bump
 

 got an error with vignette generation due to availability of web file. fixed now but need to bump anyway.
 

 Remove warning
- Update documentation so that \linkS4class{} isn't used for classes outside the package itself. These are replaced with \code{\link[package]{class}}
 

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 1.9.3
 

 dont test diffCoexpression
 

 bump to 1.7.9, more removal of github links
 

 Add annotate_heavy_V_alleles() and annotate_light_V_alleles()
 

 Update benchmarks. Chunk gprofiler queries
 

 Fix planarian tests
 

 Fix version number
 

 Change maintainer email
 

 0.99.12 changes removing .Rproj.user dir
 

 Merge conflicts resolved
 

 Change man pages to reflect switch to using name for congtrast
 

 Fix for limma 3.66.0 switching to using the names for the contrasts
 

 Merge pull request #22 from crukci-bioinformatics/RELEASE_3_19

Release 3 19 

 Update everything with roxygen and version bump
 

 Update so that user can omit labels on PCA plot
 

 Bump version from 1.13.2 to 1.99.0 

 Merge branch 'master' into master 

 Removed old license file
 

 Update docs
 

 fixed parameter matching
 

 Handle new xgboost syntax. Now handles both prior and current versions of xgboost
 

 Last fix following the change in KEGGrest around keggconv
 

 requested deprecation
 

 Merge branch 'devel' of git.bioconductor.org:packages/scater into devel
 

 bump version
 

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    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

    commit 9a6bc51dcbe1adf7e71b02a17a7c7be25a6b27d3
    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%)
        /inst/shiny/www/set-operations/fonts/set-operations.svg -- 28.02kb -> 27.75kb (0.98%)

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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)
 

 bump GHA BioC version
 

 Merge branch 'fix_bioc_cargo' into devel
 

 fix: find_isoform_bambu unzip error if file exists
 

 bump to 1.9.1
 

 fix: library imports order in vignettes
 

 gub in examples
 

 fix error in check
 

 bump to 1.29.8
 

 Refactor print method to directly call SummarizedExperiment's show method

- Updated print.SummarizedExperiment to retrieve and call the original show method from the SummarizedExperiment namespace when tidy print is not enabled.
- Improved clarity of the method's functionality by ensuring the correct method is invoked.
 

 Merge pull request #27 from tidyomics/remove-alternative-prints

Simplified codebase 

 Merge pull request #29 from tidyomics/use-n-print-argument

Refactor print.SummarizedExperiment function 

 Merge pull request #28 from tidyomics/use-n-print-argument

Update print method parameter from n_print to n 

 Simplified codebase
- Removed design parameter from print.SummarizedExperiment function
- Updated print method to streamline functionality
- Adjusted documentation to reflect changes in print method
- Updated RoxygenNote to 7.3.3
- Added import for dplyr's all_of function in NAMESPACE
 

 bump to v1.7.1
 

 fix: args and doc
 

 docs: update vignette to reflect changes in theme/geoms
 

 ci: update GHA
 

 bump to 1.7.7
 

 Add "DotBracket" seqtype as compatible "B" seqtype (#134)

 

 Bug Fix Unit Test
 

 fix getDBs for MSA knowledgebases
 

 Trigger build minor reviews
 

 Merge branch 'devel' of git.bioconductor.org:packages/QTLExperiment into devel
 

 Improved example code
 

 Updated to v0.99.12
 

 Updated vignette
 

 Updated documentation
 

 Minor documentation changes
 

 New occupancy FDR logic
 

 Updated with new internal condition naming logic
 

 Major rewrite of occupancy FDR logic
 

 Minor changes to example code
 

 Updated with new occupancy FDR options
 

 Added bookdown as a suggest for pkgdown documentation creation
 

 Minor changes for readability
 

 Fix the figure display issue
 

 IWTomics 1.35.1: Add XVector to Suggests

The XVector package is needed by the IWTomicsData#GRangesList#list method.
This method calls the disjoin() method for GRanges objects which calls the
range() method for CompressedIRangesList objects which requires XVector.
 

 0.99.11 updates
 

 Merge pull request #22 from NICHD-BSPC/bioc_timing2

tweak examples to reduce R CMD check times

- revert to using non-package data for some examples
- switch entire examples blocks for module server/ui to using examplesIf interactive()
 

 add back --as-cran to check cmd
 

 switch mod ex to examplesIf interactive
 

 revert to non-package data
 

 Update minSlopeSize parameter, fix bug, and remove out of date tests
 

 fix group model, bump ersion, add another vignette, simplify models
 

 Minor review
 

 Hint for the recommended de.method= and aggr.ref= for SCE inputs.

This avoids the use of inappropriate defaults for single-cell references.
 

 Fix bioc check size.
 

 Fix bioc check.
 

 Fix bioc check.
 

 Fix bioc check.
 

 Fix Seurat v5 problems and add new vignette.
 

 Removed the scuttle dependency from examples and tests.

- Cleaned up code for partitioning the reference into two smaller datasets for
  combineRecomputedResults tests and examples.
- Make sure that the chosen markers actually have increased expression above
  the baseline in .mockRefData.
 

 Strip out version number when installing dependencies for GHA.
 

 correcting version
 

 remove snapshot check
 

 Update test-mainOGRDB.R
 

 export functions

#7
 

 Updated .set_meth_df_columns to use with for meth_files_columns
 

 Fixed setup to use final GRanges
 

 Cleaned make_meth_rse helper functions
 

 udpate
 

 Updated extractMethSitesFromGenome
 

 Updated make_meth_rse_accessory_functions2.R
 

 Merge branch 'master' into devel
 

 Merge pull request #176 from BorchLab/fix-seurat-assay

updated documentation and assay utilization 

 Update README.md 

 chore: Add titles to code chunks
 

 feat: Update vignettes and docs, and enable support for MZmine and MS-DIAL
 

 downcast plot class #109
 

 Merge remote-tracking branch 'conductor/devel' into devel
 

 Rm usage from gprofiler_orgs/gprofiler_namespace
 

 DESC file fix
 

 Merge branch 'tgirke:devel' into devel
 

 Merge pull request #87 from lz100/devel

fix: Add extraction of special variables to YAML input in write.yml  

 use extract() from magrittr
 

 Merge grr fixes #47
 

 bump to 1.7.6
 

 refactored testEnrichment
 

 Minor testfix to avoid unnecessary warnings about capped k.

Because CRISPR QC filtering is too aggressive on a random matrix.
 

 Only subset the neighbor search results if there are enough observations.
 

 Testfix for scoreMarkers with newly added fields.
 

 Accept a string in include.order.by= to support custom colnames.
 

 Report block IDs with the same type as the input for easier matching.

This only applies to functions that report some kind of per-block result, where
the user might want to extract a result for a specific block without coercing
the block identity to a string to match the row/colnames.

We already do this for the QC functions but we rename the field to 'block.ids',
which is easier to understand than 'block.levels'.
 

 testEnrichment now returns a DataFrame for consistency with other functions.
 

 Replace most references to base data.frames with S4Vectors::DataFrame in the docs.
 

 Remove namespacing for S4Vectors:: in all remaining functions.
 

 Preserve the type of the blocking factor in .transformFactor.

This is useful for QC functions, to ensure that the block= for filter*
functions can be correctly matched to the block= used in suggest*.
 

 Report DataFrame directly from modelGeneVariances, for convenience.
 

 Simplify logic for reporting the ordering statistic by previewMarkers.
 

 Report quantiles in the scoreMarkers.se results.
 

 fix two-sided pvalue, bump to 1.7.5
 

 fix to cdata.h
 

 Merge branch 'master' of https://github.com/fogellab/multiWGCNA
 

 Update README.md 

 Update DESCRIPTION
 

 Print statement deleted
 

 Merge pull request #30 from OumaeKaede/OumaeKaede-patch-1

Update overlaps.R 

 Added getModule function
 

 Modified findBestTrait

Made compatible with having no trait variance by adding an NA check
 

 Added description to autism vignette
 

 fix the bug when subset the cells by percentage.
 

 Fixed funtion `isCoexAvailable()` (#129)

* Fixed funtion `isCoexAvailable()`

for cases when global meta-data have more columns

Fixed dispersion function error output

* Updated tests about multi-valued global data

* Added navigation comments 

 Bugfix: drop `gghalves` package (#127)

* Dropped use og gghalves and some plots clean-up

* Solved operator conflict for zeallot's `%<-%`

Improved vignette coding style 

 migration from dependency futile.logger to logger
 

 updates for PIUMA 1.7.2
 

 retrigger checks
 

 Le's changes
 

 Normalize line endings to LF for Bioconductor compliance
 

 Add new visualizations and update documentation in systemPipeVARseq workflow
 

 feat: varseq related-files
 

 bump
 

 bump
 

 merge
 

 fix #272
 

 Version bump in devel
 

 Update github action check-bioc
 

 Update github action check-bioc
 

 Update parameters of the generatic is.CNVMetic()
 

 Merge pull request #27 from adeschen/adeschen-patch-3

Update check-bioc.yml 

 Merge pull request #26 from adeschen/adeschen-patch-3

Update check-bioc.yml 

 Update check-bioc.yml 

 Update check-bioc.yml 

 Made pathwayEnrichment test generic to prevent erroneous errors
 

 Fixed to test to prevent failure
 

 Updated reactomeDatabase data object
 

 Updated keggDatabase data object
 

 Updated hallmarkDatabase data object
 

 Updated pathwayCategories data object
 

 Changed factor column to character in sigoraExamples
 

 Comment out plyranges
 

 Version bump.
 

 Re-created srt_sc.rds to address the error related to "VisiumV1" object.
 

 update code style.
 

 Solve error
 

 feat: Enable Compound Discoverer support
 

 Vignette aesthetics
 

 version bump 

 added comment to explain name difference between `py_module_available()` & `py_install`
 

 Merge pull request #72 from PNNL-CompBio/metab-prot-integ

thanks for the comments! 

 Update DESCRIPTION

i think depends is more stringent than imports 

 added manuscript figure script
 

 Merge pull request #71 from PNNL-CompBio/metab-prot-integ

Metab prot integ 

 maybe we need vignette files?
 

 updated to make better sense of data
 

 new changes
 

 last updates
 

 Merge pull request #69 from PNNL-CompBio/metab-prot-integ

addition of a lipid/protein example 

 more updates to the vignette
 

 Merge pull request #68 from PNNL-CompBio/metab-prot-integ

Added outline of lipid/proteomic integration 

 working on  package building with vignette
 

 added reduce function
 

 Added updated function to get metspace data
 

 updated spatial diffex fro counts

added support for voom.
 

 kept this in separate branch for now
 

 testing out metabolomic/proteomic integration
 

 cleaned up line ending
 

 Merge pull request #62 from PNNL-CompBio/new-bioc-sub

Major bioconductor updates, trying to get ahead after seeing the leapR comments 

 updated ahead of new bioconductor version prep
 

 Update README.md 

 updated vignette
 

 updated vignette
 

 added python script to process edges of image automatically
 

 fixed issue
 

 Merge pull request #53 from PNNL-CompBio/split-impute

Split impute 

 cleaned up more issues
 

 updated documentation
 

 Merge pull request #52 from PNNL-CompBio/split-impute

updated split function 

 Merge pull request #51 from PNNL-CompBio/split-impute

Added split functionality and more methods to imputation 

 slight fix to vignette
 

 updated ignore
 

 fixed imputation and aded ability to split

added split functionality to help with RA anlsysi, fixed imputation.
 

 First reviewed version of Bioconductor submission
 

 Add error message to output
 

 version bump 1.47.7
 

 version bump 1.47.6
 

 Tweaked test to support release and development versions
 

 Bump version to 0.99.1 for Bioconductor build
 

 Add files via upload 

 Delete panoramic_graphic.png 

 Delete panoramic_graphic.png 

 fixed cache issue
 

 fix namespacee
 

 Bump version to 1.20.1
 

 Fix expectation in validation tests
 

 Bump JamesIves/github-pages-deploy-action from 4.7.3 to 4.7.4 (#154)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 

 Merge pull request #124 from karawoo/gha

update cache action 

 CPSM 1.3.1: Update in DESCRIPTION and NEWS.md, cross-validation updates, feature stability metrics, and documentation
 

 Streamline configure script when the output directories already exist.
 

 Added seealso links to the SE wrappers for each non-SE function.
 

 Removed some extraneous scrapple references.
 

 Collapse the neighbor search for greater speed by default.
 

 chore: Update lcmsPlotClass documentation
 

 feat: Codebase improvements for Bioconductor standards
 

 bugfix namespace, simplify .stan models
 

 merge
 

 KNN implementation
 

 Merge remote-tracking branch 'upstream/devel'
 

 version bump 1.7.6
 

 Updated comparison to work with Biostrings 2.79.3

comparable_seqtypes was changed in Biostrings to allow for seqtypes "ModRNA" and "ModDNA" to be used efficiently. Performance improvements by avoiding the constructor calls as suggested by Herve Pages were implemented.
 

 Added function to fetch signatures from https://github.com/tgac-vumc/StatescopeData and did some code cleaning
 

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel
 

 Update check-bioc.yml 

 Update check-bioc.yml 

 Update check-bioc.yml 

 Update check-bioc.yml

Switched to newer free disk space fork 

 Update check-bioc.yml

Now actually rm -rfing I hope 

 Update check-bioc.yml

Forgot # 

 Adjused autogenes environment to python 3.7 (most recent with pip <24.1
 

 Update check-bioc.yml

Claim disk space by removing unused tools, see:
https://github.com/actions/runner-images/issues/2840#issuecomment-3641541098 

 Merge pull request #21 from NICHD-BSPC/bioc_timing

make bioc check more efficient 

 use included data in ex
 

 Merge pull request #20 from NICHD-BSPC/bioc_debug

troubleshoot bioc build issues

- removed clusterProfiler from Suggests
- tweaked vignette to use data obj 

 typo
 

 fix vignette
 

 updt data obj
 

 bump R version in reqs
 

 use env-unpinned fr R CMD check
 

 bump R version to 4.6.0
 

 use 'logger' rather than 'futile.logger'
 

 Change the Examples.
 

 Update the Description for the biocheck.