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Package: psichomics
Commit: be77daf8cf983b7d0f0763aebdd70fc2f42d9c13
Author: Nuno Agostinho <nuno.agostinho@crg.eu>
Date: 2026-05-31 00:22:08 +0200
Commit message:

 Squashed commit of the following:

commit 84c6048df6d65e9bc3271fc1f4206ba06dbc2ef6
Author: Nuno Agostinho <nuno.agostinho@crg.eu>
Date:   Sun May 31 00:21:18 2026 +0200

    Squashed commit of the following:

    commit e3d5f4b68002c2be328ef453247c6e886fe80800
    Merge: f15b1eee dc206d7d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 31 00:08:18 2026 +0200

        Merge pull request #489 from nuno-agostinho/performPCA-empty-input

        Handle empty inputs in `performPCA()` to prevent crashes

    commit dc206d7d9a50a8988b331e025a954612329c4fb5
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Sat May 30 23:22:06 2026 +0200

        Handle empty inputs in `performPCA()` to prevent crashes

    commit f15b1eeeebcd2a1afda91efa9bf4944fc0c78d3e
    Merge: f2a3003c f9c2aac2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 11 09:26:45 2026 +0200

        Merge pull request #488 from nuno-agostinho/dependabot/docker/bioconductor/bioconductor_docker-3.23

        Bump bioconductor/bioconductor_docker from 3.22 to 3.23

    commit f9c2aac24d43b2041b0cbf38064258fe1b790c54
    Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    Date:   Mon May 11 00:44:53 2026 +0000

        Bump bioconductor/bioconductor_docker from 3.22 to 3.23

        Bumps bioconductor/bioconductor_docker from 3.22 to 3.23.

        ---
        updated-dependencies:
        - dependency-name: bioconductor/bioconductor_docker
          dependency-version: '3.23'
          dependency-type: direct:production
          update-type: version-update:semver-minor
        ...

        Signed-off-by: dependabot[bot] <support@github.com>

    commit f2a3003c3a46847a779952854df9218abfd14e95
    Merge: b12065f5 aeddd7d1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 7 11:15:53 2026 +0100

        Merge pull request #486 from nuno-agostinho/bump-1.36.1

        Bump version to 1.36.1

    commit aeddd7d17ebb608f4f121f0a7c94c6bd251dd6a9
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Wed Jan 7 11:15:02 2026 +0100

        Bump version to 1.36.1

    commit b12065f5ed3f3bd6b6b34b0250aded8e057109ba
    Merge: bd6a518c fc59ed4f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 7 10:46:30 2026 +0100

        Merge pull request #485 from nuno-agostinho/docs

        Fix docs

    commit fc59ed4f47b575b61f2b2492b70ce9ffd671d837
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Wed Jan 7 02:47:38 2026 +0100

        Fix docs

    commit bd6a518c2bc255f2f6bde51f56ee2a16bd6f7a9e
    Merge: afd748c7 f31ffc1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 7 01:18:09 2026 +0100

        Merge pull request #484 from nuno-agostinho/readme-update

        Update README to remove wrong instructions

    commit f31ffc1eb01a69cb39fa5b4717f7a02ed592515e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 7 01:17:54 2026 +0100

        Update README to remove wrong instructions

    commit afd748c70a5a89fa76ea86f63adfddc543027944
    Merge: 4d5cedb3 3960865a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 7 01:13:33 2026 +0100

        Merge pull request #483 from nuno-agostinho/fix-unit-tests

        Fix unit tests and update docs

    commit 3960865a7ee2d2fbbcf4ab7e562211730e66a405
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Wed Jan 7 01:12:17 2026 +0100

        Fix unit tests

    commit 4f99ac98e7c6d3b79903a83829c33954f0afdcf7
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Wed Jan 7 01:11:52 2026 +0100

        Update docs

    commit 4d5cedb3de18957fffffd4ccc01dc6252d404524
    Merge: d397f145 5be9c463
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 6 21:04:25 2026 +0100

        Merge pull request #478 from nuno-agostinho/fix-issues

        Improve psichomics

    commit d397f145660681cb7a3a6fdf3da3051d53413c44
    Merge: 84525912 2d660b28
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 6 21:03:59 2026 +0100

        Merge pull request #480 from nuno-agostinho/dependabot/docker/bioconductor/bioconductor_docker-3.22

        Bump bioconductor/bioconductor_docker from 3.21 to 3.22

    commit 845259126a5db2bba76088d0b8571236297fbd0e
    Merge: 64621141 b054158d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 6 21:03:37 2026 +0100

        Merge pull request #481 from nuno-agostinho/license/copyright-to-2026

        Update license copyright year(s)

    commit b054158d8f0573e0ecd51d4d767d219317ce3b14
    Author: github-actions <github-actions@github.com>
    Date:   Thu Jan 1 04:05:38 2026 +0000

        docs(license): update copyright year(s)

    commit 5eaf2329f1e8355b7f9ed4399a7e1b2011f09f03
    Author: github-actions <github-actions@github.com>
    Date:   Thu Jan 1 04:05:28 2026 +0000

        docs(license): update copyright year(s)

    commit 2d660b28f557f05ce2f3d181231f4ce1e8cbb583
    Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
    Date:   Mon Nov 3 00:38:00 2025 +0000

        Bump bioconductor/bioconductor_docker from 3.21 to 3.22

        Bumps bioconductor/bioconductor_docker from 3.21 to 3.22.

        ---
        updated-dependencies:
        - dependency-name: bioconductor/bioconductor_docker
          dependency-version: '3.22'
          dependency-type: direct:production
          update-type: version-update:semver-minor
        ...

        Signed-off-by: dependabot[bot] <support@github.com>

    commit 64621141cbea505991975bca70f844901607855a
    Merge: 4ef8e9a4 ebc045ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 11 21:11:44 2025 +0200

        Merge pull request #479 from nuno-agostinho/nuno-agostinho-patch-1

        Annotation list: safe-guard against NULL elements

    commit ebc045ca7be1772455d9f3cf04b9f68f8af9627c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 11 17:06:15 2025 +0200

        Safe-guard against NULL elements

    commit 5be9c463a14e08ff183ed4e4a20766531ab3918d
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Fri Aug 15 10:32:54 2025 +0200

        Fix #466

    commit 50da4b37b0e2c5beff2d096d02b22644ce7067fb
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Fri Aug 15 10:32:41 2025 +0200

        Refactor highlight points observer

    commit d8f8ebedf4e990d3a9ba4ab711d1cf2826298be3
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Fri Aug 15 10:32:06 2025 +0200

        Improve Docker instructions

    commit 10d2162e67c91f159b855271d15f2f4bec303bee
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Tue Aug 12 01:11:15 2025 +0200

        Fix loading interface on collapse open

    commit 73f266350043387668328ed76ca92d7f1115212b
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Sun Aug 10 22:20:32 2025 +0200

        Update to select latest GTEx release by default

    commit c46f2716231a8d62e598c2a7546a5210ee430eed
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Sun Aug 10 22:19:19 2025 +0200

        Fix subfolder creation erroring out if inexistent

    commit 974ab5a83646d58dcb9593c6deb07d5f06931485
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Sun Aug 10 22:18:43 2025 +0200

        Add support for GTEx v10 data

    commit 4ef8e9a492c8b6b440642bb31ffc4b6c7ef5b291
    Merge: a30e9fd9 539a472b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 14:00:56 2025 +0200

        Merge pull request #477 from nuno-agostinho/nuno-agostinho-patch-1

        Avoid multiplatform image, takes too much time

    commit 539a472be122ea4d6ba9061d4670ad24bcde118f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 14:00:43 2025 +0200

        Avoid multiplatform image, takes too much time

    commit a30e9fd9950d723794d9c141f4e9774093b77a28
    Merge: ff628ba6 3f27d051
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 12:09:00 2025 +0200

        Merge pull request #476 from nuno-agostinho/nuno-agostinho-patch-1

        Update docker.yml

    commit 3f27d0514960297a5f71fcdb2e0d439a46196c41
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 12:08:49 2025 +0200

        Update docker.yml

    commit ff628ba6b4be2021f430b29c759033c8a22ca5e4
    Merge: 65b60b1d 56b1ff52
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 03:38:27 2025 +0200

        Merge pull request #475 from nuno-agostinho/docker-building-time

        Try to reduce time to build Docker image

    commit 56b1ff52229bb1b28ad401a82fbebb7824101f95
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 03:38:17 2025 +0200

        Try to reduce time to build Docker image

    commit 65b60b1d604b2bbbb2071141d03aa597b0b4b02e
    Merge: 46041085 ea26fa77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 00:58:33 2025 +0200

        Merge pull request #473 from nuno-agostinho/latest-bioc

        Update to latest bioconductor release

    commit 46041085100eefbed6b2ac981435a562441e7a40
    Merge: 1ffc8502 0f0fdc19
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 00:58:14 2025 +0200

        Merge pull request #474 from nuno-agostinho/auto-update-docker-bioc

        Add dependabot to update base Bioconductor Docker image

    commit 0f0fdc19dc847ecaedbd9cee7c79ff5ed218f0e9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 00:57:34 2025 +0200

        Add dependabot

    commit ea26fa77cfa2fdefde200ebdb561465c949d15ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 00:51:14 2025 +0200

        Update to latest bioconductor release

    commit 1ffc85024dceff2b379488d9c3cc85c2c6838f3f
    Merge: 52a585bb 9e99cb2f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 9 00:24:58 2025 +0200

        Merge pull request #472 from nuno-agostinho/multiplatform-docker

        Build multiplatform Docker image

    commit 9e99cb2fdaa2b7d36665cf80e8ac20596cfd075d
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Sat Aug 9 00:23:56 2025 +0200

        Build multiplatform Docker image

    commit 52a585bbe423c8259052bd428256343d72b0b903
    Merge: 25855cce bf99a949
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 23:41:36 2025 +0200

        Merge pull request #471 from nuno-agostinho/update-email

        Update email

    commit bf99a949f41ec4e996949a65fe931d18899fde75
    Author: Nuno Agostinho <nuno.agostinho@crg.eu>
    Date:   Fri Aug 8 23:40:39 2025 +0200

        Update email

    commit 25855cce071ab23af21944b7c97d66cc003f6b73
    Merge: 80545498 72114e2d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 23:35:11 2025 +0200

        Merge pull request #470 from nuno-agostinho/qemu-emulation

        Add QEMU emulation

    commit 72114e2db204048a8d21f3547f5792449a455bd5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 23:34:59 2025 +0200

        Add QEMU emulation

    commit 8054549818c3a12e7cdb3afaa6ae8ae7760a0037
    Merge: e0920fe3 6623bc36
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 23:26:37 2025 +0200

        Merge pull request #469 from nuno-agostinho/multiplatform-docker

        Create multiplatform Docker image

    commit 6623bc3645d6cfef6ae318801dc3995bf6bcbcdf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 02:48:46 2025 +0200

        Update docker.yml

    commit 7567fa2e6942369954235473fbe444873bd3cf12
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 8 02:48:00 2025 +0200

        Create multiplatform Docker image

    commit e0920fe3117e6529d3efd648f5c892d0057c5358
    Merge: c90171b1 9180e39f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 1 14:04:44 2025 +0000

        Merge pull request #467 from nuno-agostinho/license/copyright-to-2025

        Update license copyright year(s)

    commit 9180e39fe61e6cf44aa051b6611146bdfe8a30cb
    Author: github-actions <github-actions@github.com>
    Date:   Wed Jan 1 03:22:43 2025 +0000

        docs(license): update copyright year(s)

    commit 06fd76ed69fafad77857a200cddf58e0cb55dc41
    Author: github-actions <github-actions@github.com>
    Date:   Wed Jan 1 03:22:29 2025 +0000

        docs(license): update copyright year(s)

    commit c90171b19e063a4d1e3406522625b1e53e250bfe
    Merge: d50294c4 6346f024
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 21:11:27 2024 +0000

        Merge pull request #465 from nuno-agostinho/dev

        Bump version to 1.28.1

    commit 6346f024f41349d319e233a868087df567bf8028
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sun Feb 4 21:10:55 2024 +0000

        Bump version to 1.28.1

    commit d50294c45f7bcd14939a667c4cb66ac77d289490
    Merge: c640c997 ce4e0fb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 21:01:03 2024 +0000

        Merge pull request #464 from nuno-agostinho/dev

        Fix GTEx URLs and unit tests

    commit ce4e0fb6c2d5f746dc6cdf82473ab3d1a8ab28db
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sun Feb 4 10:56:14 2024 +0000

        Set seed when creating PSI datasets for reproducibility of unit test

    commit e9f9ae56aa8c02fe2bfdcf1ac5f322bea995bf51
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Feb 3 13:54:37 2024 +0000

        Update function docs

    commit a50b642008b5545a4b30ed674c0149e644a37adc
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Feb 3 13:42:31 2024 +0000

        Fix inconsistency of using survfit

    commit cbd710cedb44b7f8a5545b2bed45352ac0f68880
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Feb 3 11:24:54 2024 +0000

        Fix deprecated use of size in ggplot2::geom_line

    commit 0c9b9832b4e590624daa15dfa97688fd51cb78d8
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Feb 3 11:09:49 2024 +0000

        Fix GTEx URLs

    commit c640c9973817260dbc2b2feea338cd7770d12e21
    Merge: 04032935 4cc74764
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 19 16:02:14 2024 +0000

        Merge pull request #462 from nuno-agostinho/license/copyright-to-2024

        Update license copyright year(s)

    commit 4cc74764f2725aedf3cd9228dc0ae149fba91e42
    Author: github-actions <github-actions@github.com>
    Date:   Mon Jan 1 03:09:46 2024 +0000

        docs(license): update copyright year(s)

    commit 2d98acd4197cc15aa68153f4abd1a8e74aaed040
    Author: github-actions <github-actions@github.com>
    Date:   Mon Jan 1 03:09:30 2024 +0000

        docs(license): update copyright year(s)

    commit 040329354230419338f4a530c6121540b49c1c4d
    Merge: 9aabaa8b fa213c9f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 14 16:53:11 2023 +0000

        Merge pull request #459 from nuno-agostinho/ci/fix-ubuntu

    commit fa213c9fcff3e04803c1697fa6b1134fcfee5f2a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 12 21:47:35 2023 +0000

        Avoid CI tests in Windows

    commit 6ddda87323203fa9b597350728f98704eb97f4e8
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sun Feb 12 20:11:29 2023 +0000

        Simplify R CMD check

    commit 9aabaa8be72a1ae686339ae9146427cb02fc0515
    Merge: f1ab3639 5dff73b7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:09:17 2023 +0000

        Merge pull request #458 from nuno-agostinho/nuno-agostinho-patch-1

    commit 5dff73b7ce188d3e0ab6ec52d1da0ff27be9273e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:09:08 2023 +0000

        Update pkgdown.yaml

    commit f1ab363938a5e8e9eb6cdebab407f16c339fed7f
    Merge: 3a5a144e 997b8274
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 2 23:37:32 2023 +0000

        Merge pull request #457 from nuno-agostinho/update/pkgdown

    commit 997b8274f4ad7a3014c018321f940d953c10b86a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 2 23:37:14 2023 +0000

        Update pkgdown automation

    commit 3a5a144e44f1673b4d79ee5e5a38898ac00f82f2
    Merge: d9d644a9 2c5726df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 2 23:31:08 2023 +0000

        Merge pull request #456 from nuno-agostinho/license/copyright-to-2023

    commit 2c5726df7460f0ea8259215024a9b05a388af991
    Author: github-actions <github-actions@github.com>
    Date:   Sun Jan 1 03:14:41 2023 +0000

        docs(license): update copyright year(s)

    commit f6224c47c3d063d596b227d6b9d4da51f3ade0e8
    Author: github-actions <github-actions@github.com>
    Date:   Sun Jan 1 03:14:22 2023 +0000

        docs(license): update copyright year(s)

    commit d9d644a91872e74dd1ee859a6aba4d0d50a3fa47
    Merge: f513e98f 800700a7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 26 20:34:23 2022 +0100

        Merge pull request #455 from nuno-agostinho/update/1.24.0

    commit 800700a74ad9727116618f2d17f0bfb0228bf430
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Wed Oct 26 19:33:24 2022 +0100

        Bump to 1.24.0

    commit 8d44ef550d884d8f3374d0ce4a684bc8790cec4c
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Wed Oct 26 19:30:22 2022 +0100

        Fix bugs that prevent web app from opening

    commit f513e98fb3f5ea346d8a51b0fbadcd5daa6deb0a
    Merge: 2c7d423c 60eaedec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 26 00:06:07 2022 +0100

        Merge pull request #454 from nuno-agostinho/fix/gh-actions

    commit 60eaedec374ac1cc2ed2685880ba066ffe8fa3e1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 26 00:05:58 2022 +0100

        Fix GitHub Actions workflow

    commit 2c7d423c1267edf0ae6f3a90ee642b6cc9239b67
    Merge: 182cfac1 2a07f754
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 21:17:14 2022 +0100

        Merge pull request #453 from nuno-agostinho/nuno-agostinho-patch-1

        Update NEWS.md

    commit 2a07f7543d05313860632bce4fc97a2a727d644c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 21:17:05 2022 +0100

        Update NEWS.md

    commit 182cfac13fd13421dd6e76ea5819c775752b03a1
    Merge: b609d8d8 d2f24fd0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 21:11:58 2022 +0100

        Merge pull request #452 from nuno-agostinho/dev

        1.22.1

    commit d2f24fd00651c40b77199483dcc9f3b5c4c3f9b5
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Thu Jul 14 13:27:29 2022 +0100

        Updated deprecated setting to remove ggplot2 guide

    commit 78a7fc91ebd7ff4f43a62ec49838ff395064e6e4
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Thu Jul 14 13:21:49 2022 +0100

        Update UniProt REST domain

    commit 65a85de3dad562e70b8c50cae938b5e88c2df09d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 11:45:23 2022 +0000

        Fix UniProt API search query

    commit 134083f3ac57d509907197183e3d0a2a44ed3dba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 11 17:34:42 2022 +0000

        Fix UniProt REST API call

    commit 7562b5f9f46590a90a6d774de2b791dbd8a7af7f
    Merge: b609d8d8 5c880794
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 11 18:20:42 2022 +0100

        Merge pull request #451 from nuno-agostinho/fix/gtex-loading

        Fix GTEx data loading

    commit 5c8807947cc5ece14203a3dbb3020d0af39e6e94
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jul 11 18:17:00 2022 +0100

        Update changelog date

    commit b8385d62e8a694c9fd9227371f3eb4e02710bf8f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 11 17:15:02 2022 +0000

        Fix loading GTEx v8 data

    commit dc70999b0ccb9ed58d317c1e0d66f29479e84e9a
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jun 20 19:10:07 2022 +0100

        Bump version

    commit d25c0ca418c7b7a25346e0c359657e1ad0ba4047
    Merge: 08247299 f3fe8f33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 20 19:06:48 2022 +0100

        Merge pull request #448 from nuno-agostinho/fix/tutorial-surv-plot-list

        Update CLI_tutorial.Rmd

    commit 0824729992cec87dc2b238d338d3a66eba0ec4cf
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jun 20 19:05:49 2022 +0100

        Fix GTEx data loading

    commit b609d8d8ad645a3b9af8239e9003c18f6fb5810e
    Merge: 9a6bc51d c4b63557
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Thu May 19 13:26:23 2022 +0100

        Merge pull request #449 from nuno-agostinho:dev

        Custom Codespace container

    commit c4b63557ff5ab2c58ce85a637069ff07c4301757
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 19 12:23:41 2022 +0000

        Custom Codespace container

    commit f3fe8f33605a513c9c81f04516fef1369d342c18
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 7 21:12:39 2022 +0100

        Update CLI_tutorial.Rmd

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 13:59:56 2022 +0000

        Fix missing topics from pkgdown

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    Merge: 5b443011 c79b8fd5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:48:59 2022 +0000

        Merge pull request #439 from nuno-agostinho/fix/limmaTrend

        Fix limma-trend when using newer versions of limma

    commit 5b4430113074848e90b5169834da7ef1e0ee5d4e
    Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Date:   Sun Mar 13 02:47:55 2022 +0000

        Update license copyright year(s) (#443)

    commit 2ea84960801becee014c1dc80c7555ef2fe4b863
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:45:46 2022 +0000

        Update update-license-year.yml (#445)

    commit 991b060d25cf8b3d3f5fb3e52787e05b0b3e9d5e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:43:01 2022 +0000

        Update update-license-year.yml (#444)

    commit d8bf3c5add70774446475763346a37b343470488
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:39:50 2022 +0000

        Update update-license-year.yml (#442)

    commit 5149c2a1069294b150a4db58bdb766a40dce5fda
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:38:25 2022 +0000

        Fix auto-update of copyright year (#441)

    commit 21fbf34b6fdd0686150a0a3ec808e52f04db25d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:34:55 2022 +0000

        Auto-update license year (#440)

    commit c79b8fd5e0d82bbe5ed49c4e4ebab8481963cf2d
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sun Mar 13 02:13:23 2022 +0000

        Fix limma-trend bug when using newer versions of limma to calculate average gene expression

    commit 5160e701985f6441d71efef51b918dfcb4b247fe
    Merge: 96b67336 6e1ef6ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:55:14 2022 +0000

        Merge pull request #438 from nuno-agostinho/nuno-agostinho-patch-1

        Update pkgdown.yaml

    commit 6e1ef6ff18bfa69d275c769981cecf27dcbae17e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:53:42 2022 +0000

        Update pkgdown.yaml

    commit 96b67336960edb62e45f89420e5e7c7dcafd3708
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:46:29 2022 +0000

        Update pkgdown.yaml

    commit 89672d62235a5a4762695613a1b8f30379117bc0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 25 20:59:08 2022 +0000

        Update README.md

    commit 30929b077b136356b18a73661ef5d3a30efa94b7
    Merge: 6b958b84 8ccc8660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 25 20:46:49 2022 +0000

        Merge pull request #437 from nuno-agostinho/fix/corr

        Allow to analyse correlation more than once in GUI

    commit 8ccc8660ee14f5ee25d2b3d942b1568c5538e866
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Jan 25 09:12:41 2022 +0000

        Allow to analyse correlation more than once in GUI

    commit 6b958b848fdc0308e44a13510827030a32eee488
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 12:02:30 2021 +0000

        Update testDiscardLowCoveragePSIs.R

    commit 9bdab27c376201a8061114890ca39f54dde1a5ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 09:08:11 2021 +0000

        Update testDiscardLowCoveragePSIs.R

    commit 1296c70a4d52813c2cfc5ce3210908d5318e0221
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 24 09:19:16 2021 +0000

        Update pkgdown.yaml

    commit 9fc9299f34afb48971788e753d540948507ba929
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 23:41:16 2021 +0000

        Revert to pkgdown 1.6.1

    commit 846031b61499f7e0d5d6445e171f59321b56bbac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:18:44 2021 +0000

        Fix using template tag twice

    commit 923c64f1b29863711ecbc0238e423b2155aaa309
    Merge: 02cd795c ff7d8f27
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:01:21 2021 +0000

        Merge branch 'master' of github.com:nuno-agostinho/psichomics

    commit 02cd795cbbd9e873d02bfb36072d23d3928503bf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:01:05 2021 +0000

        Isolate GitHub Action to deploy package

    commit ff7d8f27558f202678f49f574f9b393218187081
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 3 16:30:37 2021 +0000

        Avoid Docker cache

        Doesn't update newer images?

    commit 99b289e5b61ce5280a5d6323b63ddb2ba2c71db6
    Merge: 7c8e8fac 0a22b26d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:10:19 2021 +0100

        Merge pull request #434 from nuno-agostinho/dev

        1.20.0

    commit 0a22b26dbf09e39aabc3e8bfc352ab95c4ea7254
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:09:31 2021 +0100

        Bump version to 1.20.0

    commit 1a4f5ec9a3c559507da5109abcc524cf49db3bf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 17:06:33 2021 +0100

        Update date of release based on Bioc 3.14

    commit 873f63b8decb2be1e0df4de9ba120bbd61b23330
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 18 20:30:28 2021 +0100

        Support new AS annotations

        - Create AnnotationHub cache directory on first run of psichomics and allow to set cache path
        - Improve species/genome selection
        - Add loading bar when looking for AS annotation list
        - Change option used to evaluate shinyproxy support
        - Code copy-editing

    commit 7c8e8fac14d0087fff3e1b21d56b875d1436da00
    Merge: 654122c7 ed375ca8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 18:39:11 2021 +0100

        Merge pull request #431 from nuno-agostinho/dev

        1.18.6

    commit ed375ca8c6010dac6b9e0f837d4df60725144041
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 17:06:05 2021 +0100

        Update Rcpp

    commit 1b3e34c4273ebb23e6c239201dfa633dc488e30a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 17:05:52 2021 +0100

        Fix issues with R CMD check

    commit 253eecb02608ad1ef94a9d8c1cdcff77da5c6472
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 16:29:55 2021 +0100

        Minor UI improvements

        - Show tutorial link for user-provided data loading in welcome screen
        - Show psichomics version in welcome screen and help section
        - Update current year in copyright

    commit de8fde9fdfa31c9457f6d35c5aab8df4ff0965f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 16:27:55 2021 +0100

        Upload ZIP folder instead of folder for Shinyproxy

    commit 638e900915afb29925fd893d10f30a5bfd3ebc25
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 15:26:21 2021 +0100

        Suppress data's selectize input warnings for too much choices

    commit 9c2ab0cfc611a984bb550321774bce6dd22e657b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 18:00:18 2021 +0100

        Bump version to 1.18.6

    commit 9ba66a3a42041cc0a5f7b2cb5c60d643f8c2bd0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:57:27 2021 +0100

        Clean-up survival analysis code

    commit 0989a6ea0de8c8498553a82fe5389aa7801a7d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:56:47 2021 +0100

        Update function documentation based on third-party libraries

    commit 607c36ab3c5e4593c1221edd29afa70cd4e6083d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:56:13 2021 +0100

        Improve plots and small UI enhancements

        - Show category icons for gene expression, junction quantification, clinical data and sample metadata
        - Minor changes to plot code for more uniformity

    commit b3ffddef7e6485aa482e6800017e2e50f2178158
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:40:34 2021 +0100

        Select hg38 with GTEx v8 data

    commit 2a05d7f48a2279310307af4e628b1777d9051b98
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:14:40 2021 +0100

        Fix issues with shiny 1.7.0

        - Change icon names as required by newest versions of font-awesome
        - Avoid modifying Shiny tags using generic positions

    commit 51f3082b7f7303107b0d9eaca798395ca4e98534
    Merge: e3b948c6 654122c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 25 03:10:22 2021 +0100

        Merge branch 'master' into dev

    commit 654122c761d823ddc7dbcf7b5f45227dff652ef6
    Merge: bfe3bb28 a59acc08
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 23:28:54 2021 +0100

        Merge pull request #430 from nuno-agostinho/diagram-fix

        AS event diagram fix

    commit a59acc08438f848f91bdfb58e5f8ccf0b1215291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 13:34:25 2021 +0100

        Avoid alternative regions from overlapping

    commit e2af9d36405c3d07824cff1f16b352cf2f6c2ce5
    Merge: e144419f bd575a9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 13:31:39 2021 +0100

        Merge branch 'diagram-fix' of github.com:nuno-agostinho/psichomics into diagram-fix

        # Conflicts:
        #	dev/event_diagrams.R

    commit e144419f14a7de096c9aab86ee1b4ecb0da189f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 19:07:55 2021 +0100

        Test AS event plots

    commit bd575a9ba1eed989856e1a86606a5afc094c610b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 19:07:55 2021 +0100

        Test AS event plots

    commit dd57c2982e1bb2cf184637047be8cd1a3cedc229
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 12:11:25 2021 +0100

        Fix AS event plots

        - Fix wrong colouring of reference exon in AFE and A5SS event diagrams
        - Fix colour order stack in transcript plots (reference exon in orange now on top of others)
        - Fix loading twice transcript plots when selecting a new event in the visual interface

    commit e3b948c6500e48bd5322a6c4d545577b06922eee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 12:02:01 2021 +0100

        Update NEWS.md

    commit 07ff16a97593b3c959f2952e84da8921e3b635fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:59:04 2021 +0100

        Automatically plot PCA after calculating PCA scores

        - Copy-edit text

    commit 865e5f68c5c2c91797b9cdce9271ae67319d3e89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:54:57 2021 +0100

        Fix wrong coloring of reference exon in AFE and A5SS event diagrams

        - Change order of colour stack in transcript plots
        - Avoid loading transcript plot twice when selecting AS event
        - Improve unit testing

    commit b268627c9f758589731c4b50f3d329dc0f308674
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:42:46 2021 +0100

        Load AS annotation only when opening the splicing quantification tab

    commit f5b9d8fc2148aaa343211c2703f1419aa40a1d77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:40:29 2021 +0100

        Improve responsiveness of recount project selection

    commit bcb4e0f0d637873de7d79c67eead324b186a8657
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 20 20:06:43 2021 +0100

        Rename JS file based on proper nomenclature

    commit 493b66fc8d42799c625e3ad7eb59bfb9f06121b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 20 20:06:06 2021 +0100

        Fix issues with progress bar in ShinyProxy

    commit 015087f22d8090036253dd589ad89978bb29755e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 18:17:18 2021 +0100

        Fix shinyBS.js not loading

    commit c5699a51ed407a67d4b71264adab8bcc302f703c
    Merge: 68110bf2 4e888e4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 17:43:28 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

        # Conflicts:
        #	R/utils_interface.R

    commit 68110bf2e51a763b08c59c0363367364358c6933
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 17:40:17 2021 +0100

        Add ShinyBS JS library (useful for ShinyProxy)

        - Update animate CSS library

    commit beb347789ac00b51cd1cd51e06ec0e5deb9de2cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 17 17:37:19 2021 +0100

        Fix PCA-related bug when plotting only one group

    commit 3ec5ff2f8a4eb285f4838d116c3526f827da5831
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 20:59:44 2021 +0100

        shinyproxy: try closing progress bar

    commit 4e888e4e6b85539cb045b96e0e1d027ee7531ec3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 20:59:44 2021 +0100

        shinyproxy: try closing progress bar

    commit 7d55513d4ab47e3ec437b75d405c5015c0678844
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 18:53:16 2021 +0100

        Fix getting environemnt option

    commit b0426cb505454a82f87d2e92edf440fad45f7cdc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 17:04:49 2021 +0100

        Add support to run in ShinyProxy

    commit bfe3bb28ad05f3366448ff0f477af3cbb566d4e9
    Merge: 147ae112 e1681cdd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:58:42 2021 +0100

        Merge pull request #428 from nuno-agostinho/dev

        Dev

    commit e1681cdd89689f71055713f3cc20724fb098b20d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:49:46 2021 +0100

        Bump to 1.18.4

    commit 3988b7694aced91154a8815faf0855bc1427c135
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:47:35 2021 +0100

        Update orgDB only when loading gene expression

    commit 705ceba254f5c0b34f2b0fe586a76912837cc91e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:24:49 2021 +0100

        Fix `psichomics()` not launching

    commit 7fbb69303785b55b40c682248ba203c4687bc8d9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:22:03 2021 +0100

        Remove MD5 hash check for TCGA data

    commit 147ae11217673e94ce7612c7b6c99a8e0ad11123
    Merge: 81a7850e c106b63b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:57:44 2021 +0100

        Merge branch 'master' of github.com:nuno-agostinho/psichomics

    commit 81a7850e7d9c77677daab27ce2d47ebf99dd9c97
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:57:34 2021 +0100

        Fix pkgdown error while running examples

    commit 5b3d216809ed1ecb0aca25b05fbf2ce1ba0e82c4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:40:54 2021 +0100

        Cache Docker image steps

    commit c106b63b18d224090df407a7b5a216dab76a7fc4
    Merge: 4a6f72fd 4c35844a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:26:31 2021 +0100

        Merge pull request #427 from nuno-agostinho/dev

        Push Docker images to DockerHub

    commit 4c35844a410e4b23fc5117df90d45d7410c2ecc1
    Merge: 2d1118e1 58f13e96
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 13:40:38 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 2d1118e1189ded2a2524c7ade77daebe4197461e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 13:40:34 2021 +0100

        `plotSplicingEvent()`: avoid opening browser window in non-interactive contexts

        - Fix Bioconductor build report for Windows

    commit 58f13e9633d207991f318333943a50023653131f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 11:18:21 2021 +0100

        Push Docker images to DockerHub

    commit 4a6f72fdec02c7be120bd60845aed7112bfc0c75
    Merge: 5e58444d 15d5a462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:47:19 2021 +0100

        Merge pull request #425 from nuno-agostinho/dev

        1.18.2

    commit 15d5a4621e4b88316f7667cbdd80b8ec97dd0b85
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:46:36 2021 +0100

        Bump version to 1.18.2

    commit b781bd868ec318caf3cdeb01f925b9642377af2d
    Merge: cb6c0347 caf4bbe7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:45:52 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit cb6c03478d4484d221a26155193f745705eb1d70
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 12:29:06 2021 +0100

        Fix issues with Bioconductor build system

    commit 5e58444d4202f4a3f872735541138d22ea55c1a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 3 11:18:47 2021 +0100

        Update docker.yml

    commit caf4bbe7b433adbdd9ad04927f220dd5f0225dc1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 2 21:30:28 2021 +0100

        Update docker.yml

    commit be79fc80b7052f2e4734c427e2102bb3a045b515
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 2 16:44:50 2021 +0100

        Fix issues with Bioconductor build system

    commit c585cecdc180a789d46cde82c5f52b3642a5d623
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 27 16:48:10 2021 +0100

        Fix link to Bioconductor Docker

    commit f25daead424f1abdb9587df8ca9521e859643a98
    Merge: 800a9497 b09a55ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 27 10:42:35 2021 +0100

        Merge pull request #424 from nuno-agostinho/dev

        Bump version to 1.18.1

    commit b09a55ce3133b85fa7d664dfcaa0c73b2025a61b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:50:21 2021 +0100

        Bump version to 1.18.1

    commit a136b3277c7cd6345d09e0e5b182cbbbec341e35
    Merge: 4ed660dd 800a9497
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:43:58 2021 +0100

        Merge branch 'master' into dev

    commit 4ed660dd456eec62d194aa51054d52490f30fd23
    Merge: 7af5ed78 08d79a95
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:42 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 7af5ed7815f903863eca6be95ee75c7a54754c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:35 2021 +0100

        Rename custom data tutorial

        - Minor copy-editing

    commit 800a9497227a2952a51962819840d4029f57a9b7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 21:37:01 2021 +0100

        Fix Docker install instructions

    commit 3d89ab07e2870eedec3558c73cbc2ec9f041e18f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:19:52 2021 +0100

        Use GitHub Container Registry

        - Release `latest` tag
        - Update Docker action versions

    commit 5ce0e06d24febbc6a000db17ab540b779f2c6c36
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:17:04 2021 +0100

        Simplify dependencies install in Dockerfile

    commit 31adf199ce9b5abde5f3cd5e51349848d832ce74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:14:57 2021 +0100

        GitHub and Docker install instructions

    commit 08d79a95acdd38bca6367b2b35295e66c513aea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 17:29:58 2021 +0100

        Update README.md

    commit 72dd83cc5ffdce789cba11c17d09149032972ac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 16:01:24 2021 +0100

        Update docker.yml

    commit 02fa0bb25c07eb9b7d9660a00bf1cd3cd09b7433
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:58:00 2021 +0100

        Update Dockerfile

    commit 046ccaa16ccbb0196e83d13638bd637e82334e4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:57:17 2021 +0100

        Include cache in docker.yml

    commit 6b6eea05c1c25febfc53ca1229836fefe6b878e0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:53:19 2021 +0100

        Update docker.yml

    commit b4dfaa5c8bec6e5bee8c13bb88227ce89c895be5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:52:27 2021 +0100

        Temporary test

    commit b0ed55070f7225db992becd6eab75cf15951cac9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 14:46:56 2021 +0100

        Update docker.yml

    commit 729c0ec030f8301fa1dd87d0ab13fd81a97b1566
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 11:42:24 2021 +0100

        Update docker.yml

    commit c72aa7cb9ec3f4cb83d2a1b5a7faaaa12bdb2145
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:50:44 2021 +0100

        Simplify Dockerfile to the bare minimum

    commit 409d56b0289259d2aa6405dd5cb77d6b983176f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:16:34 2021 +0100

        Revert to working docker.yml with new registry

    commit 247013fb0d49dab26cec19d1f3d8eb43bb0de622
    Merge: 09d3d385 debcc26e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:48 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 09d3d385a633832b71391aeb006aa0f97f6c1ec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:42 2021 +0100

        Fix spelling issues

    commit debcc26e145239d23368ab36ed8ad5d6995ad1df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 11:54:40 2021 +0100

        Update docker.yml

    commit 7bdfbd87b2579f5d63f5b7cdae0e6f44723f7c49
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 10:43:13 2021 +0100

        Update docker.yml

    commit fd6dd049b71f72d21f6ac3a899574137697eada9
    Merge: b5380673 ba7412e1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 19:22:09 2021 +0100

        Merge pull request #422 from nuno-agostinho/master

        Update dev from master

    commit b53806731c44ff936b200238e00375023da76dd3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:51:51 2021 +0100

        Update docker.yml

    commit ba7412e14ae3aac94fa6bb70e404db554bcace7c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:16:45 2021 +0100

        Update check-bioc.yml

    commit 95ca4df14220a184de1b4c713fbe4712143028ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 16:58:50 2021 +0100

        Update check-bioc.yml

        Update usage of environment variable

    commit ff60092684c225f8da7daa5ca74d61eda8ffc851
    Merge: 3c039cf6 32205d23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 14:48:47 2021 +0100

        Merge pull request #421 from nuno-agostinho/dev

        Dev

    commit 32205d23dd284807e79c26e65c68a095e6d87cd6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 20:23:41 2021 +0100

        Avoid problematic unit tests in Bioconductor

    commit 2e7b506736eb923a4ea6229f58b3464f731cd205
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 12:48:38 2021 +0100

        Update NEWS.md

    commit 08302a37027e18169519859fa435014b25a5987f
    Merge: e2f0ae2c 3c039cf6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:35:12 2021 +0100

        Merge branch 'master' into dev

    commit e2f0ae2c838d418bfc01245afcaf8f7d9eb62bf5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:49 2021 +0100

        Bump version to 1.18.0

    commit e5003caf9a98ab9981e0c8c02448d232ebf6f9e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:34 2021 +0100

        Fix issues with R CMD build/check

    commit b846abece509ea86a1998f8bd5bc31eeba16ef81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 16:18:43 2021 +0100

        Update documentation and resolve minor issues

    commit 445dacade2d8745957b2a42dbc5663159f98861b
    Merge: de048440 2ea05d6f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:38 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit de048440a477c16339030886703ac2d1f9417021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:19 2021 +0100

        Fix `plotDistribution()` for listed groups (e.g. in the CLI tutorial)

        - Fix issues with unit tests

    commit 2ea05d6f66a31aadc63fd81efbaab2e4d655734b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 14:09:56 2021 +0100

        Avoid using set-env to set environment variables

    commit 2e536f9e4573549df3a1af7f5b0991e2aec7364b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:45:23 2021 +0100

        Only animate spinning wheel when effectively loading data

    commit a9362fe77814ff22f8b092fd4a804becc2f8bc81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:29:26 2021 +0100

        Improve plotting of AS events

        - Allow to use `plotSplicingEvent()` directly with a PSI table
        - Improve support diagrams for IR events
        - Fix IR diagrams in distribution plots not displaying introns
        - Fix parsing of VAST-TOOLS IR events as SE for certain annotations
        - When searching particular splicing events, fix results based on the wrong genomic coordinates
        - Fix other AS events display in Y axis for distribution plots
        - Minor copy-editing

    commit 283e137bcca44e07a451296dab8c44655184748b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 19:28:03 2021 +0100

        Improve distribution plots

        - Allow to invert axes
        - Avoid redundant code
        - Render event diagram based on axis containing PSI distribution values

    commit 0e9e88251500d9d4a063d641240090b118ef3be2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 13:01:27 2021 +0100

        Suppress snapshot date message

    commit 5dd040a4800f71e4bc93ca86b4fb45d1d58ffc64
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:28:24 2021 +0100

        Minor improvements

        - Place distribution plots on top of event diagrams
        - Timeout GTEx data retrieval after 3 seconds without server response
        - Avoid unnecessary messages when loading Firebrowse interface
        - Avoid "Matching subjects to their samples/Matching process concluded" loop

    commit 28b2c303bad579cd2a25093bb9f0388a4150991a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:18:53 2021 +0100

        Support gene symbol conversion for any species with OrgDb

        - Remove 'org.Hs.eg.db' dependency
        - Allow to select OrgDb species to use for gene symbol conversion
        - Minor code copy-editting

    commit efb0bd138e1abb07cab0034bab8bca749f860b91
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 11:00:36 2021 +0100

        Bump version to 1.16.1

    commit 74cc2347872c24788419a3ccb96b3ec7851b53c6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 10:59:49 2021 +0100

        Fix parsing of VAST-TOOLS intron retention events as skipped exons

    commit d651dd530ea5e05e987b7f12f342de4dda51d5f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 19 13:37:06 2021 +0000

        Improve distribution plots

        - Allow to plot violin and box plots
        - Hide rug plots with 500 or more values (by default) for performance reasons
        - Add jitter to rug plot (helps to discern multiple numerous points)
        - Display IQR per group in tooltip
        - Easily add subtitles to distribution plots
        - Avoid redundant code
        - Reorganise code

    commit 3c039cf6f68722e0a1def624c607aca18c8910ec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:33:22 2020 +0000

        Fix setting environment variable

    commit a6feeadad42e93163d6614d1fb89a50ac5f30faa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:05:11 2020 +0000

        Avoid bioc-devel while R-devel is not available

    commit 35b2cc0dcb02e20eacd1a4a8c2594945cd1322fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 18:35:05 2020 +0100

        Fix comments in bash commands

    commit f159bdc8ea2800c6482e439ea8f495575b52db1c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:50:53 2020 +0100

        Fix unit test function

    commit bdc246c1708d7ed3957cf74bd830467c42ab9f23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:19:13 2020 +0100

        Move unit tests to correct folder

    commit 87344cdc4a8e92eb6a3fa3c0857cd7e559986e01
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 7 15:26:06 2020 +0100

        Minor changes

        * Warn about discarded events when quantifying/loading PSI data
        * Print elapsed time of loading local files
        * Improve verbosity when quantifying or loading PSI values
        * Add dev/ dir to add files of interest to the project
        * Copy-edit CLI tutorial, code and documentation

    commit 37f209a0799b21c71faffb6c21c101f115c27ba0
    Merge: a84aeb84 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 18:41:27 2020 +0100

        Update NEWS from origin

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS.md

    commit a84aeb84b669683aa20fddc20852b9599cc0b845
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 17:39:49 2020 +0100

        Improve performance of `discardLowCoveragePSIvalues()`

        - Move reusable `progressBar()` C++ function to header file

    commit 15c4e2712d424ce0e3835e30fbf8c6be1c77fda8
    Merge: 3cfc873d 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:54 2020 +0100

        Merge pull request #415 from nuno-agostinho/dev

        1.14.4

    commit 13b0d736d14f623658fffad4da31be115624dee4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:12 2020 +0100

        Update NEWS.md

    commit 358819f2127b3340d2624489d06c1135f5808d50
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 17:15:14 2020 +0100

        Correct spelling

    commit 230f03f3e6704626e13d60417d340a1aa3adbe60
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 16:33:23 2020 +0100

        Improve file/directory browser dialog

    commit 18344b16cc4bcd251c9c01b23011e10b20750ffd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 14:59:37 2020 +0100

        Improve file/directory browser dialog

    commit 989b5aac54dc7799b9f187349a901370b402beea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 28 18:54:44 2020 +0100

        Improve file/directory browser dialog

    commit e37c62c848e3dc0091076d7dd7894aa4f9fe62da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 15:13:58 2020 +0100

        Bump version to 1.14.4

    commit 1bb928810f71d63daf7ae3f840b6c59f06d79d8f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 09:18:27 2020 +0100

        Fix file browser dialog selection of single file in macOS

    commit cc63bdb5a69a6e0c9fbdd2cb860629a6bfec404c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 26 19:02:54 2020 +0100

        Improve data loading

        - Speed up loading of GZ and BZ2 files
        - Increase verbosity while loading files
        - Speed up loading of VAST-TOOLS' inclusion levels
        - Fix loading of VAST-TOOLS' inclusion levels sometimes returning an error regarding duplicated row names
        - Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS' inclusion levels

    commit cae16fb330bf82aff77ac9b6beda26e4f5462519
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 24 18:17:36 2020 +0100

        Copy-edit tutorials

    commit 3cfc873db5f20c82d408f71b0522f52d7c3bf2b4
    Merge: 0db81dd6 b766d090
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:29 2020 +0100

        Merge pull request #414 from nuno-agostinho/dev

        Expect to contain "ensembl_havena_gene" in logic_name

    commit b766d0908894fb121a93ccb575037741e22967e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:05 2020 +0100

        Expect to contain "ensembl_havena_gene" in logic_name

    commit 0db81dd670f572886d9398b38bbbea7f536e3400
    Merge: b31fc62a ed83e8a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:21:00 2020 +0100

        Merge pull request #413 from nuno-agostinho/dev

        1.14.3

    commit ed83e8a169ccaf55867e225c4e236ccd7aa1b232
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:02:32 2020 +0100

        Bump version to 1.14.3

    commit 91198ec580ae300566c318391287d7e9540f83a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:48:36 2020 +0100

        Fix upstream changes from Ensembl API response

    commit 339e0d6f658074fb96e9996014c8d9da84271d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:47:32 2020 +0100

        Run R CMD check regularly

    commit c04f25193841c87d7a9df28ad37bc4c7af682f97
    Merge: 548ae1f5 b31fc62a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:30:40 2020 +0100

        Merge branch 'master' into dev

    commit 548ae1f5984a6858b777a4dadc474b482bc44ca4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 00:33:07 2020 +0100

        Fix undefined global variables on renderBoxplot

    commit 616f2804081e240a1cedf920164015a178dfc998
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:32:08 2020 +0100

        Fix incomplete final line

    commit f7f34ccde450d5666d2253c36e7436d350580771
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:13:24 2020 +0100

        Pass codecov even with 1% of differences

    commit 21864c25fb5dc270d6f4d0eee9cf84aaf5a5d3e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 15:17:15 2020 +0100

        Publish Docker images based on dev branch

    commit 278f77ebe6bc1b50861df5c6cad21d8f3b279609
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 10:05:50 2020 +0100

        Minor copy-edit

    commit b31fc62a23d4a2eeb8f993baa0cadce22d3b89b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:29:36 2020 +0100

        Avoid publishing Docker image on master push

    commit 75706aac561c5cee7e2bccb911187e7a78940df1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:26:33 2020 +0100

        Update README.md

    commit f9d0f85e50aae13d81e4394d4c85d60c35fa60b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 00:24:03 2020 +0100

        Fix pkgdown deployment

    commit 96942cc2abc3e3bd8a835c0f0807be8cd13a96f1
    Merge: 49ca4891 14364a71
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 23:26:58 2020 +0100

        Merge pull request #412 from nuno-agostinho/dev

        1.14.2

    commit 14364a719e271169cc4198cdf66974cb06606d2c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:49:36 2020 +0100

        Fix unit tests for VAST-TOOLS' data loading

    commit 40d7f93c716a914200f456c12d4013234721975b
    Merge: 31fc5ac5 140ab018
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:01:28 2020 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 140ab01862eb4e021430593492a0799a0f3c6333
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:00:42 2020 +0100

        Update NEWS.md

    commit 31fc5ac577e056bee88e00c3565f29f2fab52291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:29:27 2020 +0100

        Improve loading of VAST-TOOLS' inclusion levels

    commit 48cc9ee5617d5a4b08e21ba7954b3e11eb719fd2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:27:58 2020 +0100

        Fix asking multiple paths in file browser on macOS

    commit cfa5ec8e6c08baf3374545828f59470038d7a2ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 10 10:16:59 2020 +0100

        Table with supported file formats in psichomics

        - Include more information on manually loading FireBrowse and GTEx data
        - Reorganise information

    commit a3f81cfa4816ab3bdc1b3185a025d0a8d9d6a83e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:19:54 2020 +0100

        Copy-edit NEWS.md

    commit 3f2a23257ed3f8735c8ea07e3f8f892378a7f80a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:12:55 2020 +0100

        Publish Docker image in GitHub Packages

    commit 88b307d9598e608666281bd135c2b09ae3a92550
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 20:51:07 2020 +0100

        Fix VAST-TOOLS data loading unit tests

    commit 1977f5fe2f9038998c81577edbe0ecf745e43a39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 19:27:58 2020 +0100

        Test VAST-TOOLS data loading

    commit c56b728553c133747c685f7b1112555a6aa48a6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 12:11:23 2020 +0100

        Fix testing expected error

    commit e751c549cfb39d44e4ff69891b94d7f3304c005e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:46:05 2020 +0100

        Fix returning only one data column for loaded data

    commit f4e6750492448d5bdd6193ada0c342cb0bf72c35
    Merge: 1301be60 23881204
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:25:04 2020 +0100

        Merge branch 'vast' into dev

    commit 2388120475c3f585440dd15cc320863b6109ed13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:24:47 2020 +0100

        Replace CI tools with GitHub Actions

    commit d78cef99c576bc6922310245055b37a544cfe375
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:22:39 2020 +0100

        Avoid using deprecated boxplot function

    commit 1301be607968ea9febcec01adba5dfa5873da8f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 10:28:16 2020 +0100

        Avoid running interactive example

    commit 30a9b4786c606cf013d766b6a3d20538ab2c36b0
    Merge: 8d83c327 75748c4f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 09:37:29 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

    commit 8d83c327e7e37f4e4fc69ebbf9adff3d66724b34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs whenever talking about the cRPKM dataset
        - Copy-edit CLI tutorial
        - Use Gene (singular), not Genes in calculateLoadingsContribution()
        - custom_data.Rm: Show usage of both gene read counts and cRPKMs in CLI

    commit 75748c4f9610e6aa078e1034dc0a2b5488f55025
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs
        - Copy-edit CLI tutorial

    commit 49d76fd13e0e57205efc684d3194a9eb67b14ae7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:03:09 2020 +0100

        Raise error (instead of capturing it) when perfoming PCA/ICA

    commit 03e69817e4dfe7bfbbf03d9e714c8e65cde0ffb0
    Merge: 2f41e2dd 1804e4f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:06:16 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

        # Conflicts:
        #	R/data_geNormalisationFiltering.R
        #	man/normaliseGeneExpression.Rd

    commit 2f41e2ddc9aef85bbe70dc2424b3ba9d0f72df9f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:02:48 2020 +0100

        Replace label of `plotLibrarySize()` from "Gene expression" to "log10(library size)"

    commit 26beab6c7291874fa2fadeca79940017079fcea3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Toggle specific statistics based on gene expression values when filtering
        -
        - Allow to change object attributes to unset attributes only
        - Improve gene expression documentation
        - Copy-editing

    commit 1804e4f38074cc9fb07a2db616f7c78e78f89fed
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Allow to change object attributes to unset attributes only
        - Copy-editing

    commit 868139d711321b01d291c9e6eacb8f5daff6fad6
    Merge: 364bbe0b 49ca4891
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:57:18 2020 +0100

        Update with master and fix conflict

    commit 364bbe0bd4201884f093aee244667e0925d6bcbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:30:10 2020 +0100

        Copy-edit

        - Keep event data on PCA results
        - Copy-edit welcome screen
        - Rename exported function `getSplicingEventInformation()` to `getSplicingEventData()`
        - Rename internal function `getEventData()` to `findEventData()`
        - Put group creation table preview above other elements in the page
        - Minor copy-editing code and documentation

    commit 68770871054fbe55172a3b7ebe683e37cf782002
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 14:08:25 2020 +0100

        Copy-edit documentation

    commit a86b1bbd7b7a934767b413f51d7dfca26e8b8ac7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 13:54:35 2020 +0100

        Fix cognate genes when creating groups from differential splicing results

        - Change group title depending on creating group from differential splicing or expression results

    commit 2c2cbfdc5f19a4fd403f344736c75dfd3650d418
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 19:14:09 2020 +0100

        Minor changes to visual interface

        - Improve groups interface, including larger margin between buttons when decreasing window width
        - Copy-edit text of GTEx tissue selection context

    commit 3ca2e456984732b1d3fbcde5e68d5e0829f71033
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:43:55 2020 +0100

        Toggle individual parameters when filtering PSI data

        - Fix filtering settings not being reported after quantifying PSI

    commit 769e05e499d88cde8b892b93d7f7f3a9bb09229c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:06:27 2020 +0100

        Improve interface for group preview

    commit cde100637ec21e0ef51b05540ec5f1bde2bd367f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 11:53:19 2020 +0100

        Copy-edit custom data tutorial

    commit 231a81728c4145517d3abc2739faff64992c0076
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 23:06:30 2020 +0100

        Improve group creation and correlation interface

        - Show an alert when there is no data to create groups
        - When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
        - Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
        - Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app) when performing correlation
        - Avoid creating automatic groups based on gene lists when respective genes are not available
        - Rename RBPs to make it clear they are human RBPs
        - Minor copy-editing

    commit 8b018cc96486b55f95ff3f75c00382269607cded
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:44:53 2020 +0100

        Preserve eventData for results from differentialAnalyses

    commit 916e3f257bd71754b6824811fd266b335410130f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:38:05 2020 +0100

        Copy-edit

        - Improve information on loading user-provided data and include it in the custom data loading tutorial
        - Improve function documentation
        - Copy-edit tutorials

    commit b4a187d34e2db7bea482648ec1d839b3c1f3029e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 11:02:56 2020 +0100

        Fix warning in Roxygen regarding link to unknown function

    commit 594df5196876340607c3ce0ecd94062706328d7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 23:59:21 2020 +0100

        Fix issues in R CMD BiocCheck

    commit c16c21c691dc8dd40bd651d9a570efea0621ff76
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:47:21 2020 +0100

        Fix R CMD check issues

    commit 671b9de8b6be89484540f15655695a052e454432
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:17:01 2020 +0100

        Fix unit test issues

        - Fix plot distribution of single values
        - Fix wrong results when calculating fast row-wise stats of vectors
        - Fix error when quantifying splicing with no genes in the annotation

    commit 2ee32f8f8b25deb90bab250ae96f4d4dc53895fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:35:36 2020 +0100

        Minor copy-editing

        - Replace icons for consistency
        - Improve vertical distance of primary buttons when window width is small
        - Avoid permanent progress bar after loading list of GTEx tissues

    commit 4ae464c767abd9b4a8c15d7a01200fd669f10912
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:18:53 2020 +0100

        Fix issues with PSI filtering

        - Fix not filtering by event type events quantified via psichomics
        - Fix error when calculating stats for a single row containing missing values
        - Fix not being able to search for event types in selectize input

    commit a897e1f734a1c60ce7620f818be513959f79c6fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 17:28:26 2020 +0100

        Fix not filtering splicing event (sub)types if stat filtering is disabled

        - Improve speed of filtering VAST-TOOLS by reordering steps
        - Improve filtering settings attribute
        - Copy-edit

    commit 06fb9cacdc5f74e0268536861d084842b6f1ef14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 25 10:20:50 2020 +0100

        Improvements on parsing and directing user to differential page

        - Improve speed of joining all coordinates
        - Ensure groups are NULL when going to differential page from PCA loadings
        - Ensure AS events are correctly parsed by setting the alternative splicing quantification information when setting the event
        - Load test data with unparsable events
        - Correctly identify alternative splicing events: consider a string as splicing event if data's attribute dataType is "Inclusion levels"
        - Improve tooltips of PCA and volcano plots (loading plots now show cognate gene, event subtype and event position in tooltips)
        - Show AS event identifier at all times in the selectize event input and tables below volcano plots
        - Fix crash when there's no splicing event information
        - Copy-editing

    commit 850d2f7b2f27629b2276aae18f16817b5ac2fca2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 16:20:18 2020 +0100

        Improve PSI filtering interface

        - Filter by min/max individual PSI values
        - Discard VAST-TOOLS values based on quality scores

    commit 0cf47d34fc134ad02ec377317733d3e8b150228d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:02:36 2020 +0100

        Copy-edit documentation

    commit 6feb0f564baeb49857528bb7f685f3a39eac1756
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:00:44 2020 +0100

        Remove redundant datasets from loaded data (ignoring attributes)

    commit fb0a764d4995dd34167af81be9cb1c813ade6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:48 2020 +0100

        Correclty discard events containing only missing values

    commit eeb388ee789460220b0f4c214abef95ce2635811
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:20 2020 +0100

        Fix VAST-TOOLS' IR-S event type not being parsed

    commit 4337b2452869d07fdb5ae47db7d8d413ad1d4ef9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:56:29 2020 +0100

        Vastly improve preparation of alternative text when there are no AS event diagrams

    commit 3b7414ee228b4502fc6ce9899729637a50d10392
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:40:59 2020 +0100

        Improve filtering of PSI values

        - Discard low coverage PSIs from VAST-TOOLS
        - Allow to filter by event type or subtype
        - Use faster calculation of row-wise max and min
        - Improve code for row-/col-wise stats

    commit e8a0538af6cb0e523d73f59f51e0557854ce5021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:38:51 2020 +0100

        Get splicing event types from a given dataset

    commit 0c7b1fa05e2d707ce82d2c512ec38eab34b722ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:37:20 2020 +0100

        Improve VAST-TOOLS file support

        - Support loading output from `vast-tools tidy`
        - Use ENSEMBL gene names when gene symbols are ambiguous
        - Correctly name RI events as expected in psichomics

    commit 17e5e2c819c3a99523066ccee1a86591f342516a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:32:12 2020 +0100

        Fix eventData passing from transposed PSI for dimensionality reduction

    commit 4be272d9bc5f531d68d5056b50fad6efcea08c6c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:12:04 2020 +0100

        Add exported function getSplicingEventInformation()

    commit adfc058c6ca8f0b2ad283e290a5f4b81ea1f20d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 11:53:09 2020 +0100

        Improve calculation time of row- and column-wise statistics

    commit 0589f7a51f76de753fab53ad954c50f2845a6fea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 10:24:35 2020 +0100

        Improve consistency of function names

    commit 1e02261a0891870725ad2749528304d2ae4e8a9a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 09:36:36 2020 +0100

        Improve file loading and parsing

        - Import VAST-TOOLS gene expression data
        - Check if folder exists before loading files
        - Add verbosity to file loading functions
        - Return only TRUE/FALSE when checking file formats
        - Minor copy-editing

    commit 07addf93e43abf273be6596944d176bd71ba0e51
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:28 2020 +0100

        Copy-edit NEWS

    commit 5567fcf5a6c19ba34c4b75f2d1c71425f52c260c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:14 2020 +0100

        Process psichomics PSI tables the same way as any other generic PSI tables

    commit b124bb55472c429167a5f63239a5739ee4458420
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:26 2020 +0100

        Fix misc issues

        - Correctly parse AS events (major issue)
        - Try to put tooltip always on top of every element (still problematic...)
        - Avoid showing diagram in volcano plot tooltips if event cannot be parsed
        - Minor copy-editing

    commit 2ac31028e0d646c3a706c908688770bd82280920
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:09 2020 +0100

        Fix suggested attributes in group creation not being updated when changing to datasets with no attributes

    commit b5605b22ce54ba396cfb54819c54b6d855982f0d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:35:50 2020 +0100

        Support SRA metadata automatically

        - Update user-provided data loading tutorial

    commit 0a6ef1ea0a509671a2fcc10d2483d1fadeb3f75d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 14:17:52 2020 +0100

        Fix expected events type from a VAST-TOOLS PSI table

    commit d8d18f3ba2177cc1565f8a2d2245022106df5d65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 13:59:25 2020 +0100

        Support loading PSI tables with arbitrary (i.e. unparsable) events

        - Expect warning (instead of error) from `parseSplicingEvent()` only when running in the R console

    commit 1d43fac671ca8e72872eb59f73c5fceece715dc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:12:24 2020 +0100

        Use cache for inclusion level summary plots

    commit 0333d6e65c6df9391286504b7bee022c87c7f824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:00:34 2020 +0100

        Minor improvements

        - Fix gene expression summary plots not showing in specific situations
        - Fix legend not hiding in plotRowStats
        - Minor copy-editing

    commit 796838fe55a3f30ce877350526af91f0dd23ecf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:55:43 2020 +0100

        Alternative splicing quantification filtering

    commit b66f2d762dc6cbcb0bcffe044de207767bcf68ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:51:02 2020 +0100

        Avoid leaving missing values in type when there is subtype information

    commit 7787bd2caa9a73da856d624dcb1af3a38048cac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:35:23 2020 +0100

        Improve data loading visual interface

        - Discard file browser input selection
        - Show helpful context messages in panel interfaces
        - Minor copy-editing
        - Avoid re-matching subject to their samples

    commit d076540dec323a59e38e17d2684e37226b4fb62c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:29:01 2020 +0100

        Use fan as loading icon for AS event selectize element

    commit b41f94365b0754e95f905c600ae1d7dc19224906
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 17:46:01 2020 +0100

        Improve gene annotation page

        - Persistent user tags when querying PubMed
        - Allow to select more species/assemblies and freely add more
        - Fix no AS event plot diagram in information
        - Minor code copy-editing

    commit 0fc04c8c5df2501789d5f0553dd68dcfc5c816ad
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:57:12 2020 +0100

        Fix rug plots in the middle of density plots

    commit c2e1d5babcfd4ca370ec70f85064773c4e89f3f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:43:00 2020 +0100

        Use group colours in density plots of differential expression table

    commit 9d1ea065b6a16820965b0e3ae1dea7ae81b31910
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 10:24:59 2020 +0100

        Improve differential analyses and other fixes

        - Correctly set splicing event when clicking in PCA loadings or in differential analysis table
        - Remove deprecated psi argument from diffAnalyses
        - Avoid plot issues with plot titles
        - Avoid errors when parsing event ID
        - Correct issues when plotting event diagrams in information
        - Copy-edit code and minor changes

    commit 4b1c028128094288811c0eeaffa437f9f9e59ab5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 1 19:29:18 2020 +0100

        Allow to search using an event ID directly

    commit 623951ee40cc71090debea80b18cf45e47a938fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 23:28:45 2020 +0100

        Improve volcano plots' tooltips

        - Fix tooltip position
        - Include diagram of AS event

    commit 4d7fff2fe3a0b849dba599cd184ee0dc79fd887b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 17:06:20 2020 +0100

        Improve relevance of PubMed article results

    commit 1f4ff7e5d6e01659afaffab9c6aa79bd9ab5ed30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:13:10 2020 +0100

        Fix crash when changing to a PSI dataset without selected AS event

    commit 16aab679e2b369a2d38baf9b3cdfce0528d93604
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:10:57 2020 +0100

        Improve "gene, transcript and protein information"

        - Select species and assembly directly in annotation (automatically picked based on loaded datasets)
        - Suggest genes based on loaded datasets

    commit 105a405b3af2c15453ff58b48259aa5144fa70df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 13:28:25 2020 +0100

        Fix issues with plotting VAST-TOOLS A3SS and A5SS events

        - Improve searching AS events in AS event selectize, including unhighlighting search results when no query is typed and avoid including SVG code (from diagrams) when searching for AS events
        - Avoid plotting AS event regions if events could not be parsed
        - Copy-edit code

    commit 94c19167715f7acfa56a1e397a462e636584c49e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 12:45:59 2020 +0100

        Avoid searching SVG code from AS event diagrams

    commit a6c38080eb07cdad11c3688a05fbb08af4dac76d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 09:58:03 2020 +0100

        Fix plotting A3SS and A5SS events and always show full coordinates of unsupported diagram events

    commit 312c0b4ddb73880f176b93e9e896c06086953462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 19:11:03 2020 +0100

        Simplify group selection interface

        - Replace button to edit groups with a greyed out dropdown item, simplifying the design of the group selectize element
        - Copy-edit interface

    commit 3713216a46a2496f9317305b76f5547e9f6e6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:28:23 2020 +0100

        Rename vignettes

    commit 2107da0d81411a3b68c6796ae29dddad24206bde
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:27:25 2020 +0100

        Fix progress bar not animating

    commit d0498355caa2bfd90d3cbb8f54791f6fc5de4a38
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:46:43 2020 +0100

        Fix problem with geom_density_2d

    commit 2aa7fe5a22d783a55d413137d276dbb7a618cfb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:43:55 2020 +0100

        Fix unexpected VAST-TOOLS types

    commit c32bf742128c44616c9c78479fccbc9878e38b8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 17:33:45 2020 +0100

        Hide message about filtering gene expression

    commit f5ed4139e81a187e68745c6b054feb02ee3815f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:45:15 2020 +0100

        Show loading indicator when searching for events

    commit bcf4b99ee598fd37db903c97594a5a77b889b5d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:42:45 2020 +0100

        Improve printing of gene list object

    commit 5d38f45edab0f266e3de62b405c69aa9cd049512
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 09:43:29 2020 +0100

        Allow to import VAST-TOOLS' inclusion levels table

        - Add attribute "rowData" to inclusion levels containing AS event information, allowing to parse and plot alternative splicing event identifiers from VAST-TOOLS
        - In the visual interface, if plotting is not supported for some event, show its full coordinates
        - Use attribute "rowData" when quantifying psichomics' inclusion levels
        - Improve gene parsing when quantifying splicing with psichomics
        - Create "sticky" objects to preserve their attributes even when extracting data
        - Rename "intron retention" to "retained intron" for consistency
        - Copy-edit code and documentation

    commit 49ca48915fca6612b372e6222fca1d1f75fa3922
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 10:42:28 2020 +0100

        Fix unit tests for R 4.0 (#408)

        - Update required R version

    commit c3f588538530c7707c9a109fe821a1488abb1953
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 12 16:56:18 2020 +0100

        Print AS event diagrams

        - Export functions to print AS event diagrams
        - Only print AS event diagram if possible (instead of table)

    commit 205a30a34f065a1227e46df636cb9ddf57d4030c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 22:59:31 2020 +0100

        Improve custom alternative splicing annotation

        - Include gene symbols in custom annotations if available
        - Support more flexible filenames for VAST-TOOLS, rMATS, SUPPA and MISO

    commit 4340f89b9af23a6dd1d47d604510e4b122fbc0ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 13:31:49 2020 +0100

        Copy-edit NEWS

    commit 635ea7f799c4e572686ca959f3c7531a246a8776
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 17:44:16 2020 +0100

        Fix settings not showing for alternative splicing quantification

        - Display filename of gene expression and alternative splicing quantification from recount

    commit 026ce50e441453d4dd0e19e9955b9aa81470b6d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 10:52:51 2020 +0100

        Improve TCGA code

        - Copy-edit function names
        - Correctly take the most recent Firebrowse data

    commit dea5e14c85289cba3c9a22f9a33329d8a939b9a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 1 12:16:45 2020 +0100

        Improve rendering of summary plots

    commit d49a5805bdfef5bd76a8a28bc861843cbc2d3752
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 29 17:43:57 2020 +0100

        Parse gene symbols containing underscores

    commit b179ec03939d22a80388765cc0ef576f008f322d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 15:00:08 2020 +0100

        Copy-edit code and function documentation

        - Fix unit tests regarding changes in R 4.0

    commit 947ed62290a80b7cec9fed50b1e136e14dd4af74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 14:43:29 2020 +0100

        Allow to create Docker images based on code revisions

        - Improve startup message to include psichomics version
        - Avoid unneeded functions that may mask other package functions (rowMeans and rowVars)

    commit c360449e0d364afc1b39e3184c2c3c8fa91be413
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 26 15:37:32 2020 +0100

        Create function `plotLibrarySize`

        - Fix library size plot not working properly
        - Improve function documentation of plotRowStats and minor copy-edits

    commit 19ab1733af38042a9df952faa59b70e778cb1d93
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 25 15:39:35 2020 +0100

        Fix file browser dialog not opening and warn about selecting mandatory GTEx data options

    commit 5d94ba4f7e5aabb58d762ee9531bd89f54b69857
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 22 16:06:56 2020 +0100

        Support GTEx V8 and older releases

        - Improve loading of GTEx data and local files

    commit dd4feaf7f443bce01109dbcb487a046e9043bf30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 31 15:51:58 2020 +0100

        Try to load cached AS annotations if a timeout is reached

    commit 97023f2a69897f86e2c446563f104b096d7bb287
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 12:03:33 2020 +0000

        Fix HTML sanitization in popovers

    commit cf9fc483aa2267caa6b87690c0b22fb1f254c3ba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 10:56:27 2020 +0000

        When plotting density plots, hide Y axis when only showing their rug plots

    commit da7404c3a21434453055cddda867465852167945
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 11:07:53 2020 +0000

        Include search in pkgdown website

    commit e0df41302b0dceb0e55ba982b400bb804a72454e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 7 14:28:45 2020 +0000

        Include search in pkgdown site

    commit 2ae72bf49708a8d63f4ae8ecb435b9893d1b5ad4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 14:16:32 2020 +0000

        Simplify Travis CI config

        - Include link to GitHub page in pkgdown site
        - Fix warnings from Travis CI config validator
        - Use Linux with bioc-release for code coverage and
        - Start code coverage and deployment as soon as possible

    commit a9bb71aff254442561f5ae25d43596a50a9d2b02
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 10:06:34 2020 +0000

        Minor changes to pkgdown and function documentation

        - Include link to GitHub page
        - Improve pkgdown reference
        - Copy-edit function documentation

    commit 8ea7f504b74a2c4a18f482e468421e846ac2a754
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:59:34 2020 +0000

        Update pkgdown

    commit 27587d6647229f8ba513a60b8bad0ccbc7b0e7a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:31:01 2020 +0000

        Copy-edit tutorial, NEWS.md and README.md

    commit 9d956f1685543ecae353c30257999375889b7dfc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 11:02:23 2020 +0000

        Fix warning of Unicode symbol translation in Windows

        R CMD check raises the warning: "unable to translate '<U+2206>' to native encoding". Column names are translated to native encoding if directly set.

    commit c7b18c7c55bdad08cc6f9d8b5841ea739be66d33
    Merge: 415a02f6 52f3b141
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:14:11 2020 +0000

        Merge branch 'master' into dev

    commit 415a02f6eebed57472516438edf3f2dc87892f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:11:44 2020 +0000

        Avoid Bioconductor warnings when comparing signed and unsigned ints

    commit 52f3b141d985ab2d2de50867953090fc4ed0ce9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:50:46 2020 +0000

        Dev (#403)

        * Improve Travis CI

        - Run jobs through steps
        - Add words to spell checker
        - Test code coverage and deploy even if bioc-devel or macOS jobs fail
        - Only deploy on master branch

    commit d9bfab3374682ea450bdb41d4d34e5ea01cae899
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:31:31 2020 +0000

        Only deploy on master branch

    commit d4a68aaeb9e3aa255152f5ab016c4cbbe693520e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:04:44 2020 +0000

        Add newline

    commit 002dd77093673121994dba9db00e49a9205beb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:02:48 2020 +0000

        Test code coverage and deploy even if bioc-devel or macOS jobs fail

    commit e20bf5344b947aa74a7c14836cb55a7d2cd017ac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:01:45 2020 +0000

        Add words to spell checker

    commit bb6fa2cf973f794d5d9ee2b21767bf14cb7fbde4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:16:32 2020 +0000

        R in Windows still not supported at Travis CI

    commit 3cb8dcdc1786559c3ae83b3d931a94ca11819395
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:13:18 2020 +0000

        Improve Travis CI

        - Test on Windows
        - Run jobs through steps

    commit bfb6318485cf3216c93b0ccfedb10a6cd93ebf41
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:40:34 2020 +0000

        Update NEWS.md

    commit b4e13768bb28355901c8ec0c50785ff11493200e
    Merge: 8e5fc8aa 1b6fc0da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:35:51 2020 +0000

        Merge pull request #402 from nuno-agostinho/dev

        Improve usage of pkgdown site

    commit 1b6fc0da6070527caf29c9eee97c556ce7c3257f
    Merge: 98996ded 8e5fc8aa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:34:51 2020 +0000

        Merge branch 'master' into dev

    commit 98996ded5f67ffdb9b329f5b11467c6c344a7b92
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 10:38:36 2020 +0000

        Improve usage of pkgdown site

        - Include links to MiMB chapter
        - Replace vignette links from RPubs to pkgdown
        - Direct to quick reference instead of listing
        - Update license to current year
        - Copy-edit welcome message

    commit 8e5fc8aa362f97fd97156ad46ff3cc317fc0b919
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 00:21:19 2020 +0000

        Revert last commit (did not solve Travis issues)

    commit 64919795f1ebf9111aa2c2c82ef10da3e56f9490
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 23:48:48 2020 +0000

        Set up SSH keys between Travis CI and GitHub

        Following tutorial on: https://github.com/alrra/travis-scripts/blob/master/docs/github-deploy-keys.md

    commit b0ce9cf85a1541909f6043072d00639418af8758
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:54:08 2020 +0000

        Ask for verbose deployment of pkgdown site

    commit 0a9c9d2c59348c90591edb3e4233d0df25cf9bbc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:16:18 2020 +0000

        Import shiny::fluidPage

    commit 82767daa06239159bf7a2e9febc5688d0369e681
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:16:18 2020 +0000

        Fix AppVeyor using release version of R

    commit ab0189024fde749153c28982ae86a7dfc803c35d
    Merge: c2cd46b2 bdc1e3c9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:07:55 2020 +0000

        Merge pull request #401 from nuno-agostinho/dev

        psichomics 1.12.1

    commit bdc1e3c90cd8ac7fb70acafb04d0989c608d8c1a
    Merge: 7f1a9834 c2cd46b2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:05:42 2020 +0000

        Merge branch 'master' into dev

    commit c2cd46b237b06dd61a2bba714220b7d370708a78
    Merge: 27b677b4 7c933a20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:55:10 2020 +0000

        Merge pull request #400 from nuno-agostinho/imgbot

        [ImgBot] Optimize images

    commit 7f1a9834e8faaed78558eb56fb05461f2d07dec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:29:48 2020 +0000

        Avoid test failure by skipping it on CI tools

    commit e23f89dae16a1f10f627a560795d0a43127abe23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 15:02:03 2020 +0000

        Minor changes

        - Fix unit test issues
        - Fix error when using `plotDistribution()` for a single value
        - Copy-edit NEWS.md

    commit 475b712449f5db139901453e85356ebdf74b228f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:38:35 2020 +0000

        Browse list of AS event diagrams

    commit e038ea32fc8c01066d7117ffa40cd3b89afe35f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:37:40 2020 +0000

        Filter AS annotation list

    commit f7477f5e51ee57e7c67fd9f9bdfdf8eae04a9184
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 23:57:32 2020 +0000

        Fix issues with R CMD build/check

    commit e3c650251cdf2023ea275d6b897ccba2331995d6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:34:13 2020 +0000

        Correct spelling issues

    commit 983944d3b0cf7f975021b81700d6efc9804c5551
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:22:59 2020 +0000

        Fix issues with taking into account another exon as reference

    commit ce61e2c7ecf183ce11be7284d9b7acdaca3b605b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 17:18:25 2020 +0000

        Fix UCSC external link not working based on gene position

    commit 38d61368a649e870f93d061d0fe5f24d96b8feb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 16:58:51 2020 +0000

        Fix SRA project not loading if extra information fills only one extra column

    commit 4e4ebdd510d70ff8022dbd05e1a95b5c699d0164
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 20 16:35:40 2020 +0000

        Show available annotation information and query PubMed even if Ensembl is down

    commit 7c933a202268984ba77b179faba66e8b7d9be8a6
    Author: ImgBotApp <ImgBotHelp@gmail.com>
    Date:   Sat Jan 18 12:11:22 2020 +0000

        [ImgBot] Optimize images

        *Total -- 2,817.81kb -> 2,014.38kb (28.51%)

        /vignettes/img/UHRF2_expression_prognosis.png -- 97.26kb -> 46.80kb (51.88%)
        /vignettes/img/UHRF2_exon_10_inclusion_prognosis.png -- 47.44kb -> 23.25kb (50.99%)
        /vignettes/img/pca_results.png -- 347.44kb -> 197.16kb (43.25%)
        /vignettes/img/NUMB_exon_12_inclusion.png -- 110.03kb -> 66.18kb (39.85%)
        /vignettes/img/UHRF2_exon_10_inclusion_differential_splicing.png -- 77.23kb -> 47.89kb (37.98%)
        /vignettes/img/UHRF2_differential_expression.png -- 170.04kb -> 108.91kb (35.95%)
        /vignettes/img/3_quantify_splicing.png -- 89.61kb -> 58.73kb (34.46%)
        /vignettes/img/5_pca.png -- 146.58kb -> 97.32kb (33.61%)
        /vignettes/img/4_survival.png -- 84.17kb -> 56.04kb (33.41%)
        /vignettes/img/2_normalise_gene_expression.png -- 70.54kb -> 49.50kb (29.82%)
        /vignettes/img/4_group_tables.png -- 64.14kb -> 45.53kb (29.01%)
        /screenshot.png -- 293.99kb -> 209.80kb (28.64%)
        /vignettes/img/4_data_grouping.png -- 50.17kb -> 36.50kb (27.25%)
        /vignettes/img/1_load_data.png -- 55.78kb -> 41.42kb (25.73%)
        /vignettes/img/diff_expression.png -- 525.58kb -> 421.29kb (19.84%)
        /vignettes/img/diff_analyses.png -- 327.87kb -> 265.16kb (19.13%)
        /vignettes/img/4_save_groups.png -- 42.34kb -> 34.70kb (18.05%)
        /vignettes/img/Correlation_NUMB_exon_12_and_QKI_GE.png -- 189.59kb -> 180.42kb (4.84%)
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    commit 9cbef932c55f8edf806cee6be9822af8c13aedd0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 18:02:25 2020 +0000

        Fix tooltip colour when hovering rug plot points

    commit 6dc691bd1a13937d8b4775f2d5b6abc5d06f33a2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 15:38:06 2020 +0000

        Create pkgdown site

        - Copy-edit README, documentation, etc.
        - Improve alternative splicing annotation tutorial

    commit ac83c06f7f2950f6cb8762447f1fe35208bcfff1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 14:12:24 2020 +0000

        Add automatic spell checker and copy-edit documentation

    commit 8450709045cd166beefe3a4c19c37984a7fa1cae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 11:29:02 2020 +0000

        Minor improvements

        - Fix plotSurvivalPvaluesByCutoff example
        - Rename vignettes
        - Copy-edit CLI tutorial
        - Fix R CMD build/check/BiocCheck issues
        - Copy-edit function documentation
        - Add unit tests for SRA metadata loading

    commit 85c54c9e052ca61ad76c4d823046ab85ca091afe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 10:11:56 2020 +0000

        Add AS event diagram to distribution plots and annotation page

        - Avoid app crashing when searching for PubMed articles to many times

    commit 28ee94df2c70355fb76f71bb7748a799eaf20429
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 13:07:32 2020 +0000

        Copy-edit NEWS

    commit e5ddf7c9e37160c77ba689f283dbf99562061442
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:36 2020 +0000

        Fix R CMD build issues and copy-edit code

    commit 726a5adbbeb3db4f8d9eb53a21ed01764e887ccd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:03 2020 +0000

        Fix package dependencies

    commit 08555fabd4260d005c14cbd531e42b24271a43c0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 10:10:41 2020 +0000

        Fix: add code for subset plot

    commit 81f6f1174ad6339d34a7bae00ab8e7b9af9b94fe
    Merge: de9d66b5 94f39514
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:41:12 2020 +0000

        Merge branch 'dev2' into dev

    commit de9d66b54ded617f41bf29a2dc60673a079939d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:38:01 2020 +0000

        Remove unused function

    commit f2c47bdb34cd80c71d85cf82b506d5ff0f9d2358
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 13:47:52 2020 +0000

        Improve data grouping

        - Improve import/export of data groups from/to a file, including colour support
        - Fix discarding of samples not associated with any subject when exporting groups
        - Fix issues related with importing groups based on a file with groups of splicing events and/or genes
        - Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
        - Show number of genes in pre-made gene lists
        - When creating group of genes based on pre-made gene lists, discard genes that are not loaded

    commit 04b163d7f1c72f8ee713913db8b3f287079fbd82
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 17:02:03 2020 +0000

        Copy-edit code and NEWS

    commit 20e61243055c4d63b32672bf3611f8b04bb2c258
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:56:29 2020 +0000

        Fix slow preparation of diagram representations of AS events

    commit f9c74c8e4a69a9628d0166e8d8222efa619a7489
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:50:33 2020 +0000

        Fix error when trying to set page_size for Firebrowse web API

    commit a379bb5798e60bc6e61c3cca34bbacb1e73b89fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:29:06 2020 +0000

        Update documentation regarding survdiffTerms

    commit fa33d46c6f897ee868a1c8c5a1ceedef7a5ec837
    Merge: 1d7116ec 27b677b4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:26:13 2020 +0000

        Merge branch 'master' into dev

    commit 94f395143e5a5a4ef2d1075f97ed6854275e8b4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:20:28 2020 +0000

        Fix 0 (valid) rows error

    commit 1d7116ecb67fdbfb43db06d78c23b9ca897e1f87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:19:29 2020 +0000

        Include reshape2

    commit f95f8e20c99ecd90fd35844f5f121025bd5f3222
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:11:21 2020 +0000

        Diagram representation of alternative splicing events

        - Redesign AS event selection; highlight search results using jquery.mark.min.js (built-in highlighter has many bugs)
        - Rename internal CSS/JS files
        - Update jquery-template from 1.3.4 (2016-04-19) to 1.8.5 (2019-02-17)
        - Remove validator.min.js (not being used)

    commit 6806235f5404304cb749b6693cfbd87054acdbbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:53:40 2020 +0000

        Copy-edit code and function documentation

        - Separate utils into different, related scripts
        - Update Roxygen to 7.0.2

    commit f58c252a9c739899ca4d9c4c9fa062fca939de1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:22:14 2020 +0000

        Improve density plot

        - Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
        - After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
        - Rug plot labels now show data values if sample names are not provided
        - Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
        - Fix misguiding example in function documentation

    commit 84f9ec3b0f69b8729c5c3176fb0cf7e66206cc0e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 17:41:20 2019 +0000

        Fix loading of a portion of TCGA data if too many cohorts are selected

    commit 91c46c3a69363d5d98b36a111b02dcc7d773c98b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 13:34:08 2019 +0000

        Improve function documentation

        - Include information on function family
        - Clean up documentation of aliases and deprecated functions
        - Change patient to subject where appropriate
        - Copy-edit CLI tutorial

    commit c569febbc2f8f77a8003f6c4b9dd6304db5d1bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Dec 19 16:43:17 2019 +0000

        Fix issues with junction quantification files

        - Improve tutorial on loading user-provided data
        - Warn when discarding rows with duplicated rownames
        - Warn when discarding rows containing random, alt and Un (unknown) chromosomes
        - Fix error when returning NULL dataset after processing
        - Copy-edit code
        - Test junction quantification file loading

    commit 5fbc5bdc8ab3de2aec982a9b3c8febfe94809b5a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Dec 17 15:08:42 2019 +0000

        Support junction coordinates from chromosomes M, Z and W

        - When loading custom junction quantification files
        - Copy-edit information on the format of custom files

    commit e4e8e918cd6b4830b31ed7b0a07abdb462481042
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 7 14:46:07 2019 +0000

        Add ORCID identifiers

    commit 27b677b4d6929ab5a0690b3abc21a77077a13736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:18:58 2019 +0100

        Update README.md

    commit 77ff8427f0f4a810ece914cbc99db54a646df4a8
    Merge: 50ebb496 4550109a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:16:59 2019 +0100

        Fix Windows warnings in CI tools

    commit 4550109aac0d2180d44e45b01598f7552517c569
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:49:29 2019 +0100

        Avoid using Bioconductor-devel (wrongly trying to use R-devel)

    commit 05dec272fdc65906c1c73c7e37e69eff1317cd3d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:45:19 2019 +0100

        Bump version to 1.10.2

    commit f403ca10dd6f9595af5e7ed534a6101efbb760d1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 10:05:40 2019 +0100

        Install r-lib/remotes from CRAN instead of GitHub

    commit 7f4ad886741271dc774ce750222dda1b0b03eb94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 09:59:53 2019 +0100

        Fix link to ggrepel::geom_label_repel not being found on Windows CI tools

    commit 50ebb4961783ce4751ef4b492c8428b837802a65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:13:38 2019 +0100

        Bump version to 1.10.1

    commit 2e2abe34478ccf8fb14d177f2ce0eeaae817996b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:04:23 2019 +0100

        Avoid test timeouts in CI tools and Bioconductor

    commit 3f3f8872b35e321f524599ae8913aa3ca4a40eaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 19:20:58 2019 +0100

        Fix AppVeyor (#387)

        Install *org.Hs.eg.db* and *GenomeInfoDbData* packages via source (instead of binary which is unavailable)

    commit 6f41576364d55a3dd9a0299a78d08c8c3069c62a
    Merge: 8711c313 6d9f0824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 16:34:43 2019 +0100

        Merge pull request #388 from nuno-agostinho/travis-mac

        Support macOS testing via Travis-CI

    commit 6d9f08241245a75c1469c7ad1d5fac455ab2fbf7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 15:46:34 2019 +0100

        Support macOS testing via Travis-CI

    commit f912e3d65be79c9bd52e38e58cff285bd2d8cd94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 24 17:17:46 2019 +0100

        Improve dialog when trying to load a local folder without any supported files available

    commit 6f714d3578ce7a6d2f89a400f10907b6c88acc1b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 17:33:17 2019 +0100

        Improve GTEx data loading

        - Export getGtexDataTypes()
        - Improve available examples

    commit a1ca8d232ff76a824fd935f2690e4628d5cdfdba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:51:22 2019 +0100

        Fix alerts crashing the app

    commit e07766a3583da3c318be50eaa3477b9322a96658
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:06:35 2019 +0100

        Improve AS annotation loading

    commit d0745def60c2469178b0341697c110b086497040
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 3 13:54:24 2019 +0100

        Fix prepareGeneQuant not working for stranded datasets

    commit 4fc0ed6e3872a15a6091f5c656164be7fa806e77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 14:05:13 2019 +0100

        Fix Firebrowse function not loading all expected data

    commit 8711c313fd02fb095c496a2b9242193d5d1e7b4d
    Merge: e87a817f 15236616
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:33:33 2019 +0100

        Merge pull request #384 from nuno-agostinho/evalWithTimeout

        Replace usage of deprecated function

    commit 1523661611913ceef6a3f3bd6e1b89c9ce3ac716
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:08:51 2019 +0100

        Replace usage of deprecated function

    commit b952a879b3bf23f3759312c86677ad8b0a16f764
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 2 14:26:14 2019 +0100

        Fix p-value plot bugs

    commit e87a817f84eb88df17a3a4f53fef2b94e7a560c1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:20:05 2019 +0000

        Update .travis.yml

        Based on https://github.com/Bioconductor/BiocManager/blob/master/.travis.yml

    commit f15ab1875b318554d568022228f33a8a3e3def20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:16:02 2019 +0000

        Fix appveyor.yml

        Based on https://raw.githubusercontent.com/Bioconductor/BiocManager/master/appveyor.yml

    commit 3cf6a9b743356485fd354175173440fb270a35f8
    Merge: cad23d89 1f121b7a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 13:24:40 2019 +0000

        Merge branch 'dev'

    commit 1f121b7a9263a9bc1348fe95ed10a32f93b4113b
    Merge: db6c24f4 6ab7ab5b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:53:02 2019 +0000

        Merge branch 'dev-2' into dev

    commit 6ab7ab5b7faf8f0755df4585415f0cb281ed1aea
    Merge: b91903c6 cad23d89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:52:17 2019 +0000

        Merge branch 'master' into dev-2

        # Conflicts:
        #	NEWS

    commit b91903c6b07bf50e1cbe67bf46b06343a39d9320
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:51:23 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit db6c24f4af2b371c061b96577479a59aca9097ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:45:11 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit 71e896c1c008fce02fbad5de282327816ef39a33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:28:24 2019 +0000

        Improve and fix function examples

    commit e29243d6e5d2783019182604c4ada9b96dba7582
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:47:16 2019 +0000

        Fix issues in R CMD build/check

    commit db83ac6395086c9ab0d244fff1eced5734c41965
    Merge: 17e2fbd3 1deea8a5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:31:49 2019 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 17e2fbd3026f133b864b60a08bbb742a373b2f53
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Fix issues in R CMD build/check

    commit 1deea8a5ceb0c77ff269cffe6e4762d205433468
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Copy-editing

    commit 1190319ef6dab35921c8fb3c9870a29c5befe51a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 10:04:36 2019 +0000

        Fix issues using EList's gene expression for correlation analyses

    commit d6ecc35918e88ce390a51026234c38824cd18581
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 16:00:29 2019 +0000

        Code copy-editing

    commit 0fefbe1d1cc79a2c554321ef62af02ce37647cb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 15:58:12 2019 +0000

        Make it clearer that TCGA data is loaded from Downloads folder by default

    commit 885ed2cc3315d2efaa7795679597f7b2e29f4810
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:22:18 2019 +0000

        Plot p-values by cutoff

    commit 388aef18906d504e4edfef4294d8152935b63322
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:14:01 2019 +0000

        Minor bug fixes and improvements

        - Allow to edit path in file/directory browser elements
        - Automatically set dropdown width for group attribute selection
        - Fix warning when displaying group preview only based on subjects or samples
        - Prepare for code escaping in newer JavaScript versions

    commit 37a0afa77baec0645d9378d24cd0acb57d1af1de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 15:11:35 2019 +0000

        Fix issues with R CMD check

    commit d1246e4b8322f3cce87fcacb76894dc2e34ccb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 14:55:48 2019 +0000

        Require human gene annotation

    commit 87a2d3d83d46f2660576f905222a3c1df1638da7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 11:21:05 2019 +0000

        Fix table filtering based on plotted points

    commit 3cb42cf98e05b35bd2006ab9ae5f85833e707032
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 18 15:43:04 2019 +0000

        Improve and fix plotting of gene expression and alternative splicing quantification data

    commit 1caf8bada79c40a23afb39422050550f2c9aae6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 15 16:22:27 2019 +0100

        Plot specific combinations of gene and alternative splicing events after performing correlation analyses

    commit 387d63051f11ccee7856271f8369b38570b3d556
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 14:24:35 2019 +0000

        Improve AS and GE filtering

        - Present PSI filtering settings in the visual interface
        - Minor interface tweaks
        - Fix plot PSI error

    commit 0a094a868e124e5ec115d1f5f3c169ae057fdafe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 13:45:24 2019 +0000

        Update citation details

    commit b6d0909be72ed3d54fabd3378aae050e14ec4082
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 7 15:27:54 2019 +0000

        Allow to use selected splicing event in correlation analysis

    commit 1fb75cbb1f6de14bbcff49a1fa2ed1f942a0e3ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 18:58:47 2019 +0000

        Fix error when subsetting edgeR::DGEList

    commit b0be91e288bab1d1a3f2917dc4ea0a917400382d
    Merge: 47bee247 76ba81ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 14:50:34 2019 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS
        #	R/data.R

    commit 47bee24752a09aae6052235133a41d5c30e71f14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 03:01:52 2019 +0000

        Minor copy-editing

    commit 972e5582a5cc7664a89542dc37edf926e7b27e65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 02:59:35 2019 +0000

        Improve correlation plots

    commit 25ece479739d264f1f86898a98b703b6355ffbe6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:36:02 2019 +0000

        Fix missing attributes of gene expression normalised via voom

    commit a949e3a91ad0a650c39a57e0351e9bae1f702b73
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:34:12 2019 +0000

        Fix error when creating groups containing only samples and no matching subjects

    commit a063ae9c3e8485ec8321719898a43a2e1eced67b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Default to load clinical, junction quantification and gene expression data when selecting TCGA data
        - Minor copyediting

    commit 76ba81ea5f6d3f13761ab733550daa2e703252bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Minor copyediting

    commit f344fc0607fdf20cf78e91ecaf4e40f8ff337493
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:50:28 2019 +0000

        Fix article title formatting

    commit ad81788ad9241386b34349bb6d912824a7ff51e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 28 11:57:54 2019 +0000

        Improve gene expression filtering and normalisation and PSI filtering

        - Plot distribution of gene expression per sample
        - Plot distribution of library sizes
        - Plot gene-wise expression mean and variance across samples
        - Plot PSI mean, variance and range
        - Filter PSI values
        - Perform voom and respective normalisation if desired
        - Sample filtering
        - Filter lowly expressed genes using edgeR::filterByExpr
        - Convert ENSEMBL identifiers to gene symbols
        - Show labels for distribution plots

        Bug fixes:
        - Fix distribution plots requiring all samples in a group
        - Show sample names in distribution plots
        - Fix inconsistency of delta median and variance

    commit 795d17597f7d639681aa2cf33937ecd8a0c7eea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:15:56 2019 +0000

        Improve SRA data loading

        - Accept a vector of files as the first argument (easier to use with `list.files()`)
        - Ask to overwrite file if one exists with the same name as the output file

    commit 161f9c2da7bf5139bda1a56c0bd8aebf76268b9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:03:53 2019 +0000

        Minor copyediting

    commit 2fb74587d87c9a8a6fc2e85c1c429faf4ea1d3b6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:02:33 2019 +0000

        Update copyright references to 2019

    commit 808b219acfb5b317afc0fe232cb268a49a51cd52
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Feb 13 17:05:57 2019 +0000

        Fix colours/opacity in the rug plot within the distribution plot

    commit 7536285cb2fcea357ff945ce96192b6aff815396
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 7 17:46:53 2019 +0000

        Fix wrong information in table of differential splicing results

    commit cad23d89b8f07420b6cd90067b9ede60a4651881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 14:59:22 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit a1510c15977c36b6c9863b0a0ba0140243b9b8c5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 11:54:33 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit 676ecb0b64f593ce3a9b4d3d5fbc4adae17fd1d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 29 23:10:02 2018 +0000

        Fix crash when loading psichomics with test data that is not locally available

    commit 5bf83e4e96ac73180b6187239c7d2f570da21c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:39 2018 +0000

        Fix R CMD check and BiocCheck errors and warnings

    commit bb78b2be6e8c9457b5772435a574e728c870504e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:27 2018 +0000

        Fix progress bar when quantifying alternative splicing

    commit 19fea9e64f53c3e0479b61db08adee359ced772d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 15:46:13 2018 +0000

        Improve documentation of exported and internal functions

        - Minor code copy-editing
        - Minor tutorial copy-editing

    commit 23e38acd50866c16438a4dc6399173d98e52259b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:47:25 2018 +0000

        Minor improvements

        - Bump version number
        - Allow to show dataset icons in "Data"
        - Improve data grouping interface
        - Fix inconsistent group names when creating groups based on pre-made gene lists
        - Avoid error when user cancels file browser dialog to load groups from a file
        - Copy-editing code and documentation

    commit 65cc716dd58d1ea9a577e34d898c24b92308853a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:25:38 2018 +0000

        Ask before replacing correlation analyses

    commit 661a73a2bc12c54227a97c0003eccb022dfdab28
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:24:40 2018 +0000

        Copy-edit tutorial on custom alternative splicing annotation preparation

    commit 09210d45c4a69f37355299acff1d074e3e3c2349
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:21:38 2018 +0000

        Improve console logging of alerts

    commit e81cee95712934e4ba04b8100e7cee13d99874cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 6 15:44:19 2018 +0000

        Decrease loading time after alternative splicing quantification

    commit d65138081a2c0f25c4c4f59e8cac3aa99fe68cf2
    Merge: 950fead2 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:45:15 2018 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 950fead2c87b45eef1c57ba0ecc5221405648e07
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:43:56 2018 +0000

        Change which AS event types are quantified by default

    commit af7d87997ca811bc3dae0c9bca5e964eb92ff713
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 31 17:37:25 2018 +0000

        Load pre-made gene lists and improvements to correlation analyses

        - Display correlation results in a table
        - Display correlation analyses progress
        - Load those groups by default and allow to create them in the group interface
        - Initial support for RBPs in Sebestyen et al. 2016
        - Allow to use such groups in correlation analyses
        - Improvements to interface for correlation analyses
        - Minor copy-editing and interface improvements

    commit 757f821eacadef804a39c948dc8752bec86bba88
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:37:13 2018 +0000

        Fix link for AS annotation creation and loading

    commit cc0ddc5999ac10060c83dcff1cdf35356e5e5aa7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:29:53 2018 +0000

        Fix word break-related visual issues

    commit f59713d9a5b76005ca392b10477376fa3fb4c941
    Merge: 650c0bcd 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:32 2018 +0100

        Merge pull request #366 from nuno-agostinho/dev

        Update citation link

    commit 0166a5578b61fcb0af3c4a9643402d3ac886869c
    Merge: c78f8054 650c0bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:13 2018 +0100

        Merge branch 'master' into dev

    commit c78f80540dbb9a3bef754317251d16403c57c8df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:42:49 2018 +0100

        Update citations to link to article in Nucleic Acids Research

    commit 650c0bcdc1728a113a1a11e095c16b07c3a10881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit ebb47d9cc359f8539e319b67ee7512dd55a92eb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit ed1ad926df259ee936a9c0175a3f59024595895e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 1614e3e3a35a4c8f15a05a45623584d234c98f20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit fbb70cc6b0a0a892716fd4fe6b0e7a9734bf1aff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit ae48e0e42ecd7c2217e7e5acc6ef1af5514aadaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit ad6777fd7a401b37b659bb5440449a79b8450545
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit e08b64dd60fa56ee697557beb2090724f8f28896
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 3229d8ce5f23237f67119ce45eb23e545aabc4c3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit 9953f4f41d7b573653e23bb4ac45df864cbab160
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 5fc56fd9162549d11daf7aa6271274b9c2323112
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit f7921b88d00b7da95c5acd379abd56d14088cf5c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit c9fa821990d83f6fe223aa97de8b9265d2050ab1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit 4f4cd0fe701f891d536bd13d227a908878b8e722
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 54dea1bdb5f19a49683e3a24cc6f33964657e9fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 8b5e1b106d6b4a3556bd6c57dd1bd1786053a660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit b4fcaeaef1238f77a19b6262a6bbbea88e265940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit 2a2c46a84954e56ae792f075207a1fc7c6eb1f74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit ad607e31af37c0a65de674140e4f45ba04cef0e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 2e29f55d2a884216e4eb623772018a6f61683624
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit 4593c1ffe040e390b5ec049c449a82ad725c6dcb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 2f7c7e695f269a454f0a7de1e17872ec6c835217
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit d3218e2997a5c238827332cf8d1e16a33fbbf496
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 327bf525aeb1fb599f400b05c5ae51074db77c44
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit dace8973cd449c327d17e068fa680c1af0851bc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit 8c6e49459bf060426fd4dec5c97a0437b9fb8295
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit 9f57a89e0a585cf095b39298c276a3a5385afd0a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit a766175c2c1814c06ae700cefc2dbedf54e09272
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 72c7322885372c86ec86a7160ff366549f1e7c04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit 6ef892922d492ea1b23bd36ddd970bb72c27caca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit 644b5514e8ddc046e3ea9b4db38a25928da50ef3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4ba02ed2c43d15f44f7c04a68c9c04f6b854536b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4d7e49cf6e5884f7b70bd31cf5809b7ad407f3b8
    Merge: 193ac794 660ff9d8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:50:12 2018 +0100

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 193ac794afb5ba5ecc87a8434e6d98a8ad5b264e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 826edf1ecb8a4d56472cf35392919ae485e53a6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit d2a64dbf7f7ab3189334b6de72623685b47f920d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 10cb3df4c0304152629e18fec97a1fa880bcef8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit 486d43c20f70f1f18f4b6ea3988c31558f719940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit bddf111e81a70a988d8c06c31147518592098412
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit eae64553ff843b09a8013c6565f9a75bb47f9876
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 48189e1b1a8a49b2f45816c448da9b0cc5e71149
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 660ff9d802bd2f9d7eb920b519dfe0d74906904b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 788366fff3a0e37fd5a4bb7f5829b7c3fde6a9d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit d7792511a47552b836047659736db4cf7fc1462b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit d5f8c587115cc23b4a07e496c8f07a5ba86bfe58
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 40aeed67aa0e24588ab126f7fd03537583d09ac4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit ca61fe24d1f043edd937be09e816f40ed1f0c9c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 455faf68c9dc1ebee8bd1cba8d0f0e6743b5154a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 7e2e449e90b11da3ff93247ccbc58e33dfb6218e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 8b4a7e91d71b858ea16b763d6929643d1b216f04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit 3b246807f63fa611d8ace55e3245965aaccac351
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit e392f34ebc314e4e7360ccbb3685fe4119734718
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:09:09 2018 +0100

        Update README.md

    commit bf424d7bc72d8c9eff2cf92c920b883ec7ea9552
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:01:13 2018 +0100

        Update README.md

    commit 66e932b545d0e533d7a3025de1216fb989465321
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 19:57:39 2018 +0100

        Update README.md

    commit 946af16ddbe473f074e560ba248e40b54f8359c6
    Merge: 0aac8a4d 9ea793f8
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Thu Jul 5 16:45:04 2018 +0100

        Merge pull request #361 from nuno-agostinho/dev

        Version 1.6.1

    commit 9ea793f87b94f1d916200d7431eea90e90bcf2d7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:59:26 2018 +0100

        Add placeholder

    commit 99e7b05fd75667a856b3d7254d2444b5063430b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:11:47 2018 +0100

        Add more options when plotting gene expression versus PSI values

        - Change font size
        - Change plot height
        - Improve presentation of scatterplot options

    commit c4cbb939fdc4f0c0eb83e5a556895650974fb285
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:26:46 2018 +0100

        Simplify code for file format recognition

    commit 0f976abc5570ae7407fdd0ea19af92ee62a15f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:09:37 2018 +0100

        Improve group creation and manipulation

        - Greatly improve speed at which a big file is marked as incorrect (by loading just the first row instead of the first six rows of a file...)
        - Fix error alerts not appearing when trying to create groups based on invalid parameters
        - Add error alert when trying to load file without group information when such data is expected
        - Improve style of group preview table

    commit 864fd363e59a050aa89f5dc614c207d130d998a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 11:45:03 2018 +0100

        Fix unit tests for parsing splicing events

    commit cd795942df7123e959bef96c36c03a0c8d956b4c
    Merge: cb459489 0aac8a4d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:11:41 2018 +0100

        Merge branch 'master' into dev

    commit cb459489889a9f185d4b15ee792bb3cd6becf05f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:06:35 2018 +0100

        Minor changes

        - Copy-edit NEWS
        - Change order of analyses (makes more sense this way)

    commit 09c0622f25d775e282d415c20a0bdb828a5669bb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 4 18:18:57 2018 +0100

        Display alternative splicing events in transcript plot

    commit 0aac8a4d1f5f9e3352612a1d3b901faacc7723b7
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Wed Jun 27 17:21:32 2018 +0100

        Travis-CI and AppVeyor fix (#360)

        * Fix issues with GenomeInfoDbData and DelayedArray installation in AppVeyor
        * Use binary packages to speed up Travis-CI builds

    commit 47cd9d40d6b374ad1ffd5f397a4b7920bd4fcf4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 18:58:47 2018 +0100

        Fix issues in R CMD check and BiocCheck

    commit 9de9492c581732f7cfd296f9f44478eb4b7cf699
    Merge: 92236436 30ff9e8a
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Tue Jun 26 17:45:49 2018 +0100

        Merge pull request #359

        Version 1.6.1

    commit 30ff9e8aa73036e42a2a0203de606787729574fc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:40:46 2018 +0100

        Rollback to before introducing event-wise Cox models (re-think if this is the best solution or not)

    commit 36d3163410f32578a195eec7d204d6334ddcbe65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:02:34 2018 +0100

        Improve data grouping

        - Preview groups based on selected attribute before creation, closes
        #218
        - Correctly suggest how to select variables in subset expression and
        give more examples on how to use this feature, closes #220
        - Fix subject/sample attributes not being updated for selection for the
        GREP interface
        - Minor copy-editing

    commit dfdcb3fdfb06591c0a050e22bbdac8d1fef33f9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 16:59:31 2018 +0100

        Update NEWS

    commit 5de4ee0251eab26e9f205d793190dec57f2aed4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 25 16:26:12 2018 +0100

        Recommend installing psichomics through BiocManager

    commit 2a9f6ab5820cb39fffbb470a1b92e20a635ce394
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 23:26:17 2018 +0100

        Fix error if named samples are given

    commit b3cd480ba9acd37f5948be7532f5923ab6fbc335
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:47:28 2018 +0100

        Minor improvements

        - Improve display of filtered genes
        - Update default minimum samples used based on available samples
        - Render position of splicing event when plotting transcripts

    commit a155800df9380649e461bbd5aa8d0bbe8711d451
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:20:07 2018 +0100

        Improve support for loading custom data

        - Prepare gene and junction quantifications (STAR output) and SRA metadata to be loaded into psichomics
        - Add tutorial on how to analyse SRA and user-owned data
        - Update other tutorials
        - Fix data not being loaded when fread returns a warning related to issues with previous fread commands

    commit fb347b1842f935e9251f60f1cf8d8c4ff5131e1a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:33:20 2018 +0100

        Fix warning when using deprecated function limma::toptable

    commit a79e15837ca633766d0397432f1704ecd1de30ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:30:14 2018 +0100

        Fix crash when quantifying splicing for a single sample

    commit ba626a461dbdc236499392d798564c3b53a04eac
    Merge: caa07c20 9c1b3da2
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Sun May 20 16:49:14 2018 +0100

        Merge pull request #356 from nuno-agostinho/recount2

        Add support for recount2/SRA data

    commit 9c1b3da2306a4a60b3f97c5a0fe6e54262f4f50e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 16:40:48 2018 +0100

        Minor improvements

        - Bump version
        - Update NEWS
        - Fix issues with R CMD check
        - Hide close button in progress notification

    commit 203a0fd493387983ce8f50caa2cf9118b62f0d7f
    Merge: 6702d93c 32213531
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 15:54:53 2018 +0100

        Merge branch 'recount2' of https://github.com/nuno-agostinho/psichomics into recount2

        # Conflicts:
        #	R/data_recount.R

    commit 6702d93c929e7818ec2a8f992936032d583f5dee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects
        - Update documentation (including copyediting)
        - Improve hg38 splicing annotation

    commit 3221353188fa26be22296c0fa596efa5040e8c6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects

    commit b22a2ca081d095d87fd7581f6a9384f6575ed6f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 10 15:18:36 2018 +0100

        Minor revisions to survival

        - Add link to survival page from Cox regression results withing the table containing the results from exploratory differential splicing analysis
        - Use minimal p-value to decide the optimal PSI cutoff (makes more sense)
        - Improve p-value plot, including labelled line with the p-value threshold and
        - Minor copy-editing

    commit d0304ffd165e31e25cc665c3067db3877b4a5b4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:29:57 2018 +0100

        Perform event-wise Cox models using PSI values

    commit 20e84802e4827d7161276129577bd2fcc626b08a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:10:34 2018 +0100

        Fix crash when inputting non-sense as the axes for the splicing scatter plot

        For instance, discard:
        - Non-numeric values
        - Numeric values when min > max

    commit f3645f0247f8e01f6e5873f09ac8c765fe3904d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 14:51:32 2018 +0100

        Allow to start app with test data (for dev purposes)

    commit caa07c20f35289f48fdf0deeecd3f8437a16bbb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:17:41 2018 +0100

        Fix TCGA sample metadata not showing samples from all junction quantification files

    commit 2fa6cf42035a2c62fd03fd910a9d5fbf203d834a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:15:29 2018 +0100

        Fix TCGA sample metadata not being shown when loading TCGA files from local folder

    commit 92236436b040442b484060209e959af947d76503
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 16:29:05 2018 +0100

        Bump to version 1.4.5

        - Update NEWS
        - Add links to original article in bioRxiv
        - Update package description within the GUI
        - Update mentions to NMorais Lab and iMM
        - Update copyright years to include 2018
        - Minor copy-editing

    commit b4d0e8748a3160e6838b6f68bc2a11795be92de2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:30:06 2018 +0100

        Copy-edit GUI tutorial

    commit b25b9124e57cf2758b710e980e1dde74f30b4a66
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:16:38 2018 +0100

        Replace dataset no longer distributed with car package with a built-in R dataset

    commit a09c8ee50a9ae185438c2b37e554ef9086a24655
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:37:29 2018 +0000

        Update Contributor Covenant Code to version 1.4

    commit 58a1f137b2985b97d188f87e67f14437dec757f3
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:35:17 2018 +0000

        Update README.md

        - Direct article link to the latest version available
        - Direct reference to original article (instead of references)

    commit 7783adb3be5bf6a1095a9f1cdc4b7fb899ba05ff
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:28:12 2018 +0000

        Update README.md

    commit 584cce4cf4da01e3da5450c4ec889e15d3cb8ddb
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:06:00 2018 +0000

        Update README.md

    commit 751e3f52c2539032b615c2e10e3d3fbb774e1455
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 01:54:53 2018 +0000

        Update NEWS

    commit ccecd6b7c2a1164470fa3e23bec53a7f876c24be
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:28:11 2018 +0000

        Fix R CMD check issues

    commit 26b3e0d375f4916ad2570f8421ab344286986e34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:13:08 2018 +0000

        Improve differential analyses

        - Fix highlighted events not filtering table for differential expression
        - Update selected gene in gene information according to selected
        splicing event
        - Select splicing events or genes for differential analysis
        - Set selected gene when performing survival analysis

    commit 5fef2819224bfc3cd3af6aefadc34cba94ca66d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:06:45 2018 +0000

        Fix problems related with DT versions >= 0.3

    commit ac6dfae6e30064dd2f8ccf1aac9c1e58091ba676
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:04:23 2018 +0000

        Update vignettes to include case studies

        - Correctly export required functions
        - Copy-edit documentation
        - Rank variable that most contribute to selected principal components
        - Update CITATION file to direct to bioRxiv article
        - Update information in welcome message
        - Show number of contained items for selected groups
        - Update authors and bump version to 1.4.4
        - Update .gitignore

    commit 882eb627227e20e61ce9b4379d493fa06c5820ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:03:04 2018 +0000

        Fix optimisation problem when calculating optimal PSI cutoff for survival by extending search bounds

    commit 860ce90adea912abdaa7da6d775060748499e457
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 23:30:52 2018 +0000

        Select samples to be used for survival analysis

        - Automatically select primary solid tumour samples (if available) when using TCGA data

    commit 8c2cd8af6f5fff32f63174e0f3f459db9140df7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 13:51:55 2018 +0000

        Automatically set sample types as groups when loading TCGA data (GUI)

        - Fix potential issues when dropping matrices
        - Show groups after creating groups based on clusters

    commit 8311aa1488253356b25e7f98285fc4b18526e7e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 19:26:23 2018 +0000

        Improve gene expression pipeline (perform limma-trend by default)

        - Improve gene filtering
        - Copy-editing

    commit bace4ac2e6dcec6df18e3131ae7e94db95cd9773
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 17:58:24 2018 +0000

        Stratify patients for survival analysis based on optimal gene expression cutoff

    commit f55dcfbf6af1719efc8aff413bf0fd4624d17f72
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 15:00:13 2018 +0000

        Quantify AFE and ALE events through AS-centric and exon-centric methods

    commit 8451fe2aad4865b20cb35ecd548771326b31028d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 14:41:38 2018 +0000

        Tolerate 5% of missing values for both PCA and ICA (by default)
Package: Rarr
Commit: 1795c676e2ac81a9ba2a592c7210cc59036544b6
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-30 17:04:10 +0200
Commit message:

 Bump version
Package: Rarr
Commit: b241fba6e8f2c2897b3f4b20c04bfd6bf13a8e23
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-30 17:03:54 +0200
Commit message:

 Document missing breaking change

Follow up from #174
Package: Rarr
Commit: 9f681bd1bcb9e257ae041f97fedee77faa548fc5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-29 17:58:27 +0200
Commit message:

 Revise unnecessary isTRUE()/isFALSE()
Package: Rarr
Commit: 177fb41800cc694eea75b8544241f5558dd6002e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-05-29 11:14:50 +0200
Commit message:

 Remove extra .normalize_array_path() calls
Package: universalmotif
Commit: d32921e61f9ad6d59db21b4b6a3fb15083668b13
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-30 16:08:17 +0100
Commit message:

 bump version
Package: universalmotif
Commit: c4c44caadf883d018a598776aa10483ef7ae03ae
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-30 16:06:08 +0100
Commit message:

 perf: keep the original fast two-axis path in match_bkg()

Restore a dedicated GC x length code path for the common no-covariate
case, so it runs at the original speed and produces byte-identical
output rather than paying the N-axis generalisation overhead. The
general path is reached only when covariates are supplied.

The fallback search logic is shared between both paths through a
ring-gatherer function passed to find_candidates(), so there is still a
single copy of it; the two-axis and N-axis gatherers each compute their
cell keys inline without allocating a matrix per offset. Benchmarked
against the pre-covariate version, the no-covariate path is back to
parity on time and memory, while covariate runs keep a small constant
-factor overhead that only applies when covariates are actually used.
Package: universalmotif
Commit: 5299f99b77e85d2301df4d98b22f3b0696c269bf
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-30 15:52:53 +0100
Commit message:

 docs: regenerate man pages to match roxygen prose

Re-sync compare_motifs2.Rd, enrich_motifs2.Rd, motif_finder.Rd, and
scan_sequences2.Rd with their roxygen sources, which had been edited in
an earlier wording pass without the man pages being regenerated. This
is prose re-wrapping only, with no change to arguments or behaviour.
Package: universalmotif
Commit: 22db49bbc66dd9082f8f38168904ae1072992d9d
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-05-30 15:52:07 +0100
Commit message:

 feat: general covariate matching axis in match_bkg()

match_bkg() now matches on arbitrary external per-sequence covariates
alongside GC and length. The new covariates and universe.covariates
arguments take a data.frame, matrix, or numeric vector aligned to the
target and universe sequences, and each column becomes an extra binned
axis controlled by n.bins.covariates and bin.type.covariates (quantile
or equalwidth).

The two-axis GC/length grid was generalised to N axes via
make_match_axis(), a mixed-radix encode_bins() that reduces exactly to
the old index for two axes (so existing behaviour is preserved), and an
N-dimensional ring_offsets() replacing the hardcoded 2-D ring search;
the ring cap now grows with the number of axes. Covariate matching
needs an explicit universe with universe.covariates and is rejected
together with genome, because internally-sampled windows carry no
covariate values.

return.indices gains a target. / universe. column per
covariate, and plot_match_bkg() takes a new indices argument to facet a
density panel for every matched axis. Adds tests, NEWS, and bumps the
version to 1.31.31.
 </pre>
    </div>
  
    

      Package: ImageArray

      Commit: 1dccd3a787b25ceff99068e3294277a3547fcd7a

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2026-05-30 09:55:36 +0200

      Commit message:


	  
		
 Include core dimensions (XYZCT)  (#46)

* Update parameter name in rotate example from 'degrees' to 'angle'
- fixes #36
* update gha to r/bioc devel
* Update .AXES to include additional dimensions 'z' and 't'
* Update ImageArray creation to use dynamic axes based on image list shape
* Enhance BFArray constructor to dynamically set image axes from metadata and adjust shape handling
* make sure dim takes unnamed shape
* Refactor BFArray tests to remove unnecessary dimensions in expectations
* use invalid axes
* remove spurious dimensions
* Refactor BFArray indexing tests to remove unnecessary dimensions in expectations
* enforce the correct shape
* add 4D example to vignette
* some small updates
* add links and bump version
* edit NEWS and bump version

---------

Co-authored-by: Alexander Blume <alex.gos90@gmail.com> 

    

  
    

      Package: ImageArray

      Commit: ccb572d13b0954353c2813d5d8374c29e8a64783

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2026-05-28 14:33:32 +0200

      Commit message:


	  
		
 R-Universe/BioC CI (#47)

* new r-universe bioc workflow
* update gha 

    

  
    

      Package: universalmotif

      Commit: 05d108f55ac089e98ff02d7b26594bdce0939e7e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-30 08:22:59 +0100

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: universalmotif

      Commit: 21cf59dc5f269add1b4ecd311ace1b06403b2cd8

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-30 08:22:08 +0100

      Commit message:


	  
		
 docs: wording tweaks across vignettes, roxygen, README, and NEWS

Tighten the prose in the recently-added documentation: the new
ChIP-seq workflow and curated-database vignettes, the v2-function
sections of the sequence-search and comparison vignettes, the
descriptions of the new v2 functions, and a couple of small NEWS and
README phrasings. Also fix a few stray slips in passing (a mismatched
motif name, a subject-verb disagreement, and a singular/plural verb).
 

    

  
    

      Package: AnVILPublish

      Commit: 06e578a38e1073777c4773bcbf3c1632afa80cf7

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2026-05-29 23:35:42 -0400

      Commit message:


	  
		
 version bump 1.23.5
 

    

  
    

      Package: AnVILPublish

      Commit: 93ada720bc12847e5787379213d5913131b2c786

      Author:  LiNk-NY <marcel.ramosperez@roswellpark.org> 

      Date: 2026-05-29 23:35:37 -0400

      Commit message:


	  
		
 normalizePaths for windows paths

- update unit tests
 

    

  
    

      Package: gdsfmt

      Commit: dbb2225dfbc1cfb996c55759c5c29ba4d580ef33

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-05-29 21:20:28 -0500

      Commit message:


	  
		
 tweak cleanup.gds()
 

    

  
    

      Package: BiocCheck

      Commit: 5e21b85d8184b7a64e09ee34602be123d7faa375

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 21:41:47 -0400

      Commit message:


	  
		
 version bump 1.49.9
 

    

  
    

      Package: BiocCheck

      Commit: f4969c163b3b545799fc5a01da0041b57280fb59

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 21:09:59 -0400

      Commit message:


	  
		
 update support site registration section in vignette
 

    

  
    

      Package: BiocCheck

      Commit: f55b2a4ae7cba7acd3e570c56b051ad7d96f42a6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 21:09:26 -0400

      Commit message:


	  
		
 add timeout to checkWatchedTag and improve info and error messages
 

    

  
    

      Package: dnaEPICO

      Commit: b9e91db6e53cf72c0d4872c44f44503d503442bd

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-05-30 09:34:27 +1000

      Commit message:


	  
		
 0.99.23 Bioconductor Vignettes, bioweb not display,  and R error test
 

    

  
    

      Package: scRNAseqApp

      Commit: 81c8d7b67adde1a29c8b5b06f2fd5fafaaef7716

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-29 18:15:16 -0400

      Commit message:


	  
		
 update the version number.
 

    

  
    

      Package: scRNAseqApp

      Commit: f566ac33647a3f071f630ca3031f7e19ac0baecf

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-29 18:13:19 -0400

      Commit message:


	  
		
 change some files default path.
 

    

  
    

      Package: BiocCheck

      Commit: 7dff3804defde540180b66f9489288b875492588

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 17:32:47 -0400

      Commit message:


	  
		
 version bump 1.49.8
 

    

  
    

      Package: BiocCheck

      Commit: e1b88a3abc7c328a06cd901c1a316e1448094b0b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 17:32:44 -0400

      Commit message:


	  
		
 minor updates to comments in unit tests
 

    

  
    

      Package: BiocCheck

      Commit: 252bdefcd8c41a90f94c436268659fed0b096bf2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-29 17:32:15 -0400

      Commit message:


	  
		
 add req_timeout to checkSupportReg and convert timeout / connection issues to warning instead of error
 

    

  
    

      Package: BiocCheck

      Commit: b4743a43329f606457361f763a85229e179528b8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 10:34:45 -0400

      Commit message:


	  
		
 version bump 1.49.7
 

    

  
    

      Package: BiocCheck

      Commit: cb41945b1a9c7bf0933da7ac3d86bcbbea6ca17f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 10:34:25 -0400

      Commit message:


	  
		
 update .Rbuidignore and .gitignore
 

    

  
    

      Package: BiocCheck

      Commit: 48b1a823caf0dd31cb52d5781f2234d0edd4f712

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 10:33:35 -0400

      Commit message:


	  
		
 mention VignetteBuilder instead of VignetteEngine DESCRIPTION field, closes #246
 

    

  
    

      Package: BiocCheck

      Commit: 8e2488535c7fa42bb1fe4bdcb249fcbacef3b4ec

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:54:20 -0400

      Commit message:


	  
		
 version bump 1.49.6
 

    

  
    

      Package: BiocCheck

      Commit: a9bcf4246da776ddc2ac90abc2aaafa8e605c1fc

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:54:12 -0400

      Commit message:


	  
		
 reformat BiocCheck.R with air
 

    

  
    

      Package: BiocCheck

      Commit: be874f6e5938b60747ebda60d295eb57f969b223

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:19:11 -0400

      Commit message:


	  
		
 version bump 1.49.5
 

    

  
    

      Package: BiocCheck

      Commit: 73856b336cb0463bfc06d38260dc7dc81837c3f7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:19:04 -0400

      Commit message:


	  
		
 update to roxygen2 version 8
 

    

  
    

      Package: BiocCheck

      Commit: dc9dbb8f62f427ac850d1ca9e75450b411f67dea

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:16:52 -0400

      Commit message:


	  
		
 update getFunctionLengths unit test with integer type
 

    

  
    

      Package: BiocCheck

      Commit: dcf531f1328d070d43c7ac6cc981d3aeb44c904d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-11 15:15:47 -0400

      Commit message:


	  
		
 improve checkFunctionLengths and getFunctionLengths

assisted-by: gemini-3-pro-preview
 

    

  
    

      Package: BiocCheck

      Commit: 4196aade50f3726c8d0da57531312039966fd419

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 18:07:02 -0400

      Commit message:


	  
		
 version bump 1.49.4
 

    

  
    

      Package: BiocCheck

      Commit: e7188b2a861f37b5ae444322c66fd82fc1a2fc12

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 18:06:58 -0400

      Commit message:


	  
		
 make ORCID invalid for check
 

    

  
    

      Package: BiocCheck

      Commit: d89975666d6a8a784f47b1a25385ef22f39f627f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:44:36 -0400

      Commit message:


	  
		
 version bump 1.49.3
 

    

  
    

      Package: BiocCheck

      Commit: 1e08fbc28a530e422872f4e882018752307e3f26

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:44:31 -0400

      Commit message:


	  
		
 use dummy ORCID
 

    

  
    

      Package: BiocCheck

      Commit: 494015128be5062dbd01e836e7bc70fbcedc065c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:18:25 -0400

      Commit message:


	  
		
 version bump 1.49.2
 

    

  
    

      Package: BiocCheck

      Commit: 03a35173850e223a36bd76759c2b2f2ce5d09bd7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:18:23 -0400

      Commit message:


	  
		
 remove return call
 

    

  
    

      Package: BiocCheck

      Commit: 13b8aae2dc8d1f83a2c76b867e8d2d1722002a53

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:18:14 -0400

      Commit message:


	  
		
 generate CRAN url with paste only
 

    

  
    

      Package: BiocCheck

      Commit: c0fba5c0d924deea1353d6fb4e3ab25e3a5ad444

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 17:17:21 -0400

      Commit message:


	  
		
 resolve path linter false positive
 

    

  
    

      Package: BiocCheck

      Commit: 7a89bbc0a1e2440c71b9139fdc06bc646944c6e1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:47:04 -0400

      Commit message:


	  
		
 version bump 1.49.1
 

    

  
    

      Package: BiocCheck

      Commit: 7eaa1944f72d7f516da8ac6d7549d922cc8719ee

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:36:00 -0400

      Commit message:


	  
		
 use integer values for single scalars
 

    

  
    

      Package: BiocCheck

      Commit: c04976dffd83cc4ce37834acdb6473d213accc85

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:34:48 -0400

      Commit message:


	  
		
 add spacing after paren and around =
 

    

  
    

      Package: BiocCheck

      Commit: 26fd8216437473c3e3f3fbf2f9910eb3b6629ee2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:09:18 -0400

      Commit message:


	  
		
 use file.path for portable paths
 

    

  
    

      Package: BiocCheck

      Commit: 5f4e9412f9399312ac622280dc57005db890fa80

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:08:47 -0400

      Commit message:


	  
		
 remove unused objects in code
 

    

  
    

      Package: BiocCheck

      Commit: b05986a7f0ba117e48372f6c052012f06c8bd652

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-30 16:08:17 -0400

      Commit message:


	  
		
 import utils URLencode
 

    

  
    

      Package: BiocCheck

      Commit: d7b9689c10443c3d066f0eaf09be287128ad6e76

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 14:29:36 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 

    

  
    

      Package: BiocCheck

      Commit: c9893fa0788a7f0a50117ef76b8069a3266bfceb

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 14:29:36 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 

    

  
    

      Package: BiocCheck

      Commit: 8a22310f669d9d91243999bb2787e9db0d8f039e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-21 10:13:51 -0400

      Commit message:


	  
		
 version bump 1.47.26
 

    

  
    

      Package: BiocCheck

      Commit: cbc4366f396bee6fa07ab528ab1255636fe8175a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-21 10:13:25 -0400

      Commit message:


	  
		
 minor formatting updates
 

    

  
    

      Package: BiocCheck

      Commit: fa30033ef6453add2a9764482b97e37a023e3057

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-21 10:11:37 -0400

      Commit message:


	  
		
 add NAMESPACE checks doc for BioCheckGitClone in vignette
 

    

  
    

      Package: BiocCheck

      Commit: 798f0ba62d59ea7776e8dc6f73a7617eba81a4c2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-21 10:02:35 -0400

      Commit message:


	  
		
 check for Remotes field in BiocCheckGitClone, closes #245
 

    

  
    

      Package: BiocCheck

      Commit: e70fe5301922ec209eeffe8b889688da723f4fe7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-10 14:23:36 -0400

      Commit message:


	  
		
 version bump 1.47.25
 

    

  
    

      Package: BiocCheck

      Commit: 825871c14e84ab889573fc080124d5a7eb887694

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-10 14:23:32 -0400

      Commit message:


	  
		
 add progressive indentation
 

    

  
    

      Package: BiocCheck

      Commit: b555469b33bdc6287656daf3f1b4ce2b50131461

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-10 14:10:12 -0400

      Commit message:


	  
		
 version bump 1.47.24
 

    

  
    

      Package: BiocCheck

      Commit: 7d0e7e199e6e917e9eac12b3e99bff19e694e8c0

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-10 14:10:07 -0400

      Commit message:


	  
		
 add indentation to bulleted list
 

    

  
    

      Package: BiocCheck

      Commit: f6643a3fa02e7160cbd12df18c31164cb0e79250

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 17:55:47 -0400

      Commit message:


	  
		
 version bump 1.47.23
 

    

  
    

      Package: BiocCheck

      Commit: fce72e3ead6917ceff0655ff2f03e89142bc9b9d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 17:55:41 -0400

      Commit message:


	  
		
 use URLencode for emails in checkSupportReg and checkWatchedTag
 

    

  
    

      Package: BiocCheck

      Commit: 0d1374fd13cdc5307ed3da787ece92b754557d45

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 17:28:01 -0400

      Commit message:


	  
		
 anaylize parsed Authors@R and only run within env after valid result
 

    

  
    

      Package: BiocCheck

      Commit: a109f5b487ca24a24f15b83dc301d8d1a785af0b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 15:20:47 -0400

      Commit message:


	  
		
 remove unused function
 

    

  
    

      Package: BiocCheck

      Commit: 97298d8f9300795cf381451729a9944bc1912550

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-04-02 15:11:40 -0400

      Commit message:


	  
		
 Update container and CRAN URLs in workflow 

    

  
    

      Package: BiocCheck

      Commit: 9d088908463514723bb60e1ce20dcec42ec4fd36

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 15:03:05 -0400

      Commit message:


	  
		
 version bump 1.47.22
 

    

  
    

      Package: BiocCheck

      Commit: 8e9ec4a33b3c52f5b8d93d9b504a5be702954d98

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 15:03:00 -0400

      Commit message:


	  
		
 remove old TODO
 

    

  
    

      Package: BiocCheck

      Commit: efdeea1df8a5bd6e4264c90ab7f4dcad32349c16

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 15:02:19 -0400

      Commit message:


	  
		
 combine validation logic
 

    

  
    

      Package: BiocCheck

      Commit: 2ab96b1cb902d6e67d3cb7c2bfc6497d321cf450

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 15:02:07 -0400

      Commit message:


	  
		
 format code in util.R
 

    

  
    

      Package: BiocCheck

      Commit: b606a59931a69552936fe89ab1c8cef192a813ba

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 14:43:23 -0400

      Commit message:


	  
		
 version bump 1.47.21
 

    

  
    

      Package: BiocCheck

      Commit: 5cf8a9428a298445c9cec155086b5ecf0bc4a0ce

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 14:43:16 -0400

      Commit message:


	  
		
 use safe URLs for VIEWS files
 

    

  
    

      Package: BiocCheck

      Commit: de89badbbf01c81e6114f15578f87aeaa7d18926

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-04-02 14:36:11 -0400

      Commit message:


	  
		
 update r-pkgs URL
 

    

  
    

      Package: BiocCheck

      Commit: 1310f87fdedfa0a53260c7f3337badcfe0fe21f2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:20:21 -0400

      Commit message:


	  
		
 version bump 1.47.20
 

    

  
    

      Package: BiocCheck

      Commit: 84e665245e59faeb0dc010ec225d33201e76637e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:20:18 -0400

      Commit message:


	  
		
 use markdown code chunk for preformatted code in docs
 

    

  
    

      Package: BiocCheck

      Commit: 3d8b5c21bc3ae23e6d9da73a3effc048f11a4218

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:19:55 -0400

      Commit message:


	  
		
 use markdown instead of emph in docs
 

    

  
    

      Package: BiocCheck

      Commit: ba97491f6690447ca7d9d7d37ca440b2fa474c7f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:19:15 -0400

      Commit message:


	  
		
 use markdown for code in docs
 

    

  
    

      Package: BiocCheck

      Commit: 9b5dbffc213405eb8cc05118ddcd127391f64fd5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:10:49 -0400

      Commit message:


	  
		
 use url delimiters <>
 

    

  
    

      Package: BiocCheck

      Commit: cbb7604157532c54c40fda165add8befe525e6ab

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 14:08:38 -0400

      Commit message:


	  
		
 use markdown for class links
 

    

  
    

      Package: BiocCheck

      Commit: bcebc614fddfd866600b4433c701d483c42095d1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 13:45:35 -0400

      Commit message:


	  
		
 version bump 1.47.19
 

    

  
    

      Package: BiocCheck

      Commit: d3f339fa3197d0a3bfcb1c9ea87c841c45690363

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-12 13:45:29 -0400

      Commit message:


	  
		
 convert Sys.setenv ERROR to WARNING, closes #243

- update justification in vignette
 

    

  
    

      Package: BiocCheck

      Commit: 6c837ecef28c866522947452a22908a0accadb7a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 16:01:48 -0500

      Commit message:


	  
		
 version bump 1.47.18
 

    

  
    

      Package: BiocCheck

      Commit: e8d1059c8c7b7c3b6c5cddfa8d259d60673a2a41

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 16:01:44 -0500

      Commit message:


	  
		
 fix non eval calculation for rmd vignettes
 

    

  
    

      Package: BiocCheck

      Commit: ba266693ddb0a69b94bccba3111f900bcd34f2d8

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 14:36:00 -0500

      Commit message:


	  
		
 version bump 1.47.17
 

    

  
    

      Package: BiocCheck

      Commit: d484e6d0473639dc29d7d6763d56fda7b0c3a972

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 14:35:54 -0500

      Commit message:


	  
		
 combine values then sum
 

    

  
    

      Package: BiocCheck

      Commit: 2bc685ae769d2f6d0ad9845ce840003b9ba9d567

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 14:35:14 -0500

      Commit message:


	  
		
 use simple assignment
 

    

  
    

      Package: BiocCheck

      Commit: b43fc13c44b44e38828987845e9d9fcf781c8a06

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 14:04:06 -0500

      Commit message:


	  
		
 remove comments
 

    

  
    

      Package: BiocCheck

      Commit: aa39fdf9e7fdec677e7e438de231845e73fbb8e2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 14:03:57 -0500

      Commit message:


	  
		
 update chunk detection to separately count non eval chunks
 

    

  
    

      Package: BiocCheck

      Commit: 8bdf5c7b119a55bdc04c2c9836935758ee1f0f73

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 13:58:38 -0500

      Commit message:


	  
		
 rename chunk related value names
 

    

  
    

      Package: BiocCheck

      Commit: 13702bc7e3e3ffed757cd061681d9ad035643850

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 13:54:41 -0500

      Commit message:


	  
		
 use knitr pattern for html chunk end
 

    

  
    

      Package: BiocCheck

      Commit: 1cebecfdd1e381f017f4c968578562f79a095365

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 13:51:11 -0500

      Commit message:


	  
		
 identify eval false {{r}} in qmd
 

    

  
    

      Package: BiocCheck

      Commit: b9f5059550b781b9cddda0db90b896854be61f80

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-02-02 13:50:04 -0500

      Commit message:


	  
		
 identify eval:false in qmd
 

    

  
    

      Package: BiocCheck

      Commit: 74b0876885d1c9b59868235eb536a7a62d957747

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-25 12:23:40 -0500

      Commit message:


	  
		
 version bump 1.47.16
 

    

  
    

      Package: BiocCheck

      Commit: d3b933bb06a0ecc6b167da6c7d92d7c025dfb9f1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-25 12:23:31 -0500

      Commit message:


	  
		
 use triple colons in tests
 

    

  
    

      Package: BiocCheck

      Commit: 718d5933a8739c2ca028c2899bd766533f1f5188

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-25 12:18:22 -0500

      Commit message:


	  
		
 version bump 1.47.15
 

    

  
    

      Package: BiocCheck

      Commit: a1a3b9f46b85859b17b45e59cd4224d9e88d6961

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-25 12:18:15 -0500

      Commit message:


	  
		
 add unit tests for Rhtml
 

    

  
    

      Package: BiocCheck

      Commit: 3607a1b20bfdfb36c6ea14429fb16325dcfae630

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-25 12:17:12 -0500

      Commit message:


	  
		
 exclude Rhtml from checkVigMetadata
 

    

  
    

      Package: BiocCheck

      Commit: a45d03358e2ac8c3408d400746b9681222fb4b92

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-21 23:48:14 -0500

      Commit message:


	  
		
 add support for rhtml vignettes
 

    

  
    

      Package: BiocCheck

      Commit: 232ad7bad6b4d40385120b6be04f4569faee5fa3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-23 22:09:25 -0500

      Commit message:


	  
		
 version bump 1.47.14
 

    

  
    

      Package: BiocCheck

      Commit: fc33ab18d3e904df645fc66fe388e8d54e0622e3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-23 22:09:20 -0500

      Commit message:


	  
		
 use zero length integer value when search is out of range
 

    

  
    

      Package: BiocCheck

      Commit: 20e11fa5ad2148bb74678e2368585f474388cad3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-20 20:03:27 -0500

      Commit message:


	  
		
 version bump 1.47.13
 

    

  
    

      Package: BiocCheck

      Commit: 0a3877285c54b9179373513479d09a8a9d28004e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-20 20:03:17 -0500

      Commit message:


	  
		
 coerce to expected type, closes #241
 

    

  
    

      Package: BiocCheck

      Commit: 4b91d27bae62c9b96c7ceceab362ddbfde429bd6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 16:02:56 -0500

      Commit message:


	  
		
 version bump 1.47.12
 

    

  
    

      Package: BiocCheck

      Commit: 9ee6d2861d992251ce8bf8895856a9471b09f99e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 16:02:50 -0500

      Commit message:


	  
		
 convert error with purling vignette to warning
 

    

  
    

      Package: BiocCheck

      Commit: 05d378ac6c121fbedd4eae05edcb7e406172d0e2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 15:42:45 -0500

      Commit message:


	  
		
 version bump 1.47.11
 

    

  
    

      Package: BiocCheck

      Commit: d931fcd5feb1929912e22617f0c4399a206fe6e9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 15:42:40 -0500

      Commit message:


	  
		
 skip checkForValueSection when there are no Rds in package
 

    

  
    

      Package: BiocCheck

      Commit: 14ff817b69dd070e5e73164219283295a4256d5a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 15:35:13 -0500

      Commit message:


	  
		
 version bump 1.47.10
 

    

  
    

      Package: BiocCheck

      Commit: 5a793c6dcd4cfc79556654e0feecc5ca9b2725d2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-15 15:35:00 -0500

      Commit message:


	  
		
 get symbol ranges when function has no curly brackets for the body
 

    

  
    

      Package: BiocCheck

      Commit: e409b5eb85739f79aa816a85453bca28891b9ecb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-14 16:39:17 -0500

      Commit message:


	  
		
 version bump 1.47.9
 

    

  
    

      Package: BiocCheck

      Commit: e8d5a97c4cd9df2f06eb1c860737ad80c2379214

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-01-14 16:39:10 -0500

      Commit message:


	  
		
 remove extra error and warnings related to yaml front matter delimiter
 

    

  
    

      Package: igblastr

      Commit: 1b542fba6edd24855e669983567ed9420bf247ca

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-29 12:42:44 -0700

      Commit message:


	  
		
 Add two built-in germline dbs for human: _OGRDB.human.IGH+IGK+IGL.202605
and _OGRDB.human.IGH+IGK+IGL.202605.src

These new germline dbs were obtained by importing the following
AIRR-community/OGRDB germline sets for Human:
- `IGH_VDJ`:     version 10 (released on 2026-05-27)
- `IGKappa_VJ`:  version  5 (released on 2026-05-27)
- `IGLambda_VJ`: version  4 (released on 2026-05-27)

For more information about these new germline sets, see:
  https://wordpress.vdjbase.org/index.php/ogrdb_news/human-ig-sets-updated/
 

    

  
    

      Package: DEGraph

      Commit: 00311b35c592acaf21018ba2a781abe1aac65e6e

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:42 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: DEGraph

      Commit: c223c096b9d8c21ef86181b250efbda21627b283

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor
 

    

  
    

      Package: BiocHail

      Commit: 62f9fd20af6341697a82ccf2806428f30d3483a5

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:41 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: BiocHail

      Commit: 8c0ac8841e393414d4ae59bb77298ad277e2caee

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor
 

    

  
    

      Package: ReUseData

      Commit: 8d2f1ee0ddf4904ca5374179620916d86b311604

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:40 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: ReUseData

      Commit: 576a8f40e4b4020184de061333c257bdf1acb37e

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor
 

    

  
    

      Package: muscData

      Commit: d208f34f69c596f0e1e6ddc198709f3762881c42

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:39 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: muscData

      Commit: 02542174381946859cc2def2a286442adf295fec

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor
 

    

  
    

      Package: gmapR

      Commit: fbd5ff0dde123b9f4b244ae5e4023125785ec7b5

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:38 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: gmapR

      Commit: a171bb6399960d4e456737c3842793869491d708

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

- Replaces .BBSoptions UnsupportedPlatforms in R Universe build system
- Excludes specific binaries from distribution via Bioconductor
 

    

  
    

      Package: biobtreeR

      Commit: dc3de3092237f7e81a70f986709feb644a35e5ab

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:37 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: biobtreeR

      Commit: 2c98e95b46e8de94c2d87e9f18777ece7618e92f

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

      Commit message:


	  
		
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      Package: Ibex

      Commit: e9edf776063f5b6eeedae67cdf0cd44381534868

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      Date: 2026-05-29 14:37:36 -0400

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      Package: Ibex

      Commit: e0fa12efe43b07f6856e0c181572e63693bd278a

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      Date: 2026-05-29 11:55:39 -0400

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      Package: imcdatasets

      Commit: b6b5be5e35b52e127ea29ea2aaebd9876ca97e45

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      Date: 2026-05-29 14:37:35 -0400

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      Package: imcdatasets

      Commit: 86c4cc273c355acecb8496f80f81e37edb05f1db

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      Date: 2026-05-29 11:55:39 -0400

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      Package: octad.db

      Commit: ab0fa96ac3100fbe83199fd19c1b5b127cede8e0

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      Date: 2026-05-29 14:37:34 -0400

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      Package: octad.db

      Commit: 3351f3077da643ac2c98ccda8864831acce2c12f

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      Date: 2026-05-29 11:55:39 -0400

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      Package: NCIgraph

      Commit: 56c4d75d400a41c39d1622ff9c1534cff69f3cac

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      Date: 2026-05-29 14:37:33 -0400

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      Package: NCIgraph

      Commit: cd05a2d302807c2fd21ea824a90d248294ea5594

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      Date: 2026-05-29 11:55:39 -0400

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      Package: rifi

      Commit: 75de92622d1d34795969a366a250c13e8d98fa88

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      Date: 2026-05-29 14:37:31 -0400

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      Package: rifi

      Commit: 07bcf7d1f21c2532949419c6961f97903f0739c6

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      Date: 2026-05-29 11:55:39 -0400

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      Package: MACSr

      Commit: af3b8214c67d0e6f8f95fb29fa85f991c4618dee

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      Date: 2026-05-29 14:37:30 -0400

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      Package: MACSr

      Commit: 39c21037038f813dfaa1f86ee3eb6210cf27f483

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      Date: 2026-05-29 11:55:39 -0400

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      Package: GeneGA

      Commit: 9e9d8f2feb23d2f00b263c04b7322919ab4f7968

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      Date: 2026-05-29 14:37:29 -0400

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      Package: GeneGA

      Commit: 457933ff913a2d0d7f4c733ae8f544989873a412

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      Date: 2026-05-29 11:55:39 -0400

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      Package: beachmat.tiledb

      Commit: 1b587bd9f9f04f7f13f013824b4c7dcbfcc8f07e

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      Date: 2026-05-29 14:37:28 -0400

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      Package: beachmat.tiledb

      Commit: 0e38acf53bf62343a259324799be34ed3483a7bf

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      Date: 2026-05-29 11:55:39 -0400

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      Package: VDJdive

      Commit: e6b1f6bd749238aaec49033f84304d66c13eca6a

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      Date: 2026-05-29 14:37:27 -0400

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      Package: VDJdive

      Commit: 8f4fa33818b2ca631db508a173cedbdddefef7d2

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      Date: 2026-05-29 11:55:39 -0400

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      Package: iBMQ

      Commit: 29a65d30ccfa3b6f41972a1699f600d8574772c0

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      Date: 2026-05-29 14:37:25 -0400

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      Package: iBMQ

      Commit: be39a4dd5d20b940762625f76e723e62702c62d2

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      Date: 2026-05-29 11:55:39 -0400

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      Package: igblastr

      Commit: 039ae17036bcd9f8ed4ab38f389e558f4064806e

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:24 -0400

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      Package: igblastr

      Commit: e9bd161b9e0a8fffc44d41e1a6ebd7b37c026d35

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: HilbertVisGUI

      Commit: 4027df17dcb3607ea3f2b920fc16008f8c63311b

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:23 -0400

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      Package: HilbertVisGUI

      Commit: 64ce0f02961a9a1cdade34a854166c49ba30f3d2

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      Date: 2026-05-29 11:55:39 -0400

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      Package: conumee

      Commit: afd7c582f853c3bfe7f23522fb2cbd890886a930

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:22 -0400

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      Package: conumee

      Commit: 29b731a2a060d527d9835cd94c9a6012cd0f3180

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: octad

      Commit: b39886ce482f24b666cd7eef0cfc3fd1ca1ee8b7

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:21 -0400

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      Package: octad

      Commit: 08ebbf46959d6cb299287a962e42dad00a0a1835

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: Rcollectl

      Commit: add4e35ead201dd8faa2dccff2c6fac1377e674e

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:19 -0400

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      Package: Rcollectl

      Commit: 32baa69c487b71e4fdf2a39e42f48b4a5d7ca9a9

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: ChIPXpress

      Commit: 36af3a0e31b0dc036c9964eebabfd65182719320

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:18 -0400

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      Package: ChIPXpress

      Commit: 63c44b70b2a12445e7b94a4195a5aac8c772054a

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: R3CPET

      Commit: 43f1f69e0efee863b0d8ff1492a72c7b394faeff

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:17 -0400

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      Package: R3CPET

      Commit: 2e75b6bc918590792a3cc1d40e259765f7e245f8

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:39 -0400

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      Package: ChIPXpressData

      Commit: 96d6703dba93b87daae0522fcdb11e85cdbc3320

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:16 -0400

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      Package: ChIPXpressData

      Commit: 069f382d7ccd6dc08b594fe3a7434a7070d4d088

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

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      Package: CoverageView

      Commit: 17f9e533f6124c9b5701ee3e5587dce14816cee5

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:15 -0400

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      Package: CoverageView

      Commit: f1671b9d737764d7776d5ef8b25b74927ba925b8

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

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 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: GenProSeq

      Commit: e67e085a30c6939aa6ac75d3e0ffaf98fb97d7ba

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:14 -0400

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      Package: GenProSeq

      Commit: 19ce2a26f67768a45410549f8eb0a823088476e0

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

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 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: runibic

      Commit: 058bc3648dd80aa527b43594318c250b785f90da

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:13 -0400

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 Bump version
 

    

  
    

      Package: runibic

      Commit: 87750a27aa94c875ec0011664655461569c24b0c

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

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 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: ExCluster

      Commit: d9404b890d5654e111aa70c90a731f23535eae72

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:12 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: ExCluster

      Commit: e8208b2f54123d98f65840aa8a35b163d1845963

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: SICtools

      Commit: 344a04ae6c54136414ee064dd5c347429b07ca24

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:11 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: SICtools

      Commit: 4b0df87df59cbe7f29e94aa0653ee3a00ca65e53

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

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 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: rsbml

      Commit: 3c724c8869db24d5f2e3c5ce2635912c71b2a782

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:09 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rsbml

      Commit: 6396d239c031b13cbbfc0e4b6eeb061ea76c156f

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: HiCool

      Commit: 3cffa64ad0dbb2b379ee9994259882e7f74a6b9a

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:08 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: HiCool

      Commit: 10b4a491094da5e339cb20c292ed88bcb16aa62c

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: NetPathMiner

      Commit: 0421150dede87b90971ec447d8dccb263e0401e9

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 14:37:07 -0400

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: NetPathMiner

      Commit: 2dd16bdad82cc62087e098f722bdb4652164373a

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: scRNAseqApp

      Commit: 69dacca146363abbba9adad6a97e5d5f88ff4395

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-29 12:37:18 -0400

      Commit message:


	  
		
 Add Z-axis
 

    

  
    

      Package: scRNAseqApp

      Commit: b1b2df87102ac8a1cb506c84595b10367b2813e2

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-28 21:09:20 -0400

      Commit message:


	  
		
 fix the typo
 

    

  
    

      Package: scRNAseqApp

      Commit: d19b6ca0b6b834d3bcd4051b9f30d9e19d74eeb0

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-28 21:04:14 -0400

      Commit message:


	  
		
 Fix the issue if DefaultBoundary is centroids.
 

    

  
    

      Package: annmap

      Commit: 6bccb78da99e75f955ccacb9ac5b4497125bc1f2

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 12:18:21 -0400

      Commit message:


	  
		
 Bump version to 1.55.1
 

    

  
    

      Package: annmap

      Commit: eb665a973d3034f5f30a0e56755fddfa1f1f1a3d

      Author:  A Wokaty <awokaty@users.noreply.github.com> 

      Date: 2026-05-29 11:55:38 -0400

      Commit message:


	  
		
 Add Config/Bioconductor/UnsupportedPlatforms

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      Package: universalmotif

      Commit: 83fc9c00b5d64d603081e07a2267a9141a7278d8

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-29 14:44:51 +0100

      Commit message:


	  
		
 address audit2 performance findings (safe, result-preserving subset)

Precompute integer alphabet-power tables in the C++ k-let counters and
sequence generators instead of calling pow() at every sequence position
(P1): klet_counter / get_lastlet / eulerian_walk / markov_generator /
create_sequences in shuffle_sequences.cpp, and klet_counter_NA in
get_bkg.cpp. Replace the 11 pow(x, 2.0) calls in the per-column
compare_motifs metrics with plain multiplication (P8). Hoist the
loop-invariant tscore out of the inner j loop in the motif_pvalue
multi-split DP (P6). Add a 64-bit overflow guard in expand_scores_cpp so
the exhaustive path stops cleanly rather than overflowing a 32-bit int,
independent of the R-side cap (P4). Drop the per-column NumericVector
temporaries in the scan PWM quantisation (P2; the audit's parallelise
suggestion is unsafe because it touches the R API).

All numerically identical; the targeted test suites pass unchanged.
Informal benchmarks show roughly 10-20% on the affected paths.

Bump version to 1.31.29.
 

    

  
    

      Package: HMMcopy

      Commit: 0c9a92e4a0f3ff937a637f0b7c38ae0b65802fac

      Author:  Andrew McPherson <andrew.mcpherson@gmail.com> 

      Date: 2026-05-29 08:02:41 -0400

      Commit message:


	  
		
 Update maintainer email and bump version
 

    

  
    

      Package: igblastr

      Commit: 13ec75fa2813ab3eacbb5d40df883e69a7e40364

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-29 03:50:09 -0700

      Commit message:


	  
		
 igblastr 1.3.4

install_IMGT_germline_db() now emits a warning if the computed
"internal data" that it includes in the germline db has disagreements
with the "internal data" shipped with IgBLAST.

Add show_intdata_disagreements() to show disagreements (if any) between
the computed "internal data" included in a germline db and the "internal
data" shipped with IgBLAST.
 

    

  
    

      Package: Rsubread

      Commit: 5513571bdb88d4400f1f29dc621f3769aab045dd

      Author:  Yang Liao (Monash University) <yliao@m3v103.massive.org.au> 

      Date: 2026-05-29 16:09:34 +1000

      Commit message:


	  
		
 ranged get base value
 

    

  
    

      Package: Rsubread

      Commit: 91b8aa77530543869150d5addc241629c5c55d86

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-29 15:49:30 +1000

      Commit message:


	  
		
 tried different ways for optimisation.
 

    

  
    

      Package: Rsubread

      Commit: 52778582b3f661442d4cfa2e0d49d9fa79863688

      Author:  Yang Liao (Monash University) <yliao@m3v103.massive.org.au> 

      Date: 2026-05-29 13:23:50 +1000

      Commit message:


	  
		
 Minor changes in cell-counts
 

    

  
    

      Package: Rsubread

      Commit: 77ba2414b5d424848b7b0ca46f7a39efc4b8303d

      Author:  Yang Liao (Monash University) <yliao@m3v103.massive.org.au> 

      Date: 2026-05-29 12:33:25 +1000

      Commit message:


	  
		
 optimised IVT tab
 

    

  
    

      Package: gemma.R

      Commit: b4f107bf727073c07841b42f9af69951fb1fbe96

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-05-28 17:49:20 -0700

      Commit message:


	  
		
 add keyword do visualize_dataset
 

    

  
    

      Package: gemma.R

      Commit: 17c0bcdd2c9aa354bc5954141bab470837d4048d

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-05-28 17:41:33 -0700

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: gemma.R

      Commit: 3fecc0e46a55d78833e1a55e74e3f45bcf3a6a3b

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-05-28 17:40:43 -0700

      Commit message:


	  
		
 documentation bump
 

    

  
    

      Package: gemma.R

      Commit: 91f7dca6a014b11a023d483527bc3c0f66c636b8

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-05-28 17:21:14 -0700

      Commit message:


	  
		
 fix tsv reading for large files
 

    

  
    

      Package: gemma.R

      Commit: d29063d87ee091ebdfbe62c59ce59af1bab4b0ce

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-05-28 16:58:38 -0700

      Commit message:


	  
		
 viridis palette
 

    

  
    

      Package: gemma.R

      Commit: 3dd9591c98b4e8b500b8e0a2912e1044d872acf5

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-05-14 16:00:42 -0700

      Commit message:


	  
		
 allow setting headers with gemma_call
 

    

  
    

      Package: gemma.R

      Commit: eda190ae2ca2dd3542bf62a2e4cc4f53e6f8c2a7

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-31 16:03:56 -0700

      Commit message:


	  
		
 interaction baselines fix
 

    

  
    

      Package: gemma.R

      Commit: 2a1cb07743d704076ebf8cdcb03e5ff3bfa883ff

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-09 18:20:45 -0700

      Commit message:


	  
		
 require R 4.1.0
 

    

  
    

      Package: gemma.R

      Commit: afe812313a8eba75f5413f148ff168c99d4ebd70

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-03-04 15:57:31 -0800

      Commit message:


	  
		
 add "local" to setGemmaPath
 

    

  
    

      Package: gemma.R

      Commit: 7789b0dee4e1dab92a64f12895bc0ff7322bb7ae

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:22:37 -0800

      Commit message:


	  
		
 remove p vals from plot
 

    

  
    

      Package: gemma.R

      Commit: 2f285e40c800a967114d2fc3feca6b892df80c25

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:21:14 -0800

      Commit message:


	  
		
 better printability
 

    

  
    

      Package: gemma.R

      Commit: f14fb1714ffe2710cc89fe7f8e7b466011358430

      Author:  OganM <ogan.mancarci@gmail.com> 

      Date: 2026-01-29 13:07:03 -0800

      Commit message:


	  
		
 diff exp plotting
 

    

  
    

      Package: gemma.R

      Commit: c6b1666bacaabdcfde0186e0023db5d817d0435a

      Author:  OganM <ogan.mancarcii@gmail.com> 

      Date: 2026-01-22 15:38:08 -0800

      Commit message:


	  
		
 expression processor fix for single cell
 

    

  
    

      Package: CycleMix

      Commit: b3a3c456183e2d9f9d390b79a5926cfb9f20785d

      Author:  Tallulah Andrews <tallulandrews@gmail.com> 

      Date: 2026-05-28 16:58:02 -0400

      Commit message:


	  
		
 fix author description for bioconductor
 

    

  
    

      Package: dnaEPICO

      Commit: 65bbf248d4e52d70151d3e6f04b0c3d91f512de4

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-05-29 05:50:14 +1000

      Commit message:


	  
		
 Bioconductor 0.99.22 Vignettes not being push to bioweb
 

    

  
    

      Package: gVenn

      Commit: 8ea4fed99211f56ca6e93de3293897de04e3191d

      Author:  Christophe Tav <christophe.tav@gmail.com> 

      Date: 2026-05-28 14:50:07 -0400

      Commit message:


	  
		
 bump version to 1.3.2 and fix plotVenn default fills for partial overlaps
 

    

  
    

      Package: AnVILPublish

      Commit: 4cc757b47df53978ff102b2b8221dd8b2a1c8a71

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 13:58:22 -0400

      Commit message:


	  
		
 version bump 1.23.4
 

    

  
    

      Package: AnVILPublish

      Commit: 6276354378726f4f631d7723ba90dcf0bb5fe669

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-28 13:58:15 -0400

      Commit message:


	  
		
 return a message when dry.run = TRUE and quarto sysdep is not installed
 

    

  
    

      Package: CLAMP

      Commit: 6531757d118b2e7abb6f73a0c15f01adb57663f1

      Author:  msubirana <mb2subi@gmail.com> 

      Date: 2026-05-28 11:40:51 -0600

      Commit message:


	  
		
 Bump version to 0.99.2
 

    

  
    

      Package: CLAMP

      Commit: d821a11c8a3e80b41e208b00633834d5ac219a0f

      Author:  Alexander McKim <alexander.mckim@cuanschutz.edu> 

      Date: 2026-05-28 08:28:39 -0600

      Commit message:


	  
		
 Bump version to 0.99.1
 

    

  
    

      Package: CLAMP

      Commit: d405d8bc56cbdc2dd9e6755b3711fff2c9410a96

      Author:  Alexander McKim <alexander.mckim@cuanschutz.edu> 

      Date: 2026-05-28 08:15:39 -0600

      Commit message:


	  
		
 Add Makevars and Makevars.win for cross-platform BLAS/LAPACK linking
 

    

  
    

      Package: igblastr

      Commit: 77aa1b159aab0e7c3b19ee2c5a2027661509c455

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-27 23:03:30 -0700

      Commit message:


	  
		
 Improve the auxdata produced by install_IMGT_germline_db()

Improve the computed auxiliary data produced by install_IMGT_germline_db()
by completing it with the auxiliary data shipped with IgBLAST.
The completion process consists in eliminating missing values in the
computed auxiliary data where possible. This is done by replacing each
missing value with the corresponding value from the auxiliary data shipped
with IgBLAST, if the latter is available.
 

    

  
    

      Package: gDRstyle

      Commit: 207d27c84b39b4352befb78563a18bf41d8528d3

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 18:44:26 +0200

      Commit message:


	  
		
 Merge pull request #97 from gdrplatform/GDR-1014 

    

  
    

      Package: gDRstyle

      Commit: a6936a6cef16e851010a9a4a938ee98eab5fe509

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 16:30:39 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 3530ea1367eaf7ee9d9c2187f73518b3c35ffeab

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 15:41:16 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 95011a2bf27b3eb7d472d17181c3fe6281359af2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 15:17:57 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 10b6b21f9898fdd649974d0afde2262874c5ddce

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 14:20:39 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 7114b0f2b95d08410d1ec26b39f46dab61720fd4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 12:01:15 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 5ad61f206112992b9292a5755a16fdd66957001a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:55:26 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 28a25597063bb2ddab1b7bdbb1cd00c68fe21660

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:42:15 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: ea4cf28aed0fc5cdc934ee361757c79dc6c7b44f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:34:16 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 52077cfabf672281f9d3746145efbd7b06e2de33

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 10:52:00 +0200

      Commit message:


	  
		
 fix: remove cyclocomp_linter exclusion from lintr defaults
 

    

  
    

      Package: gDRstyle

      Commit: f1f65158b3c35bdb21f6225d360a976597adfede

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 09:11:59 +0200

      Commit message:


	  
		
 fix: remove unused cyclocomp from Imports
 

    

  
    

      Package: gDRstyle

      Commit: ae6214b012573ed684d6acd42be3dc4c6ed5e4b3

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:21 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: dd7148154d11eff8753f85617fdd1571801943c5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:49 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 3d00de82020cbf7d14765fe25d4051f92fda0d27

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 20:21:41 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRstyle

      Commit: 21fdeef99490cc8e97345a8251bebf7105ff229b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 20:11:20 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 5935f97e4426e5f85ce8039ea68d441d04b7fcde

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 20:08:44 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: a876a35d33652582d68bb96df5bc4d81537458d5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 20:03:20 +0200

      Commit message:


	  
		
 fix: replace non-ASCII em dash with ASCII equivalent
 

    

  
    

      Package: gDRstyle

      Commit: 59334f8a999edd72d5149b1e1b593546532eda17

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 19:54:42 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 0b29d1e92da00e98a30010a0f72d3f23ec355f7f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 19:30:14 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: b052a57e1c239685b52a6c82f95c1d1d94869d98

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:20:05 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 00844774f98eccbc66ff9314039b546ff2943507

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:18:17 +0200

      Commit message:


	  
		
 docs: generate man page for lintNewsEntries
 

    

  
    

      Package: gDRstyle

      Commit: 64b159d54d615aede8eabaff723cbe8a5a032c5c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:14:52 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 5240873c660eb1f64c2cecb5db1d8da981111808

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:06:42 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 8c3c93aa0703623f588ab43b399049ff9e292a46

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:02:08 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: e5e390cea8320643fe22543751f2601ac3ca0180

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:05 +0200

      Commit message:


	  
		
 fix: add missing infinitive verbs to VALID_VERBS
 

    

  
    

      Package: gDRstyle

      Commit: 3003cd5fe9ac5f53300c4734ce0084b1c6147d40

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:40:01 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 379a2a2c1992ef9b60c24e46f0130c7400315e05

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:15 +0200

      Commit message:


	  
		
 fix: use only infinitive verbs in VALID_VERBS and NEWS.md
 

    

  
    

      Package: gDRstyle

      Commit: dc4ee0d578f17b4fc13ef5bbe28bf3ae537661fb

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:37:15 +0200

      Commit message:


	  
		
 fix: add legacy verbs to VALID_VERBS for backward compatibility
 

    

  
    

      Package: gDRstyle

      Commit: 980d2099c6a24efeefcbb60a335ed5b037bd705a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:37 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 

    

  
    

      Package: gDRstyle

      Commit: 2ac531b009861e92f3378c7dca7d610ac171e3f9

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:21:44 +0200

      Commit message:


	  
		
 fix: only lint latest NEWS.md section, keep VALID_VERBS as infinitives
 

    

  
    

      Package: gDRstyle

      Commit: f6ad810e12d05171981bf58f911f2400124eb5b2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:21 +0200

      Commit message:


	  
		
 fix: extend VALID_VERBS to cover all historical NEWS.md entries
 

    

  
    

      Package: gDRstyle

      Commit: 7ee616b8442e8a2a0b6cab38c8c23c73093d4690

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:07:19 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: c8e73af50a79977a8febaee6148521a4aec86db4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 16:55:57 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 53f9416a07316c9df29549d33745f7e124442a82

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 16:51:18 +0200

      Commit message:


	  
		
 fix: extend VALID_VERBS to cover historical NEWS.md entries
 

    

  
    

      Package: gDRstyle

      Commit: b1844ab69ad3bc3707d6bdc141fbe4087b721509

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:54:29 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: a542be12761d0a8aacf26cbc69b803e538030977

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:25 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 

    

  
    

      Package: gDRstyle

      Commit: 65f4a555e5d9443ad04182e2f52d7383bd752886

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 13:08:19 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 29376d81729eb6dc58ce698510bdfcfc0553413f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 12:28:07 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 38d0f32643c92d45afd59379055df6cd2be2f8a2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:38 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDRstyle

      Commit: 52c1b2a5f21c56c8806a7daf6e59aa1ff3988232

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 07:52:49 +0200

      Commit message:


	  
		
 refactor: revert cyclocomp refactoring, defer to separate PR
 

    

  
    

      Package: gDRstyle

      Commit: d390c4de1c2da201a304ca3b77da02bf9550b430

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-19 10:47:31 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 15a61f53141f7a51afefeb7354e4d7882e7dfa36

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:16 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRstyle

      Commit: 4a4dba7e21e7bed02e451f5184af457cf9413b31

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:12:56 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 754dcf28abc33f4f7fb5217ef8fb65dc51cb81ed

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-15 10:10:11 +0200

      Commit message:


	  
		
 fix: export lintNewsEntries, fix self-lint violations, allow <<-/:::

- Add lintNewsEntries to NAMESPACE (was missing, causing all packages to fail)
- Allow <<- and ::: operators (needed for closures and tests)
- Fix trailing whitespace, paste_linter, seq_linter violations in gDRstyle
 

    

  
    

      Package: gDRstyle

      Commit: 19dd60e4febf767320f50877b95ba32321292480

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 12:49:32 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRstyle

      Commit: 9c87422ed133a61b9952e64ddc203926ed3bd091

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-13 21:55:09 +0200

      Commit message:


	  
		
 fix: add cyclocomp to Imports to ensure cyclocomp_linter works
 

    

  
    

      Package: gDRstyle

      Commit: 68042cf3ff032f1e8560a729eef845fd87734f84

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:31:20 +0200

      Commit message:


	  
		
 feat: forbid nrow/ncol in favor of NROW/NCOL
 

    

  
    

      Package: gDRstyle

      Commit: b60626b419416f81a9346ecd8211d6c5fb7ece64

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:30:55 +0200

      Commit message:


	  
		
 feat: forbid Jira ticket references in NEWS.md entries
 

    

  
    

      Package: gDRstyle

      Commit: 8f773f50f93f05599d5f1f299ee5234790d877a1

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:28:51 +0200

      Commit message:


	  
		
 feat: set max_chars=120 and add max_bullets=3 rule per NEWS section
 

    

  
    

      Package: gDRstyle

      Commit: 68a3d783b66730ffb747e3053ace62fe3cdee984

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:27:32 +0200

      Commit message:


	  
		
 chore: revert version bump, add NEWS entry to 1.11.3
 

    

  
    

      Package: gDRstyle

      Commit: 6f8a85341ea2d4fa4da2f1678a73104c629170e6

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:26:47 +0200

      Commit message:


	  
		
 feat: add lintNewsEntries to enforce NEWS.md entry style
 

    

  
    

      Package: gDRstyle

      Commit: ec809ed1a02f43e4846bc9f61c065d9384cd5692

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-11 15:15:26 +0200

      Commit message:


	  
		
 fix: avoid f-string interpolation of diff content in auto-changelog
 

    

  
    

      Package: gDRstyle

      Commit: d71fe13c43dfe52f51320d114958c36c545cf814

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-09 07:55:08 +0200

      Commit message:


	  
		
 fix: resolve shell injection in auto-changelog and stale CONTRIBUTING.md reference
 

    

  
    

      Package: gDRstyle

      Commit: cda7a6686f77556d123009b39b55d31484782e35

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-09 07:53:14 +0200

      Commit message:


	  
		
 refactor: unify linter config by bumping lintr requirement to >= 3.2.0
 

    

  
    

      Package: gDRstyle

      Commit: a5faedfd6ab48de2d6cdb83fed44c07bd7f26e94

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:35:01 +0200

      Commit message:


	  
		
 chore: simplify NEWS.md entry for 1.11.3
 

    

  
    

      Package: gDRstyle

      Commit: 10b08ef8ee365fd1e7790d39259cb1ab589d6485

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:34:20 +0200

      Commit message:


	  
		
 feat: add testthat linters and document all active linting rules in style_guide
 

    

  
    

      Package: gDRstyle

      Commit: f4430e4deca87f5ea01def17e09efb7d12bee1fc

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:26:24 +0200

      Commit message:


	  
		
 chore: update NEWS.md
 

    

  
    

      Package: gDRstyle

      Commit: a48c980bc2d38e4faf6ae89f256bbce9e62bfcad

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:25:36 +0200

      Commit message:


	  
		
 chore: remove CONTRIBUTING.md in favor of style_guide.Rmd vignette
 

    

  
    

      Package: gDRstyle

      Commit: 5cdd0ca8f1e738be5f73484fc7bc2a1940589a75

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:25:31 +0200

      Commit message:


	  
		
 docs: update style_guide.Rmd with new linting rules and fix SemVer description
 

    

  
    

      Package: gDRstyle

      Commit: a32516e20894de999a34debe274399af10e93b82

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:19:37 +0200

      Commit message:


	  
		
 chore: bump version to 1.11.3 and update NEWS.md
 

    

  
    

      Package: gDRstyle

      Commit: 0e5ec6c77bbe65b71f8a80565e002ca5e139c531

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:19:35 +0200

      Commit message:


	  
		
 docs: add CONTRIBUTING.md with Conventional Commits guidelines and non-blocking CI check
 

    

  
    

      Package: gDRstyle

      Commit: ecabb4bdaa515d50c00fdb5eed63018f57837710

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-08 12:19:32 +0200

      Commit message:


	  
		
 feat: extend linter config and add auto-changelog workflow
 

    

  
    

      Package: gDRutils

      Commit: 8ea9786029ca68b1e4ec0a86d813bbefea7188a6

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 18:36:29 +0200

      Commit message:


	  
		
 Merge pull request #188 from gdrplatform/GDR-1014 

    

  
    

      Package: gDRutils

      Commit: bf7dc1ac4956bcde27e582121829652754d5ab38

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 16:54:32 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: 852a36a088b9fa23f01eed6038234672b095f61f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 16:48:11 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: ca3691af3bde327ebffbb10b80b9afcbf4dbde07

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 16:30:41 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 6d258f575090d0c921ae5a4b17ccb63b3455ce8c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 15:39:56 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: a17e1606d7dc323a917059ed66a82809692b0b87

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 15:17:55 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 9108c31ce18c46f64c72393d8de8d7a7722a2eed

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 14:18:51 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: b4eba3f6fe31646acd933734417c448f34a89c8a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 12:01:13 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: c700baadb71ff5572cdf4a86a9c3e3d80ebfa8ec

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:55:27 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: eef74c9172e11edf622a468a0c3d131e6ac709e0

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:42:17 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 455a8ff987c4e43a59ce7509847debd86d31e87f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:35:26 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 41aff0f3e1b0a6f018e0cd9846eb31cbf1a8c360

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 09:49:32 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: 97265ad23cdb05f1aa4244d0e58970ab74714bb8

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 09:27:51 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: d4587f14895b7ed0488ad5e11da05aa30b4cc6a5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 08:33:32 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 2bc6b2badb7843ed6c7c5b8fc2311c588b322152

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:17 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 80bf7c9b567a1c1d4a7b77f2a2e17fecdd0a2015

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:46 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRutils

      Commit: 59c4efe8071ac65e1673a1479459f0f4fb30132b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:30 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 

    

  
    

      Package: gDRutils

      Commit: 19c6824d5ae5ed0d94643ed47f2dab58b778adae

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:12 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRutils

      Commit: 2eb9c0febb34a41af2283cd009928655877e2061

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:21 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRutils

      Commit: 5ac594256d4b9a1b24fd97e517d181c61f5123e7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:42 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 

    

  
    

      Package: gDRutils

      Commit: 64dc26eb682951dba3d334084fcb40a4bfa1bf23

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:32 +0200

      Commit message:


	  
		
 fix: add missing terminal newlines
 

    

  
    

      Package: gDRutils

      Commit: 8e65c04fee409be1951c11bf190c22d2eeee687b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:29 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 

    

  
    

      Package: gDRutils

      Commit: f8c0783306c740b87e2952c1a9d1c91e581a2188

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:37 +0200

      Commit message:


	  
		
 chore: trigger CI
 

    

  
    

      Package: gDRutils

      Commit: a9536396a7d63b4965d4dc47d2ce175b8c7d5080

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:08:01 +0200

      Commit message:


	  
		
 fix: complete nrow/ncol to NROW/NCOL replacement
 

    

  
    

      Package: gDRutils

      Commit: e63ff7c2534627538089e8ff0356139d46837d02

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:30:01 +0200

      Commit message:


	  
		
 fix: restore paste0 in merge_SE.R to avoid unwanted spaces
 

    

  
    

      Package: gDRutils

      Commit: 5736a3662d52c6ac30e4aa230519d32cad205a8a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:29:29 +0200

      Commit message:


	  
		
 fix: restore logic changes incorrectly introduced by lint fixes
 

    

  
    

      Package: gDRutils

      Commit: 3e085d988f65048fa8674f469b6b79c9bcd0b9ac

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:14:45 +0200

      Commit message:


	  
		
 fix: restore paste0 for multi-arg concatenation with collapse
 

    

  
    

      Package: gDRutils

      Commit: a62b56e0e51167c2d4cf8975ccfd4a06744ad3a3

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:41 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDRutils

      Commit: daed703409c6842c9704236fcec5bbc031df23c1

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:18 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRutils

      Commit: ca86d9dd95bad404acf05ba591c1c2c0e9e2e4a7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:49 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

    

  
    

      Package: gDRutils

      Commit: 7b000e1ce6f712a9cbd672e7932663a317fb07c6

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:38:25 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 

    

  
    

      Package: universalmotif

      Commit: a5f74a4a1eb0a3c0f080f0046ef56fd5c0b56d49

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 16:28:10 +0100

      Commit message:


	  
		
 bump version to 1.31.28; NEWS for the audit follow-up
 

    

  
    

      Package: universalmotif

      Commit: ac1a48d595a1c521a31fe053e2b82ef3dc920654

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 16:26:36 +0100

      Commit message:


	  
		
 clear two pre-existing R CMD check items

- R/match_bkg.R: roxygen markdown was interpreting "[0, 1]" inside the
  algorithm description as a link target, which expanded to a
  Rd \link{0, 1} and produced a cross-reference warning. Escape the
  brackets so the prose renders verbatim.
- R/universalmotif.R: add cor and setNames to the stats @importFrom
  list. They were used in view_motifs2 (cor) and elsewhere (setNames)
  via base::-style access that R CMD check flagged as "no visible
  global function definition".

R CMD check now reports 2 WARNINGs and 4 NOTEs (down from 3 and 5).
The remaining items are all about pre-built vignette PDFs vs.
inst/doc, the absent Enhances packages (PWMEnrich, rGADEM),
.DS_Store hidden files, an unpinned C++ standard, and installed
package size — none are caused by source code in this branch.
 

    

  
    

      Package: universalmotif

      Commit: 3cada604f7a868d0f7c59d8ec0587cd683e497c9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 16:23:06 +0100

      Commit message:


	  
		
 fix two pre-existing crashes uncovered while writing the audit tests

- shuffle_sequences: k larger than the shortest input sequence used to
  read past the end of the sequence buffer inside the C++ backend and
  crash R. Added an R-side check that errors with a clear message
  before the dispatch. Order of validation inside enrich_motifs() also
  shifted so the "widest motif" check fires before the shuffle, keeping
  the existing error message for that path.
- compare_motifs (pval_extractor): the per-comparison row search bumped
  n1/n2 each iteration looking for a matching db.scores row, but when
  it ran off the table it set row = -1 without setting ok = true, so
  the outer while loop kept incrementing past the table forever. Bail
  with ok = true on the same branch.
 

    

  
    

      Package: universalmotif

      Commit: 6ac6391392d94855c465d74e06fa65a61654f94f

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 16:19:28 +0100

      Commit message:


	  
		
 audit follow-up: fill in the coverage gaps the audit flagged

Adds new tests across most of the package's exported surface. Grouped
by the audit identifier:

- T2 (test_sequence_complexity.R, new): smoke and known-value tests for
  every method (WoottonFederhen, WoottonFederhenFast, Trifonov,
  TrifonovFast, DUST), AA coverage, and nthreads=1 vs nthreads=2
  determinism.
- T3 (test_merge_similar.R, new): mirrors the existing merge_similar2
  tests against the v1 function, which had no test file.
- T4 (test_view_logo.R, new): pins view_logo's data-emitting behaviour
  without exercising the actual plot, and adds a smoke test for
  view_motifs(return.raw = TRUE).
- T5 (test_write_motifs.R): adds read -> write -> read identity tests
  per format (MEME, JASPAR, HOMER, TRANSFAC, universalmotif, matrix)
  against the inst/extdata fixtures.
- T6 (test_read_motifs.R): malformed-input cases for every reader,
  including the JASPAR empty-matrix and missing-header paths that the
  fixes above now guard.
- T8 (test_convert_type.R): nsites = 0 / nsites = 1 / high pseudocount
  / PPM <-> PCM <-> PPM and PWM <-> PPM round-trips.
- T9: RNA + AA fixtures across scan_sequences{,2}, compare_motifs{,2},
  and enrich_motifs{,2}.
- T10 (test_motif_rc.R): non-palindrome RC, RC-of-RC identity, RNA
  alphabet, AA-should-error.
- T11 (test_switch_alph.R): DNA <-> RNA round-trip, AA-should-error,
  strand and row-name preservation.
- T12: nthreads=1 vs nthreads=2 parity tests on scan_sequences{,2},
  compare_motifs{,2}, motif_pvalue, motif_finder, plus seed-driven
  reproducibility on shuffle_sequences. The compare_motifs nthreads=2
  parity test is the regression catcher for the C2 thread-safety fix.
- T13: v1/v2 smoke parity tests for every paired function (scan,
  compare, merge, enrich, tree, view).
- T14 (test_motif_score.R): threshold bounds rejection and
  allow.nonfinite = FALSE with -Inf PWM.
- T15 (test_shuffle_sequences.R): k = 1 routing for each method and
  seeded reproducibility at nthreads = 2. The k > seqlen test was
  intentionally omitted because the euler path currently crashes R
  rather than erroring cleanly; a guard for that is a separate fix.
- T16 (test_trim_motifs.R): min.ic = 0, min.ic above all column ICs
  (the documented "completely trimmed" error), and trim.from = left /
  right.
- T19 (test_utils-motif.R): positive and negative cases for ppm_to_pwm,
  ppm_to_pcm, pcm_to_ppm, position_icscore, consensus_to_ppm,
  consensus_to_ppmAA, get_consensus, get_consensusAA, add_gap / ungap,
  prob_match.

Suite count went from 708 to 875 tests; all green.
 

    

  
    

      Package: universalmotif

      Commit: 1452139fa990031c5dae2e5ebef20e263e23a3b8

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 16:19:01 +0100

      Commit message:


	  
		
 audit follow-up: correctness fixes across C++ and R readers

Fixes the items from the audit:

- compare_motifs.cpp: pairwise similarity in compare_motifs_some_cpp was
  passing bkg[index1[i]] twice instead of bkg[index1[i]], bkg[index2[i]],
  which mis-scored every comparison whose two motifs had different
  background frequencies.
- compare_motifs.cpp: pval_extractor used to call R::pnorm / R::plogis /
  R::pweibull from inside an RcppThread::parallelFor, all of which touch
  R's internal state and are not thread-safe. Split into a parallel row
  search and a serial p-value calculation; correctness no longer depends
  on the operating system's pthread scheduling being kind on macOS.
- shuffle_sequences.cpp: renamed the local firslet/firstlet typo so the
  variable name matches the helper.
- read_homer.R: replaced ifelse(is.na(...), numeric(0), ...) (which
  silently returned NA_real_ instead of an empty vector) with explicit
  if/else so missing nsites/bkgsites parse to numeric(0) as documented.
- convert_motifs.R: motifStack pcm conversion used to pick nsites via
  unique(colSums(mat))[1], silently masking unequal column sums. Now
  checks within tolerance and errors with a clear message when columns
  disagree.
- universalmotif-class.cpp: the PCM branch of check_motif_and_type only
  inspected the nsites slot; added an equal-column-sum check on the
  motif matrix itself, with tolerance matched to the existing PPM
  column-sum tolerance so PPM-derived PCMs still validate.
- read_jaspar.R: guard ncol(motif) == 0 (and is.list(motif), the parse
  shape produced by header-only matrices) before max(colSums(motif)),
  which otherwise produced an -Inf nsites slot that only blew up later
  in convert_type.
- read_jaspar.R / read_cisbp.R / read_meme.R / read_transfac.R: error
  with "no motifs found in ''" when the regex that locates headers
  returns an empty vector, instead of silently parsing to an empty list.

The audit also flagged C3, C4, C5, and C6. Each was investigated and is
either unreachable from R (C3 is gated by R/motif_pvalue.R, C4 by the
R wrapper in R/shuffle_sequences.R) or correct-but-obscure (C5's
unsigned arithmetic is held safe by its guard, C6's offset arithmetic
collapses to offset because forj == 1 in one branch and fori == 1 in
the other). None of them fires for any caller in the current package,
so they were dropped from the action list.
 </pre>
    </div>
  
    

      Package: universalmotif

      Commit: f7d7617fe025f67d63556e8edc7529e79eb09d0e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-28 14:59:44 +0100

      Commit message:


	  
		
 convert_motifs: actually build TFBSTools-*MatrixList outputs

The list method documented PFMatrixList, PWMatrixList and ICMatrixList
as valid target classes but had no code path for them, so each motif
hit the universalmotif method's `unknown 'class'` stop. Now intercepted
in the list method: convert each motif to the singular matrix type and
wrap with the matching TFBSTools list constructor via do.call (the
constructors are variadic). Adds a test covering all three list classes
plus a PWMatrix-list input round-trip.
 

    

  
    

      Package: simPIC

      Commit: 9c476fcc17e088ab54f045893b52ea9391fc77d4

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 20:14:21 +1000

      Commit message:


	  
		
 Skip splatPop estimate tests without VariantAnnotation
 

    

  
    

      Package: simPIC

      Commit: 4e4754800a2c5a45ffa3bde7b85d48d2c743195e

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 15:11:46 +1000

      Commit message:


	  
		
 Guard splatPop estimate example optional dependencies
 

    

  
    

      Package: simPIC

      Commit: 84163fec557ed0128bb2c3e92a707b845ee259b3

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 12:59:00 +1000

      Commit message:


	  
		
 Guard Microglia example optional dependencies
 

    

  
    

      Package: simPIC

      Commit: 466edf35aa51347d0761ee9106b8cf72f4be62e4

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-28 11:17:34 +1000

      Commit message:


	  
		
 Skip Microglia vignette chunks when optional deps are unavailable
 

    

  
    

      Package: simPIC

      Commit: 1b04b52910ba81967210c6753c22cbc1ac655437

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:55:30 +1000

      Commit message:


	  
		
 Reduce test data size and install CI vignette dependencies
 

    

  
    

      Package: simPIC

      Commit: 80a39f395bb6ff862e7635e25b005a25c88a2251

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:22:18 +1000

      Commit message:


	  
		
 Install CI dependencies without pak lockfile
 

    

  
    

      Package: HiCDOC

      Commit: ee91ddbbcb8f86c7192de9c7358d25c67560868a

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 14:31:26 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: HiCDOC

      Commit: d2fbefa9f90768cb8781120ca08d4cef401b33d5

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 14:22:28 +0200

      Commit message:


	  
		
 recompile doc
 

    

  
    

      Package: HiCDOC

      Commit: 18bed5ea3c603cb68831278602e9fc55bf748170

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-28 13:14:30 +0200

      Commit message:


	  
		
 uses HiCParser to import HiCData
 

    

  
    

      Package: HiCDOC

      Commit: ea0789dd79794d7227952b1d6c5093c32fe948e5

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:58 +0200

      Commit message:


	  
		
 redocument
 

    

  
    

      Package: HiCDOC

      Commit: f99a3d9e23d506d5d0d7184a89d62ab7a31bfea3

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:43 +0200

      Commit message:


	  
		
 add script to generate example data (ignored in build)
 

    

  
    

      Package: HiCDOC

      Commit: dfb049b806a4d13ab368012d0bf551c3f693e0af

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-27 16:26:01 +0200

      Commit message:


	  
		
 uses default parameters in tests and examples to retrieved data and fix typos (bad copy paste)
 

    

  
    

      Package: HiCDOC

      Commit: 087cbb06b974a6d07949054a4db9b211c40384e0

      Author:  Elise Maigné <elise.maigne@inrae.fr> 

      Date: 2026-05-26 15:38:54 +0200

      Commit message:


	  
		
 changing default parameter for smallChromosomesThresholds to 0
 

    

  
    

      Package: gDRcore

      Commit: 4e3e80b92f1f345e7db066a77a1e26a2f8332c34

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 14:17:11 +0200

      Commit message:


	  
		
 Merge pull request #196 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 

    

  
    

      Package: gDRcore

      Commit: a73a08c482d9e3e9e81884ba45e0275f5677189f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 12:01:17 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: ca7dd1ff874e23fef58d96c2dad6fda894f8e13e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:55:23 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: d34af1ea6e0f7a1dd14dcf163e02b38196ba874f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:42:18 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: f0de2c8924df8b40ea519341b6f77492a9c2141b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 11:34:19 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: d93e7b090bc1f4fc63e9aa17bb01ff6327d1ed77

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 09:27:52 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: 88b76cd9fc561dba1dba883e56e2aa6dabb58f56

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 08:33:34 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: 78ad015ae6a27174233952fd157f0a793cdc1b06

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:09 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: 65233d6ab8853b838ef592227220954b998e56d6

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:40 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRcore

      Commit: c0e3db82b52df52e4120b7f352afc106bc74e3c0

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:27 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 

    

  
    

      Package: gDRcore

      Commit: de06d6e501374d80c51113f248bc52708341dcfd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:14:01 +0200

      Commit message:


	  
		
 fix: use fixed substring match in validate_data_models_availability test
 

    

  
    

      Package: gDRcore

      Commit: 51fefb60df5716b32d560e8a978b3b6c5c0a929c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:06:07 +0200

      Commit message:


	  
		
 fix: collapse multi-line error message and resolve merge conflict
 

    

  
    

      Package: gDRcore

      Commit: 987578755452cf19b0e06e1467b5d4e0ad861d00

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:08 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRcore

      Commit: daa3708230cfa6e5e57641a099999923d2166536

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:17 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRcore

      Commit: 5c83a5c1d43fb3bc801fb6ff7f3b45b2ba2a4cd5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:38 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 

    

  
    

      Package: gDRcore

      Commit: 10149c680e0d3598b3043338e858895723424531

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:28 +0200

      Commit message:


	  
		
 fix: add missing terminal newlines
 

    

  
    

      Package: gDRcore

      Commit: 0006e23e53c01f033e577755c848e72df919c789

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:26 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 

    

  
    

      Package: gDRcore

      Commit: 77bc7bce8f3f54cd4288062c37e4a348d0da696d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:39 +0200

      Commit message:


	  
		
 chore: trigger CI
 

    

  
    

      Package: gDRcore

      Commit: aa93fbba4e32061c4832e8cfb2b088e9bb25aeb4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:08:02 +0200

      Commit message:


	  
		
 fix: complete nrow/ncol to NROW/NCOL replacement
 

    

  
    

      Package: gDRcore

      Commit: 72a16e14899803d6c6cfbfffaaa34dd9e8756048

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:43 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDRcore

      Commit: bc62905b144a8df8d23242473e7a978d6e064a79

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:19 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRcore

      Commit: 4ca19ef4c68dffbafc9fa3863a0b04acdb5ff5e7

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:49 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

    

  
    

      Package: gDRcore

      Commit: b1ab7f09a88dcc53cae805b11dfa30b3764a3e76

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:24:08 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 

    

  
    

      Package: gDR

      Commit: aa689b6ad34be68cc8ec8b64d9748535559e4def

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:29:43 +0200

      Commit message:


	  
		
 Merge pull request #59 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 

    

  
    

      Package: gDR

      Commit: 1b0be1952756128f657442505f58a62cbc5fd6a9

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:34:25 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDR

      Commit: d224c300a082b396a1773736738a296c07bda90e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:53 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDR

      Commit: 94c47ba3c0d6dcef9351b2d5010cfe449a63ba8d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 19:40:54 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 

    

  
    

      Package: gDR

      Commit: 44e006fc3014746ea570186fbcb7b77e706d14ac

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:35 +0200

      Commit message:


	  
		
 fix: fix malformed version header in NEWS.md
 

    

  
    

      Package: gDR

      Commit: 5dc46e0acd026ba02287e9832e09d8811925845d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:46 +0200

      Commit message:


	  
		
 chore: trigger CI
 

    

  
    

      Package: gDR

      Commit: a037055172b9425e574d68f016b8040894b4b126

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:42:59 +0200

      Commit message:


	  
		
 fix: correct typos in documentation
 

    

  
    

      Package: gDR

      Commit: 4b1f3e0293f0f4364c9a7e6b3bef0b9d39aa6325

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:06:10 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDR

      Commit: 1d9eac2716e75ecc51a59e80a1d2455b912bec3e

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:18:06 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDR

      Commit: 52081f4b70dd78d799294b65f6c35477f29f5a13

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:50 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

    

  
    

      Package: gDRimport

      Commit: 6b292201b76678b4e7b0355e66bbfcdf64028256

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:27:49 +0200

      Commit message:


	  
		
 Merge pull request #121 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 

    

  
    

      Package: gDRimport

      Commit: b78f11d4d8d64562c97c9e15e9d14648de06e04a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:33:44 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRimport

      Commit: 70429f5adab4fa548653710335fdca0190cde121

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:23 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRimport

      Commit: 2ee7cfd66279ff7c4ab319b46f23712f749cec1d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:28 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 

    

  
    

      Package: gDRimport

      Commit: 2e8067ae2b17cd950043c0dd11dc6ae2f54ba923

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:10 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRimport

      Commit: b0f037c0812f785ef7cffe77834469530d3b9b38

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:38:19 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries
 

    

  
    

      Package: gDRimport

      Commit: 774b658b6a149aeaa1901b9839cdb5d332f04632

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:30:40 +0200

      Commit message:


	  
		
 chore: update date to 2026-05-27
 

    

  
    

      Package: gDRimport

      Commit: 1966941316c38b18b6c6728d9fe182b31122fc87

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 17:18:30 +0200

      Commit message:


	  
		
 fix: add missing terminal newlines
 

    

  
    

      Package: gDRimport

      Commit: 71aa2f598ac283316af8668a936d67a3d880f105

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 15:48:28 +0200

      Commit message:


	  
		
 fix: resolve remaining gDRstyle linting violations
 

    

  
    

      Package: gDRimport

      Commit: 9c19db3a41ead5aaa15cd6714d5f962f1dd757bd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:42 +0200

      Commit message:


	  
		
 chore: trigger CI
 

    

  
    

      Package: gDRimport

      Commit: 3cf8f6f7b1c525c81952baa8b69fbe60773db78d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:08:02 +0200

      Commit message:


	  
		
 fix: complete nrow/ncol to NROW/NCOL replacement
 

    

  
    

      Package: gDRimport

      Commit: b6f8aeb8ce968090c227dd514be397ecb718bc9f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:43:00 +0200

      Commit message:


	  
		
 fix: simplify matrix initialization
 

    

  
    

      Package: gDRimport

      Commit: b3c6d745cc19049860ad1383a85a9becbaed9356

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-26 10:27:43 +0200

      Commit message:


	  
		
 fix: restore qs2::qs_read calls in test-load_files.R

Reverts accidental reversion from qs2 back to qs package calls.
 

    

  
    

      Package: gDRimport

      Commit: 95087dfee143117072ddbe855706150af5f5147f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:14:47 +0200

      Commit message:


	  
		
 fix: restore paste0 for multi-arg concatenation with collapse
 

    

  
    

      Package: gDRimport

      Commit: 9928c5315089fa0fbd98d63bad6cf9741febc99f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:05:45 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDRimport

      Commit: 76e71e7d0a3d976efb26d2e8c0dbe411d020666f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 07:54:06 +0200

      Commit message:


	  
		
 refactor: revert cyclocomp refactoring, defer to separate PR
 

    

  
    

      Package: gDRimport

      Commit: 2fc1d68f3d5489eb30606ba1a0060d5cbcf9cf32

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:17:21 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRimport

      Commit: b1f4d05cc89328b588cd009433c7560d46b03b12

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:49 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

    

  
    

      Package: gDRimport

      Commit: 328ce132e7018d72532fead8a0241f75f9a9edc1

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:40:58 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 

    

  
    

      Package: gDRtestData

      Commit: 24bc077c204c89080e73211a09f1ef603ea99bea

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2026-05-28 08:26:17 +0200

      Commit message:


	  
		
 Merge pull request #76 from gdrplatform/GDR-1014

fix: resolve gDRstyle linting violations 

    

  
    

      Package: gDRtestData

      Commit: 6f6a034e99f8e5db70928050e627b821f2ad3f5a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-28 07:33:43 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRtestData

      Commit: b5b023b64e53d34b83823770dfcbb9c069284ebd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 22:05:21 +0200

      Commit message:


	  
		
 ci: retrigger build
 

    

  
    

      Package: gDRtestData

      Commit: 2c6bb832bf54d0982e85c552ddef73d7d2790826

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:23:32 +0200

      Commit message:


	  
		
 docs: regenerate documentation
 

    

  
    

      Package: gDRtestData

      Commit: 310b0f93594edbcddc59cfbb7a71bf54102dcb36

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 18:00:33 +0200

      Commit message:


	  
		
 fix: use infinitive verbs in NEWS.md entries and fix malformed header
 

    

  
    

      Package: gDRtestData

      Commit: 462a012951ca085e6e737697d500b52a9e618473

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-27 11:27:44 +0200

      Commit message:


	  
		
 chore: trigger CI
 

    

  
    

      Package: gDRtestData

      Commit: 46e2936e765648cd0928d2d637b7f621ceefa5d2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:15:00 +0200

      Commit message:


	  
		
 fix: restore paste0 for multi-arg concatenation with collapse
 

    

  
    

      Package: gDRtestData

      Commit: 00e6754595850a8c99ef6eaabe3e49ab3c61229d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-20 08:06:08 +0200

      Commit message:


	  
		
 docs: update NEWS.md entry wording
 

    

  
    

      Package: gDRtestData

      Commit: 337a8a645dc64153e8874eef6a9f2433d358bcad

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 11:18:04 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRtestData

      Commit: d827d18076bcc9e19d1cfed16e0ef6f28b33b77d

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-18 10:07:50 +0200

      Commit message:


	  
		
 fix: resolve gDRstyle linting violations

Address lint violations from updated gDRstyle rules:
- Fix trailing whitespace and blank lines
- Replace nrow/ncol with NROW/NCOL
- Fix paste_linter (paste0+collapse, toString, strrep, file.path)
- Fix seq_linter (seq_along, seq_len)
- Refactor cyclocomp_linter violations (extract helper functions)
- Fix test linters (yoda, expect_true_false)
- Remove undesirable operators (|> pipes)
 

    

  
    

      Package: gDRtestData

      Commit: e3fad77ff30a9215ccbbc0acb96fa499a3a91d6b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2026-05-14 17:41:29 +0200

      Commit message:


	  
		
 fix: replace nrow/ncol with NROW/NCOL to satisfy gDRstyle linting rules
 

    

  
    

      Package: enrichplot

      Commit: 8adce9ad89d02c81d44298917b439e4acdca66dd

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-29 12:11:21 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: Rsubread

      Commit: 2bf5428ac73feed2244d0e065c5b557d2a1ebdb7

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2026-05-28 09:57:56 +1000

      Commit message:


	  
		
 added some hints about memory alloction failure.
 

    

  
    

      Package: Rsubread

      Commit: f6bdbe14e492e2b80913633f182546a3b21307f7

      Author:  Yang Liao <yang.liao@monash.edu> 

      Date: 2026-05-28 09:24:07 +1000

      Commit message:


	  
		
 removed two bugs in file-based realign buffer
 

    

  
    

      Package: Rsubread

      Commit: c219f59ec5226ec2fffaeb50071664bccad7454f

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-28 08:57:36 +1000

      Commit message:


	  
		
 improved speed for index loading
 

    

  
    

      Package: AnVILPublish

      Commit: 4cae77a6baf74f26c96d8e66ba0a6189b2a25405

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:28:45 -0400

      Commit message:


	  
		
 version bump 1.23.3
 

    

  
    

      Package: AnVILPublish

      Commit: 89d6cfd5e030b0d4894011dc13188b8ddc0e5780

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:28:26 -0400

      Commit message:


	  
		
 update NEWS.md

assisted-by: Gemini 3.5 Flash
 

    

  
    

      Package: AnVILPublish

      Commit: 551f95edd5c9c52d4c1bb33ff75aa09e9e360c27

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:24:39 -0400

      Commit message:


	  
		
 add AnVILBase to Suggests
 

    

  
    

      Package: AnVILPublish

      Commit: 7d8f26ad0e51f06ff5a5bcb7b19804c4b28b9850

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:49 -0400

      Commit message:


	  
		
 version bump 1.23.2
 

    

  
    

      Package: AnVILPublish

      Commit: 726626c1ac2384b5ec3763851dc0483e3cbc5f4a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:46 -0400

      Commit message:


	  
		
 modularize as_workspace
 

    

  
    

      Package: AnVILPublish

      Commit: 834ba861047dff3acef235be0987eca2161fca6c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 17:16:26 -0400

      Commit message:


	  
		
 fix indentation for BiocCheck
 

    

  
    

      Package: AnVILPublish

      Commit: b3bfd09c6d777c8b7c453d09c728a398dcbb1f79

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 16:39:26 -0400

      Commit message:


	  
		
 use assignment operator <- instead of equals =
 

    

  
    

      Package: ggcyto

      Commit: 2484d0d88328e9ff72d36f422dd4eaef9755b571

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:51 -0700

      Commit message:


	  
		
 bump version to 1.41.1
 

    

  
    

      Package: ggcyto

      Commit: 23a6ad5432207cc89348bd0cfde514f4577ba767

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:39 -0700

      Commit message:


	  
		
 Merge remote-tracking branch 'conductor/devel' into devel
 

    

  
    

      Package: ggcyto

      Commit: 7ef1a8c4d40f6b73fd8d8ac9fcfc1971a04122d4

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:33:35 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#115) 

    

  
    

      Package: ncdfFlow

      Commit: 7e2647d5551571303c4c8fa5618f185113eb59f2

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:12 -0700

      Commit message:


	  
		
 bump version to 2.59.1
 

    

  
    

      Package: ncdfFlow

      Commit: 9f90a42e048651de08c36a6975076e83a806a52a

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:51:01 -0700

      Commit message:


	  
		
 Merge remote-tracking branch 'conductor/devel' into devel
 

    

  
    

      Package: ncdfFlow

      Commit: 6493dc4f3f2cad222061fb0611ec9b5399b107ed

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:35:28 -0700

      Commit message:


	  
		
 Merge pull request #59 from hpages/devel

Use new BiocGenerics::transform() with new signature 

    

  
    

      Package: ncdfFlow

      Commit: 9087d54b47c550e0c40affa9178ebd8cbd525afe

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-27 10:26:39 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature
 

    

  
    

      Package: ncdfFlow

      Commit: f91af9cafbb8e3d7c6f1347c9590189ad490aca4

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2025-01-13 10:46:45 -0800

      Commit message:


	  
		
 Merge pull request #58 from RGLab/hotfix/deprecate-zlibbioc

Hotfix/deprecate zlibbioc 

    

  
    

      Package: flowWorkspace

      Commit: 510b28a41fccfd6f637ae940bd056aaf51eba26e

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:29 -0700

      Commit message:


	  
		
 bump version to 4.25.1
 

    

  
    

      Package: flowWorkspace

      Commit: b0d5c2440db9a11a1bdf28c02732ed60da06dd02

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:10 -0700

      Commit message:


	  
		
 Merge remote-tracking branch 'conductor/devel' into devel
 

    

  
    

      Package: flowWorkspace

      Commit: b966ea1a4b404c27fed3a39eb3d5fabc0e8951b6

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:50:05 -0700

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/devel' into devel
 

    

  
    

      Package: flowWorkspace

      Commit: 37b44557ae78474e4eb79b02c941d998f4302285

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:32:57 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#408) 

    

  
    

      Package: flowWorkspace

      Commit: 103dbbe1028da62a48c5f76f2b3a7ce7a2d3e1e3

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-02-19 13:08:42 -0800

      Commit message:


	  
		
 Add cytoset_factors and GatingSet_factors classes to preserve factor levels in pData by delegating to flowSet's phenoData slot
 

    

  
    

      Package: flowCore

      Commit: 4935c7bf318697b3128ee50dae81018a6b246ab8

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:43:03 -0700

      Commit message:


	  
		
 pump
 

    

  
    

      Package: flowCore

      Commit: 371be28eaf0c47c65a93213e54babb46021bb649

      Author:  Mike Jiang <mike@ozette.com> 

      Date: 2026-05-27 13:39:04 -0700

      Commit message:


	  
		
 Merge remote-tracking branch 'conductor/devel' into devel
 

    

  
    

      Package: flowCore

      Commit: 1070ccc950e309da4782813efbd9e4b7088783f0

      Author:  Hervé Pagès <hpages@users.noreply.github.com> 

      Date: 2026-05-27 13:31:38 -0700

      Commit message:


	  
		
 Use new BiocGenerics::transform() with new signature (#281) 

    

  
    

      Package: AnVILPublish

      Commit: 17a65b390ce334bada43a13a712d80ec84a5b7ec

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 16:11:13 -0400

      Commit message:


	  
		
 version bump 1.23.1
 

    

  
    

      Package: AnVILPublish

      Commit: 56e485c8fedf896bfe1ccd8a3e3eba136ad36af9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:34:43 -0400

      Commit message:


	  
		
 add fnd role with NHGRI grant number
 

    

  
    

      Package: AnVILPublish

      Commit: a7688dc50ef7398957571ac48705b64abf56464b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:06:33 -0400

      Commit message:


	  
		
 remove qualified mentions of AnVILPublish functions
 

    

  
    

      Package: AnVILPublish

      Commit: 9f93f00702d27a18c618fefd5c646aa4d1ce1e79

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:05:57 -0400

      Commit message:


	  
		
 update system2 call in vignette to show output
 

    

  
    

      Package: AnVILPublish

      Commit: 49af015be1ab1c8027b54320b2b8d0205be6b8d1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 15:05:46 -0400

      Commit message:


	  
		
 update ref links in vignette
 

    

  
    

      Package: AnVILPublish

      Commit: 843a6bcfd8bacd01013c9fae96519920322ecd14

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:55:35 -0400

      Commit message:


	  
		
 produce error when not using quarto

- remove mentions of notedown
 

    

  
    

      Package: AnVILPublish

      Commit: 5c0c443af3d2ae09cf76c0ad83395778a6adbaaa

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:45:45 -0400

      Commit message:


	  
		
 update quarto arg doc for as_notebook and as_workspace
 

    

  
    

      Package: AnVILPublish

      Commit: 15e6a3b79f26095172d956b487d5e5f7673be46a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:42:00 -0400

      Commit message:


	  
		
 handle lowercase .rmd files in as_notebook
 

    

  
    

      Package: AnVILPublish

      Commit: cf2fa7469b92935397bd3ec3a5675cd2b6a494e6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:36:25 -0400

      Commit message:


	  
		
 minor formatting to .rmd_to_quarto
 

    

  
    

      Package: AnVILPublish

      Commit: 551aa662320c97d6b1ed64d01b39eabbf78dc2a7

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:09:21 -0400

      Commit message:


	  
		
 add quarto-cli to SystemRequirements
 

    

  
    

      Package: AnVILPublish

      Commit: da0994a42a09e6bdd4b3232eb11ae41921b724ef

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:04:34 -0400

      Commit message:


	  
		
 use roxygen2 v8
 

    

  
    

      Package: AnVILPublish

      Commit: acc73c6d780a4cf81a36637da5a4500b3b5ef0e6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 14:04:24 -0400

      Commit message:


	  
		
 add example Rmd for vignette
 

    

  
    

      Package: AnVILPublish

      Commit: 8f23b76e79c61c88f254f18436102e91ccc89b88

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:53:05 -0400

      Commit message:


	  
		
 add named chunk checkQuarto
 

    

  
    

      Package: AnVILPublish

      Commit: 7bd2977db778a5bbf366b3d138466cd622026eb1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:52:51 -0400

      Commit message:


	  
		
 update examples to use dry.run
 

    

  
    

      Package: AnVILPublish

      Commit: ef9c9a35ea9f35e909eb99c01b87b646e7b8ec01

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:51:58 -0400

      Commit message:


	  
		
 remove duplicate & unevaluated chunk
 

    

  
    

      Package: AnVILPublish

      Commit: aa864264e732ed8ecb483b740ad1c2435fc4501d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:51:25 -0400

      Commit message:


	  
		
 remove old email
 

    

  
    

      Package: AnVILPublish

      Commit: d38c017f9d1392d5903939406aea6abd13d81173

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:50:07 -0400

      Commit message:


	  
		
 add GCPtools to section title
 

    

  
    

      Package: AnVILPublish

      Commit: 247ee664469f0082f609c56ffdd1433a92b44bdd

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 13:42:48 -0400

      Commit message:


	  
		
 update install and load sections
 

    

  
    

      Package: AnVILPublish

      Commit: 24a84f9f3b573bf309d272d46410131b4b52a1b6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:31:48 -0400

      Commit message:


	  
		
 add conditional chunk on availability of gcloud
 

    

  
    

      Package: AnVILPublish

      Commit: 240236101c5a3c3caf124e9fb9a15d8793c9e998

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:26:47 -0400

      Commit message:


	  
		
 remove old email from vignette
 

    

  
    

      Package: AnVILPublish

      Commit: 9674b60e136ec75f7e7e1fafe33912d43302cd28

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:26:32 -0400

      Commit message:


	  
		
 simplify documentation and remove unnecessary roxygen tags
 

    

  
    

      Package: AnVILPublish

      Commit: d8765103ed429d6699180fb52ef68bc7b8f9ba57

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-27 12:18:32 -0400

      Commit message:


	  
		
 add dry.run arguments to add_access, as_notebook, and as_workspace
 

    

  
    

      Package: AnVILPublish

      Commit: 0365bdbf8a0c8f5806b052dba067819b9f411780

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:52:45 -0400

      Commit message:


	  
		
 add examples for add_access, as_notebook, and as_workspace
 

    

  
    

      Package: AnVILPublish

      Commit: 4f867a684be46dd68a6549e234552c26c6f5c322

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:38:02 -0400

      Commit message:


	  
		
 set install package chunk to eval=FALSE
 

    

  
    

      Package: AnVILPublish

      Commit: 9a7121115e3d95368506965861539a7821c08f71

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:37:11 -0400

      Commit message:


	  
		
 add testthat.R to run unit tests via R CMD check
 

    

  
    

      Package: AnVILPublish

      Commit: 87917d744be518ae12f05d0ce0a1ed4c10c404f5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 17:36:40 -0400

      Commit message:


	  
		
 add URL and BugReports fields in DESCRIPTION
 

    

  
    

      Package: scRNAseqApp

      Commit: da7dd5afa4544aac90f0486ec205b290f3d654f1

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2026-05-27 13:56:08 -0400

      Commit message:


	  
		
 replace size with linewidth.
 

    

  
    

      Package: friends.test

      Commit: 95d11a75a181784dd9a51d29448940f515df64b1

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 11:40:51 -0400

      Commit message:


	  
		
 Add MulticoreParam parallel tests (skip on Windows)

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 

    

  
    

      Package: friends.test

      Commit: b38c68bdbaf8e0709bf6fbcce21b29c9b091cfa8

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 11:18:30 -0400

      Commit message:


	  
		
 Fix SnowParam workers: propagate .libPaths() and use local(envir=globalenv())

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 

    

  
    

      Package: friends.test

      Commit: 979b9579b82fab4d0e58d642b419018cb75e6ffb

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 10:58:06 -0400

      Commit message:


	  
		
 Fix SnowParam worker serialization: wrap lambdas in local(envir=globalenv())
 

    

  
    

      Package: friends.test

      Commit: b39cd46f5e4ba108019684bb48a8a96ba13e0936

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-27 03:19:23 -0400

      Commit message:


	  
		
 Fix SnowParam workers; fix broken doc links; add pkgload to Suggests

- BPOPTIONS(packages='friends.test') in bplapply/bpmapply wrappers
- skip_if(is_dev_package) in parallel tests (workers need installed pkg)
- Remove broken \link{} to deleted fullmesh.enum from docs
- pkgload added to Suggests

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 

    

  
    

      Package: friends.test

      Commit: 77fcf0c151ee823445b5ebe6644b516db9211f8b

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 19:06:16 -0400

      Commit message:


	  
		
 Sync with devel: O(ncol) step fitter, BiocParallel, test cleanup

- step.fit.ln.likelihoods: new compact return format (best_ll_by_k1, best_l1_by_k1, uniform_ll)
- step.fit.ln.likelihoods.fullmesh: new function, restores full ll-profile format
- step.fit.ln.likelihoods.fullmesh.enum: removed from public API
- Tests replaced 100-random loop with 7 targeted cases (637 -> 83 tests)
- BiocParallel parallel backend (BPPARAM)
- NEWS.md and .Rbuildignore updated

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 

    

  
    

      Package: friends.test

      Commit: d3663ecd264391c6a582d7c10d57c0a957463c53

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 02:50:31 -0400

      Commit message:


	  
		
 Fix package name in testthat.R: best.friends -> friends.test

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
 

    

  
    

      Package: friends.test

      Commit: 3e03da3a72ced62c3375d8272c38dc8b3e900495

      Author:  Sasha Favorov <favorov@sensi.org> 

      Date: 2026-05-26 02:45:40 -0400

      Commit message:


	  
		
 0.99.19
 

    

  
    

      Package: Fancy

      Commit: 7f84e30fa93ba2f94fbb0d1d3680028e74dc3e2b

      Author:  wala-github <graceca.norsk@gmail.com> 

      Date: 2026-05-27 19:06:35 +0200

      Commit message:


	  
		
 Update of version number for submission to bioconductor
 

    

  
    

      Package: CoSIA

      Commit: 090a204b0e3f808a0752d33af163146ef618ffa1

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-27 11:21:22 -0500

      Commit message:


	  
		
 Version bump in devel
 

    

  
    

      Package: CoSIA

      Commit: 8d3d88f343ec59fa5d4ee93fb89e7749114411b8

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-27 11:03:24 -0500

      Commit message:


	  
		
 Merge branch 'devel' of git.bioconductor.org:packages/CoSIA into devel
 

    

  
    

      Package: CoSIA

      Commit: ac19826fc8ac105adfd2d46c85a26e9cd963cf9c

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-08 13:22:04 -0500

      Commit message:


	  
		
 Make test project paths relative
 

    

  
    

      Package: CoSIA

      Commit: abd4615418a1c9fbc5fcbbb4518ad6c5328b0f84

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-06 12:18:14 -0500

      Commit message:


	  
		
 Ensure container directory exists before SIF check

mkdir -p now runs unconditionally in ensure_sif so the bin/container
directory is created even when the SIF is already present.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: ea2ad1b2cbe0ca8196d2a66d85c66fc43ad2d2bb

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-06 12:04:11 -0500

      Commit message:


	  
		
 Add runners for test and validations
 

    

  
    

      Package: CoSIA

      Commit: 9cba678b81e0c87d8f3b133443b7cf1d0aaae5b4

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-05-05 12:19:37 -0500

      Commit message:


	  
		
 Bump to 1.11.2 and revise validation scripts for 1.11.1 vs 1.11.2 comparison

1.11.1 is the Bioconductor production version with the CV_Tissue bug.
1.11.2 is the fixed release.

Validation strategy:
- CV_Tissue: confirm 1.11.1 crashes (bug), 1.11.2 succeeds (fix), with
  structural checks and cross-species consistency check on the fixed output
- CV_Species and DS_* metrics: unchanged code paths, so values must match
  exactly between versions

All scripts now cover all six metric types with a shared set of inputs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: d6da95311bc470c0f2ed021502b9dd88a1f7560c

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 14:58:59 -0500

      Commit message:


	  
		
 Instruct Claude to read CLAUDE_CHANGELOG.md at session start

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: 0c2f99452abe817b6386834adc711eb2acec0b71

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 13:18:36 -0500

      Commit message:


	  
		
 Add GitHub Actions workflow for running the test suite

Runs devtools::test() on push/PR to devel and main using the official
bioconductor/bioconductor_docker:RELEASE_3_22 container. Caches R
packages keyed to DESCRIPTION and ExperimentHub data (EH7858-EH7863)
with a static key to avoid redundant downloads across runs.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: d8001e5bc203c047e9593c11180eaa85c98ed24b

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-23 13:08:47 -0500

      Commit message:


	  
		
 Add CV_Tissue validation scripts and update .Rbuildignore

Three scripts in validation/ compare Bioconductor release against the dev
version to verify correctness of the CV_Tissue merge rewrite:
- 01_run_bioc.R: captures reference output from installed Bioconductor CoSIA
- 02_run_dev.R:  captures output from the modified dev version
- 03_compare.R:  compares results with structural checks, exact value
  comparison for single-species, and manual spot-check instructions

.Rbuildignore updated to exclude validation/, CLAUDE.md, CLAUDE_CHANGELOG.md.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: b0fbf7a2304f275b7143c6c88a3deaf6f68f9f37

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-22 15:56:48 -0500

      Commit message:


	  
		
 Fix CV_Tissue merge loop producing duplicate columns and missing Anatomical_entity_name

The original loop fed the accumulated result back into each merge iteration,
creating a Cartesian product with cascading .x/.y column duplicates and a
broken Anatomical_entity_name column (also contained a typo in the fallback
rename). Rewritten to join each species independently against the original
id_dataframe and combine on all ID columns + Anatomical_entity_name.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: CoSIA

      Commit: 7a07a9e1ed4091f27a11298a33a29f0776c74238

      Author:  Tonie Crumley <tonie.crumley@gmail.com> 

      Date: 2026-04-22 14:24:56 -0500

      Commit message:


	  
		
 Add test suite, fix viewCoSIAn and CV_Tissue bugs, remove deprecation markers

- Add tests/testthat/ suite with 59 tests covering CoSIAn constructor,
  viewCoSIAn, getConversion, getGEx, and getGExMetrics (all 6 metric types)
- Fix viewCoSIAn: replace ifelse() with if/else so data frame slots are
  returned intact rather than coerced to a scalar
- Fix CV_Tissue in getGExMetrics: guard Anatomical_entity_name.x filter
  behind a column existence check so single-species calls no longer crash
- Remove PackageStatus: Deprecated from DESCRIPTION and .Deprecated() call
  from R/zzz.R; package remains active in Bioconductor 3.22
- Add Config/testthat/edition: 3 to DESCRIPTION
- Add CLAUDE.md and CLAUDE_CHANGELOG.md

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

    

  
    

      Package: tximeta

      Commit: d9a028e53c6f687abd621957e353ad6fb0f58b1c

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-27 11:10:53 -0400

      Commit message:


	  
		
 Merge branch 'devel' of github.com:thelovelab/tximeta into devel
 

    

  
    

      Package: tximeta

      Commit: 894467ad2a9c43cd2a207898390318ca91a2327a

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-27 11:10:51 -0400

      Commit message:


	  
		
 cleaning up getTxDb code
 

    

  
    

      Package: tximeta

      Commit: 35872c0cc73434485b8358f43bd5fe3f5c201e18

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-26 08:54:59 -0400

      Commit message:


	  
		
 adding new diagrams
 

    

  
    

      Package: tximeta

      Commit: e58c5650ab7027b2692457c56f773f228ae0260c

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-05-22 10:52:03 -0400

      Commit message:


	  
		
 adding new argument gencode_gtf_prefix, for flexibility with the GTF file that is downloaded
 

    

  
    

      Package: simPIC

      Commit: 6a69e49b24f4b71dd72dc18913a1614c944ca918

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 22:13:10 +1000

      Commit message:


	  
		
 Use development pak for CI dependency resolution
 

    

  
    

      Package: universalmotif

      Commit: 36a8a72a904a38b622810ed06245cc9123613df6

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-27 13:03:52 +0100

      Commit message:


	  
		
 ChIPseqWorkflow: attach GenomeInfoDb so keepSeqlevels() resolves

The vignette attached GenomicRanges (which re-exports seqlevels()) but
not GenomeInfoDb, where keepSeqlevels() actually lives, so the Bioconductor
build machine failed the vignette with "could not find function
keepSeqlevels". Attach GenomeInfoDb in the setup chunk and declare it in
Suggests. Bumps the version to 1.31.26.
 

    

  
    

      Package: simPIC

      Commit: acd9550073b411940f5cc1c65e4ab2bb92b6ece9

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 21:55:47 +1000

      Commit message:


	  
		
 Fix CI dependencies and deprecation warnings
 

    

  
    

      Package: simPIC

      Commit: 1ede624444aa9bd3bd7ca798d375234132efaba7

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:42:29 +1000

      Commit message:


	  
		
 Resolve devel version after upstream merge
 

    

  
    

      Package: simPIC

      Commit: eab64bbe9b21e537ec13c81ea8a32cbfbdef8b03

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:34:37 +1000

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel' into devel
 

    

  
    

      Package: simPIC

      Commit: d60e655843e7d7c13ce1ecac0ce7955d0efbc6cf

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 20:27:26 +1000

      Commit message:


	  
		
 Add population simulation workflow
 

    

  
    

      Package: simPIC

      Commit: 93c1dc6882edf066546f52617bd16163cf4acbed

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2026-05-27 16:33:58 +1000

      Commit message:


	  
		
 Exclude GitHub files from R build
 

    

  
    

      Package: simPIC

      Commit: 0897f400ce732b823d27d674c10a8b54791b01cf

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 09:58:33 +1000

      Commit message:


	  
		
 Fix CI: Remove oldrel-1 testing and refresh dependencies
 

    

  
    

      Package: simPIC

      Commit: f6b43cfcfcb4e03f5a2663541adf909a41e3da6b

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 02:35:33 +1000

      Commit message:


	  
		
 R-CMD-check badge
 

    

  
    

      Package: simPIC

      Commit: 007b0d0c1a7d54740913840299b34b668abcd340

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-23 02:33:38 +1000

      Commit message:


	  
		
 R-CMD-check badge
 

    

  
    

      Package: simPIC

      Commit: c71d97e828c7719d5eddfc2e62b2cf4e4ce22d94

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:57:17 +1000

      Commit message:


	  
		
 make sure .yml interprets R script add single quotes
 

    

  
    

      Package: simPIC

      Commit: bf01536f75a2e5de4030808dba9b67266b7c68fc

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:54:22 +1000

      Commit message:


	  
		
 make sure .yml interprets R script add quotes
 

    

  
    

      Package: simPIC

      Commit: 4324f9e3c0b809f81536298f955304040425f142

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:47:41 +1000

      Commit message:


	  
		
 make sure .yml interprets R script
 

    

  
    

      Package: simPIC

      Commit: fb2837808985fe47b32c9bab9be47adbf7c167c5

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:37:18 +1000

      Commit message:


	  
		
 Add BiocCheck workflow for devel-- fixed indent
 

    

  
    

      Package: simPIC

      Commit: 0b32bd82810a06bf67c030ea285c31bd139c3052

      Author:  Sagrika Chugh <sagrika.chugh@gmail.com> 

      Date: 2025-05-22 16:27:58 +1000

      Commit message:


	  
		
 Add BiocCheck workflow for devel
 

    

  
    

      Package: universalmotif

      Commit: c09ae09e266d94b2ea4e7c7f44ce5e5cc743cc9e

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-27 11:38:14 +0100

      Commit message:


	  
		
 README: refresh overview to cover the current feature set

Brings the landing page up to date with the package as it stands: notes
CWM support, de novo discovery, co-occurrence testing, and the faster
DNA/RNA comparison and scanning functions; adds the ChIP-seq workflow and
motif database curation vignettes to the list; introduces a CWM section
with a plotted contribution logo; and reworks the comparison example
around compare_motifs2(), merge_motifs2() and view_motifs2(), regenerating
the example figures. Also bumps the version to 1.31.25.
 

    

  
    

      Package: Rarr

      Commit: bbc893ebd576e0cfe031b82903d489e41bff3941

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:56 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 4dd1708bf9fb810f51a0b70324b27acf172b3089

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:34 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: Rarr

      Commit: 1d8a577443e3b5c457e3ec0f18e0c7646c2d3a19

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-05-27 08:52:22 +0200

      Commit message:


	  
		
 Fix compatibility with older ZarrArray
 

    

  
    

      Package: epiregulon

      Commit: 4d04502f71982894976ccaac7384e01505292c0c

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 06:32:24 +0000

      Commit message:


	  
		
 update github workflow to Bioc3.24
 

    

  
    

      Package: epiregulon

      Commit: b9f6be6a9bc56ff16646c38112fed805ded3c242

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 06:31:14 +0000

      Commit message:


	  
		
 update github workflow
 

    

  
    

      Package: epiregulon

      Commit: a8fa50e9d32144ec8e1c6ba53768ca4947787935

      Author:  Xiaosai Yao <yao.xiaosai@gene.com> 

      Date: 2026-05-26 05:58:32 +0000

      Commit message:


	  
		
 version 2.3.2. replace scran::findMarkers with internal findMarkersSimple
 

    

  
    

      Package: Rsubread

      Commit: f2c356364060e3089e1beb442a3fe7f42432ea17

      Author:  Yang Liao <yang.liao@onjcri.org.au> 

      Date: 2026-05-27 15:11:52 +1000

      Commit message:


	  
		
 used normal sort for very few items for sorting
 

    

  
    

      Package: Rsubread

      Commit: c044a6e7348db22b75e11938585f7930b78ace46

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 15:07:19 +1000

      Commit message:


	  
		
 disabled sample-level junction list
 

    

  
    

      Package: BiocGenerics

      Commit: fab8ae09376803fd8bb7d2d7a7c2638d94046ca8

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-26 21:50:21 -0700

      Commit message:


	  
		
 BiocGenerics 0.59.6: Add S4 generic rotate()
 

    

  
    

      Package: Rsubread

      Commit: 6277cc92e632aa3cf6301f1a089bb6b1e027fe2d

      Author:  Yang Liao <yang.liao@onjcri.org.au> 

      Date: 2026-05-27 13:55:02 +1000

      Commit message:


	  
		
 added some comments.
 

    

  
    

      Package: Rsubread

      Commit: 92bbda8745d398a8881806cd5c24de2761dfa353

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 13:22:31 +1000

      Commit message:


	  
		
 Added unassigned read output in cellCounts
 

    

  
    

      Package: IRanges

      Commit: 10ce23b0f4e889c60b495c18cc69b637540919ad

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-26 19:39:38 -0700

      Commit message:


	  
		
 IRanges 2.47.2: Use new transform() signature in method definitions
 

    

  
    

      Package: S4Vectors

      Commit: 6b6e8b0396cf84d00b05199a0580ea25284ed4b8

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-05-26 19:24:47 -0700

      Commit message:


	  
		
 S4Vectors 0.51.3: Use new transform() signature in method definitions
 

    

  
    

      Package: Rsubread

      Commit: a9e162b08cfa02b5b481c78533d1232ce2fc9f8f

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2026-05-27 11:19:19 +1000

      Commit message:


	  
		
 added vbuf to many file pointers
 

    

  
    

      Package: glmGamPoi

      Commit: 95cffb79b02ce1239112d3c8b4adabfb448940bf

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:40:39 +0100

      Commit message:


	  
		
 Update NEWS
 

    

  
    

      Package: glmGamPoi

      Commit: 7a4ace6be5e446ecaf46ee1b95b3f4a11b81fdf1

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:39:34 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: glmGamPoi

      Commit: a9eeed642020303b350bcf072e0b2150f593de24

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:39:28 +0100

      Commit message:


	  
		
 Change license to MIT
 

    

  
    

      Package: glmGamPoi

      Commit: 8d9a005741307f13115073687fd9dbbc239ee2f0

      Author:  const-ae <artjom31415@googlemail.com> 

      Date: 2026-05-26 22:36:11 +0100

      Commit message:


	  
		
 Add check for degenerate model_matrix in predict.glmGamPoi for se.fit=TRUE
 

    

  
    

      Package: AnVILAz

      Commit: 89e3a4bc79c91664afd02f0fb8fcc59878191a0e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 16:27:05 -0400

      Commit message:


	  
		
 version bump 1.7.2
 

    

  
    

      Package: AnVILAz

      Commit: b276ea3e2d963089ead2b7ef4b8239880378e514

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-05-26 16:26:56 -0400

      Commit message:


	  
		
 fix showClass typo
 

    

  
    

      Package: universalmotif

      Commit: 411e104c944df24322c4348da8c89654c0f24d85

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 21:09:39 +0100

      Commit message:


	  
		
 clean up news
 

    

  
    

      Package: universalmotif

      Commit: a45fb4c4175988d9c243e8dcf50c862138fa1050

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 21:02:24 +0100

      Commit message:


	  
		
 NEWS: frame 1.32.0 entries relative to the last release

The release notes should describe net changes since the last
release (1.30.x), not changes between intra-development states.
Two entries were written against mid-cycle states and don't make
sense to a user upgrading from the last release:

- Dropped the standalone "merge_similar2(return.clusters) now
  returns a universalmotif_df instead of a data.frame" entry:
  merge_similar2() is itself new this cycle, so there is no prior
  released behavior to migrate from. The return.clusters output is
  now described as part of the merge_motifs2()/merge_similar2()
  feature entry.

- Dropped the rev_comp_mat()/view_motifs2() reverse-complement
  bug-fix entry: view_motifs2() is new this cycle, so that bug
  never shipped in a release.

Also narrowed the negative-letter-stack rendering fix to
view_motifs() (the released function that actually carried the
bug; view_motifs2() is new).
 

    

  
    

      Package: universalmotif

      Commit: 6f8bb7b039e77342455adb6a30c504919aabed68

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:58:54 +0100

      Commit message:


	  
		
 NEWS: document CWM matrix I/O and the two view_motifs rendering fixes

Add the two outstanding bug-fix entries from the CWM / v2 work:
the negative-letter-stack cumulative-offset fix in
flip_neg_letters() (3+ negative letters used to overlap in
view_motifs / view_motifs2), and the rev_comp_mat() row-name fix
(view_motifs2 drew the column-reverse instead of the reverse
complement of RC'd motifs). Also note read_matrix() / write_matrix()
CWM round-trip via type = "CWM" in the CWM feature entry.
 

    

  
    

      Package: universalmotif

      Commit: 54599e74275ce439a33581d4cf6c33a5f20dbce2

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:53:16 +0100

      Commit message:


	  
		
 vignettes: cross-reference v2 functions throughout the prose

Mention the v2 siblings (compare_motifs2, merge_motifs2,
merge_similar2, scan_sequences2, enrich_motifs2, view_motifs2,
motif_tree2) alongside their v1 counterparts where the docs
introduce or describe each function, so readers discover the
leaner alternatives in context. Also tidies assorted phrasing
and trims yamtk-subcommand-specific references to the bare
project link.
 

    

  
    

      Package: universalmotif

      Commit: ba46d951acbee0e380bd047442a2618d3c10dea9

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 20:24:26 +0100

      Commit message:


	  
		
 merge_similar2(return.clusters): return universalmotif_df; CWM doc pass

merge_similar2(return.clusters = TRUE) now returns a
universalmotif_df (the to_df() view of the input motifs, motif
objects in the `motif` column and names in `name`) augmented with
`motif.i` and `cluster` columns, via a new clusters_to_df()
helper applied across the empty-input, single-motif, and
multi-motif paths. Previously it returned a bare three-column
data.frame whose `motif` column held name strings. Callers that
relied on that should switch to `name`; `motif.i` / `cluster` are
unchanged. test_merge_similar2.R updated to assert the new class
and columns; MotifDatabaseCuration.Rmd switched from
clusters$motif to clusters$name and prints the assignment columns
explicitly.

CWM documentation pass: convert_type(), create_motif(),
read_matrix(), write_matrix(), read_meme(), and write_meme() man
pages now document the CWM type / CWM argument, including the
TF-MoDISco |cwm|/sum convention, the one-way nature of the
conversion (no *->CWM), and round-trip examples. convert_type
gains a dedicated CWM @details section and Shrikumar et al.
(2017, 2018) references. A test_cwm.R case covers the
write_matrix / read_matrix CWM round-trip.

Also folds in roxygen prose tidy-ups across several v1/v2
function headers (compare_motifs, dedup_hits, motif_finder,
sample_sites, and cross-references to the v2 siblings) and the
corresponding regenerated .Rd files; NEWS updated.
 

    

  
    

      Package: universalmotif

      Commit: f7306500104e457f45cc9939f2b709d7dc572a40

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-05-26 17:03:07 +0100

      Commit message:


	  
		
 view_motifs: fix overlap in negative-letter stacks of 3+

flip_neg_letters() positions each negative letter by shifting it
down from the baseline by the cumulative height of every letter
above it in the stack. The shift table is computed at the bottom
of the function:

  letMins <- c(0, letMins)
  for (i in seq_along(lets)) d$y[j_i] <- d$y[j_i] + letMins[i]

`letMins` here is the per-letter min-y (i.e. each letter's height
expressed as a negative number after the flip). With this version,
letter i was shifted by *only* letter (i-1)'s height instead of
the sum of heights for letters 1..i-1, so any 3-or-more letter
negative stack had letters 2..N piling on top of each other. With
a CWM display the bug was glaring (3 equal-magnitude negative
contributions per core column rendering as 2 visible rows);
PWM logos with 3+ significant negative letters had the same
defect but more rarely.

The fix is the one-line cumsum the previous developer left
commented out directly above:

  letMins <- c(0, cumsum(letMins))

For 1- and 2-letter negative stacks the two formulas are
arithmetically identical, so PWM logos that used to render
correctly continue to do so. Full test suite still passes with
no new failures.
 

    

  
  


</div>

</div>