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GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

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Package: igvShiny
Commit: a1ad70ccb5cfc48585b323b11ee2795f4e1fcd39
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-09-11 08:04:41 +0200
Commit message:

 feat(tracks): add trackHeight parameter and alignment sizing options (#181)

Related: #174

Add trackHeight parameter to alignment track loaders (loadBamTrackFromURL,
loadBamTrackFromLocalData, loadBamTrackFromLocalFile, loadCramTrackFromURL,
and loadCramTrackFromLocalData), validate finite pixel height, preserve
positional compatibility with 1.9.45, and expand the option allowlist for
alignment sizing and visibility.
Package: cellNexus
Commit: 240ebe83db8f8a4ff9a3a74db77abba3326b46ce
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-09-10 15:28:27 +1000
Commit message:

 Merge pull request #158 from myushen/new_metadata_counts

Update metadata
Package: cellNexus
Commit: 851ff0b082ba294091d8e4b330476c5f26623fdb
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-09-10 12:14:24 +1000
Commit message:

 news and version bump
Package: cellNexus
Commit: f3544947b458ed8a40207e11ce2d7c7d667b513f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-09-09 21:26:25 +1000
Commit message:

 update metadata and vignette
Package: scTensor
Commit: 10a5e8036f8af8e6891f7a120fb5326018ea7bd4
Author: koki <k.t.the-answer@hotmail.co.jp>
Date: 2026-09-11 09:28:02 +0900
Commit message:

 v2.23.2: Fix DOSE enrichDGN removal and add BuildSignedCCI
Package: BiocDuckDB
Commit: 403732a8e16fb89a7ce602daad67dd369834e1e5
Author: Patrick Aboyoun <aboyoun.patrick@gene.com>
Date: 2026-09-10 17:05:07 -0700
Commit message:

 feat: beachmat/tatami fast path + DuckDBIrlbaParam for correct, fast PCA on DuckDBMatrix (#1)

* feat: add beachmat integration
* feat: add DuckDBIrlbaParam class
* fix: update benchmark_results.rds
* docs: update NEWS.md file
* docs: update the date
Package: NetSAM
Commit: f554b316d62cb21bd66f9d44a173776e1b5ff442
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2026-09-10 16:06:02 -0500
Commit message:

 add README, biocViews and NEWS, and update vignette install instructions to BiocManager
Package: NetSAM
Commit: d7e89383fe9a9dae7993ce2b84c8ce099c39cbd2
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2026-09-10 15:56:27 -0500
Commit message:

 wrap Ensembl-dependent mapToSymbol examples in try() and bump version to 1.53.1

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01FkgD1by46Brw8uxGC6nyrc
Package: DAssemble
Commit: ca195c8a7bfea072c20198ccace2a62887268d0c
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-09-10 14:52:41 -0400
Commit message:

 Merge Bioconductor devel into master
Package: DAssemble
Commit: 5ad2ebe53e7ac7beb5fb3260c093903c81c1d49b
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-09-10 14:47:11 -0400
Commit message:

 Updated vignette with an example for longitudinal
Package: DAssemble
Commit: 9cbebe5d4bf2782ff86278e6239dc3acd0fa778f
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-09-01 13:43:53 -0400
Commit message:

 updated handling of method args
Package: DAssemble
Commit: 311b862053ac10a83d347c466ca17ecf046c91f2
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-08-28 11:47:37 -0400
Commit message:

 updated enhancer for LR, maaslin2 additional functionality and updated README
Package: DAssemble
Commit: 970c744216a8436511c3ad59daf9fedb84a3665e
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-08-21 14:53:23 -0400
Commit message:

 updated news and description
Package: DAssemble
Commit: 9fa6bda0b1d43a4403fad48ae016e335673f0660
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-08-21 14:38:14 -0400
Commit message:

 updated handling of linear separability
Package: DAssemble
Commit: 07e1605447641211f25f28e6ba670da93259206d
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-08-21 13:22:19 -0400
Commit message:

 updated support for longitudinal and  multiple covariates
Package: DAssemble
Commit: fe388a2f6aea6f40ab434b119c88a8d79a45b8f5
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-07-18 17:41:38 -0400
Commit message:

 Updated bioconductor accepted code
Package: DAssemble
Commit: b7d557fb312ba5ce9a28947a0a2682f8ca31663d
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-07-09 19:51:13 -0400
Commit message:

 updated files
Package: DAssemble
Commit: 6b4585d1f696c704293656e5ea8d34b65393ed37
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-07-03 09:51:13 -0400
Commit message:

 updated bioc
Package: DAssemble
Commit: e0d71b7741dcd5891b3c6e1103fad09e3dfeb0c8
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-06-25 19:42:23 -0400
Commit message:

 updated unit tests
Package: DAssemble
Commit: 91b2edca67c496c5e138be1de81e0dfe846e334b
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-06-25 17:16:58 -0400
Commit message:

 updated vignette and citation
Package: DAssemble
Commit: d5038b5e771dd883c7f118ff77e90364391595b3
Author: Nalin Arora <nalin21478@iiitd.ac.in>
Date: 2026-06-25 15:36:17 -0400
Commit message:

 updated bioconductor submission files
Package: MSstatsResponse
Commit: 164c1d1575d5ea83ae05f4c03f820c5e895dd520
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-09-04 10:32:22 -0400
Commit message:

 Bump version from 1.3.2 to 1.3.3
Package: MSstatsResponse
Commit: 1a4ee69928178c1d923371f93e14ffde64463025
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-08-31 21:07:11 -0400
Commit message:

 refactor(createTurnoverRatios): Speed up code to use data.table (#11)
Package: MSstatsResponse
Commit: 198ef4e0f10a6440ad2655b8ae4ce1f642b2c469
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-07-20 21:46:31 -0400
Commit message:

 Update README to include TMT in workflows
Package: MSstatsResponse
Commit: 38de4ce71cd92ad5067245b3b1cf70db7bcad569
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2026-07-20 21:45:31 -0400
Commit message:

 update README with remotes::install
Package: MSstatsResponse
Commit: 16a19e9a7df3b234e472c2bb1a0dcc296ffceb55
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2026-07-20 21:34:30 -0400
Commit message:

 docs(readme): Update README with up-to-date information
Package: MSstatsResponse
Commit: 04b021d73d6788991695c1d92da42efa187031f2
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2026-07-20 15:43:05 -0400
Commit message:

 fix(turnover): handle scenarios where L_frac is NA for all timepoints
Package: scrapbook
Commit: 8d330d15f9cc8a340af13a9a95ee2feb21bcc25a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-11 03:17:10 +1000
Commit message:

 More minor wording changes in the marker detection chapter.
Package: CLAMP
Commit: 2cefda5f95f2938cb077ed21c298a6116712daa8
Author: msubirana <mb2subi@gmail.com>
Date: 2026-09-10 10:06:49 -0600
Commit message:

 Bump to 0.99.8: fix normalized whole-blood examples
Package: FlowSorted.DLPFC.450k
Commit: 5ce8b4ed6f5357b860bcffb984bce1e7eb3b6865
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 14:17:35 -0400
Commit message:

 Fix reference-data access to preserve minfi::estimateCellCounts compatibility

The initial migration exposed FlowSorted.DLPFC.450k as a plain callable
function. minfi::estimateCellCounts() (and likely other downstream
consumers) accesses reference packages via the historical lazy-data
pattern: data(list = pkg); get(pkg). With a plain function, get(pkg)
returned the function object itself rather than the RGChannelSet,
silently breaking estimateCellCounts.

FlowSorted.DLPFC.450k is now an active binding installed in .onLoad,
so referencing the bare name (matching the old data() usage) downloads
and returns the actual object, caching it for the session. Verified
against a live estimateCellCounts(..., compositeCellType = "DLPFC") run.
Package: FlowSorted.DLPFC.450k
Commit: f6aaf8bede6db56d6cffef2b3064d63a5d3f333b
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 13:55:42 -0400
Commit message:

 Move large data object to Zenodo, download via BiocFileCache

The bundled FlowSorted.DLPFC.450k.rda (130MB) exceeded GitHub's file
size limit ahead of Bioconductor's migration off its own git server.
It is now hosted on Zenodo (doi:10.5281/zenodo.21998569) and
downloaded on first use via BiocFileCache, which caches it locally
afterwards. FlowSorted.DLPFC.450k() replaces the former data(...) call.

Also removes the stray external_data_store.txt, adds Authors@R, and
title-cases the Title field to clear R CMD check NOTEs.
Package: FlowSorted.DLPFC.450k
Commit: 15cb32f55d0d0bd6b99a5030439c07f57beed86d
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 10:52:09 -0400
Commit message:

 Update maintainer email

andrew.jaffe@libd.org is no longer reachable.
Package: FlowSorted.DLPFC.450k
Commit: 69ad7300d9f0f280e95865454e355cf93442b331
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:26:58 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
Package: FlowSorted.DLPFC.450k
Commit: 6573f0236eafa54a498b8c197e1c27f750b3b92b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:26:58 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
Package: FlowSorted.DLPFC.450k
Commit: 230a32332e5ba239f1d92ca735864eb8ea88f487
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:55:00 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: FlowSorted.DLPFC.450k
Commit: b3477a40f62e534fa140f26fe19c648c035b074c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:55:00 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: FlowSorted.DLPFC.450k
Commit: c4d4188ac41085ff47770a00c0f8517db07efa24
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:54:52 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
Package: FlowSorted.DLPFC.450k
Commit: 155abe4459ccb8cef2e154c280bb931260357037
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:54:52 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
Package: FlowSorted.DLPFC.450k
Commit: dbb60629439a588a927ef4fec379d541786867f3
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:38:58 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
Package: FlowSorted.DLPFC.450k
Commit: 9c6932ecc057bc697a6a885b183c3e82fd60c144
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:38:58 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
Package: FlowSorted.DLPFC.450k
Commit: 19e2ad12d0f1cf9625008b3bd0a88b79d2f8284c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:41:39 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
Package: FlowSorted.DLPFC.450k
Commit: 3d2f4748f5601fee18ec5648cb3bea738763af20
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:41:39 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
Package: FlowSorted.DLPFC.450k
Commit: bbb9c584eaed6a0a80a1e5c0e340bb78df01bbc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:08:00 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
Package: FlowSorted.DLPFC.450k
Commit: e232946696892dd250e0767ed98fbd0c4dba3431
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:08:00 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
Package: FlowSorted.DLPFC.450k
Commit: a7338c3480ec1e2845bda6056a70389d2b8ffdd2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:35:41 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
Package: FlowSorted.DLPFC.450k
Commit: 819f6baee3293feb6d26f05c47f4891d440d2fef
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:35:41 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
Package: FlowSorted.DLPFC.450k
Commit: f5da622b24a83b927277b660426e3069aae956be
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 11:01:01 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
Package: FlowSorted.DLPFC.450k
Commit: fce417de061b6985f751d00064e58b5c23529d3a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 11:01:01 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
Package: FlowSorted.DLPFC.450k
Commit: ced8387cb470d2d816a969fc758e552560afd474
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:14:09 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
Package: FlowSorted.DLPFC.450k
Commit: 587379588d03178cc0a68db27ce15db5151144e4
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:14:09 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
Package: FlowSorted.DLPFC.450k
Commit: fd9fa33cdfccf5cd968e17d74fcddc308adb8cc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-11-21 21:39:37 -0500
Commit message:

 Pass serialized S4 instances thru updateObject()
Package: FlowSorted.DLPFC.450k
Commit: 781b9c024c05e14f907af1a6409541b6c5a422e9
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 12:09:04 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
Package: FlowSorted.DLPFC.450k
Commit: 289925a5485a096d29961f972577e58a85fdaad0
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 12:09:04 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
Package: FlowSorted.DLPFC.450k
Commit: b2b6ec5f5297e14d7a379fddee6909dce9def734
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:47:06 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
Package: FlowSorted.DLPFC.450k
Commit: 69c5d4d5663d875e0941039ff4cce43dcf39cc02
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:47:05 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
Package: FlowSorted.DLPFC.450k
Commit: 22af035a567acd8feb52992ba97385f652d0189c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:08:55 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_12 branch
Package: FlowSorted.DLPFC.450k
Commit: df7716bc207b7474b7904541e1ebeac332bef6ac
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:08:55 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
Package: FlowSorted.DLPFC.450k
Commit: ceecd951e0e3a49ee53128f4c70f8c5f8e2dc242
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:28:21 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
Package: FlowSorted.DLPFC.450k
Commit: 42e7ccf42e20af52e034107c4ed91f35e77f98c5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:28:21 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
Package: FlowSorted.DLPFC.450k
Commit: 623273a5a370199df1e4e36169ec688210f0fa5e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:37:02 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
Package: FlowSorted.DLPFC.450k
Commit: 8374a96ecf60eb64840ffc34b4425076fa86aaf8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:29:42 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
Package: FlowSorted.DLPFC.450k
Commit: 4e6268ed2f6003db06f0db22e73791c1b41a43b1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 12:06:23 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
Package: FlowSorted.DLPFC.450k
Commit: 9bb94f1ed12bbb3608eb871fea59b721a1808ee9
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 11:56:37 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
Package: FlowSorted.DLPFC.450k
Commit: ecfcd626e421432cb94713156331fcbe46320771
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:38:33 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
Package: FlowSorted.DLPFC.450k
Commit: 976258ba66d9bf66925298f29d1d6def8752aa11
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:36:23 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
Package: FlowSorted.DLPFC.450k
Commit: b7a35cc4dfc298545bd2342797d14d88e18def33
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:34:48 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
Package: FlowSorted.DLPFC.450k
Commit: 009f2d4246c8eca7832f6d13fbdb8fa8efa47b87
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:31:28 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
Package: FlowSorted.DLPFC.450k
Commit: 5fd33c7fd6036947b8c00055dd648ae896b4eeef
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 12:09:07 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
Package: FlowSorted.DLPFC.450k
Commit: 9dbccc78696152d1fff83dc048eaf653799db289
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 11:58:27 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
Package: FlowSorted.DLPFC.450k
Commit: 876cb57c1d465ba5ae79ba0391e5f9dccbae0543
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2017-08-16 19:11:10 +0000
Commit message:

 Committing experiment data for FlowSorted.DLPFC.450k
Package: FlowSorted.Blood.450k
Commit: 639d21cd37efc6cb6dd1a9564b819c0f3900e449
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 14:17:32 -0400
Commit message:

 Fix reference-data access to preserve minfi::estimateCellCounts compatibility

The initial migration exposed FlowSorted.Blood.450k as a plain callable
function. minfi::estimateCellCounts() (and likely other downstream
consumers) accesses reference packages via the historical lazy-data
pattern: data(list = pkg); get(pkg). With a plain function, get(pkg)
returned the function object itself rather than the RGChannelSet,
silently breaking estimateCellCounts.

FlowSorted.Blood.450k and FlowSorted.Blood.450k.compTable are now
active bindings installed in .onLoad, so referencing the bare name
(matching the old data() usage) downloads and returns the actual
object, caching it for the session. Verified against a live
estimateCellCounts(..., compositeCellType = "Blood") run.
Package: FlowSorted.Blood.450k
Commit: 020eb69a71b166c02f2e90897769fe884a8a10df
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 13:55:38 -0400
Commit message:

 Move large data objects to Zenodo, download via BiocFileCache

The bundled FlowSorted.Blood.450k.rda (136MB) and
FlowSorted.Blood.450k.compTable.rda (40MB) exceeded GitHub's file
size limit ahead of Bioconductor's migration off its own git server.
Both are now hosted on Zenodo (doi:10.5281/zenodo.21996983) and
downloaded on first use via BiocFileCache, which caches them locally
afterwards. FlowSorted.Blood.450k() and FlowSorted.Blood.450k.compTable()
replace the former data(...) calls.

Also removes the stray external_data_store.txt, adds Authors@R, and
title-cases the Title field to clear R CMD check NOTEs.
Package: FlowSorted.Blood.450k
Commit: dd9843778fb8698df5e4a9e135a54d31b151ff21
Author: Andrew Jaffe <andrewejaffe@gmail.com>
Date: 2026-08-18 10:52:06 -0400
Commit message:

 Update maintainer email

andrew.jaffe@libd.org is no longer reachable.
Package: FlowSorted.Blood.450k
Commit: 2be74d4e3b1d815c0e9812ca9964e196a5e231ff
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:26:12 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
Package: FlowSorted.Blood.450k
Commit: 3d4fd9cb5b7b5c7510adfcc8d34de84f7bd3ebbd
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-28 08:26:12 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
Package: FlowSorted.Blood.450k
Commit: c5501a9c037e6edcdd9be03494099bddb0720bbf
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:54:03 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: FlowSorted.Blood.450k
Commit: 5bfe7636bd3970b4c7039a93827a834323fcf5c0
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-29 09:54:03 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: FlowSorted.Blood.450k
Commit: 0f9774229b88d32347e435a39e8008fb0d5d7abe
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:24:07 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
Package: FlowSorted.Blood.450k
Commit: 49dc5596a0cd113750408eb8fb1c66c7d65d9fe3
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-15 09:24:07 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
Package: FlowSorted.Blood.450k
Commit: 87f90d6c89c87fcbf7c53d3fc25d5aee9c23fc54
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:37:31 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
Package: FlowSorted.Blood.450k
Commit: 7e1222c2b1710704c745204a0e2bd5a47c1076c4
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-10-29 09:37:31 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
Package: FlowSorted.Blood.450k
Commit: e55962233dcc5ffc3d76c15417cf2152c7f5b9c7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:40:13 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
Package: FlowSorted.Blood.450k
Commit: 080e7b03a9d7bf6ebe976c1ba12a27f81b278dd0
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-04-30 10:40:13 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
Package: FlowSorted.Blood.450k
Commit: b3269b4e5e0c3f07235bfc5a88b802ac56feae6e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:06:33 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_18 branch
Package: FlowSorted.Blood.450k
Commit: d78abba2a8b2181cf000be5be26021ff77640242
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-10-24 09:06:33 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_18 branch
Package: FlowSorted.Blood.450k
Commit: b6a8bef792ca4b374b8c15aed81ae0d316f76810
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:34:08 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_17 branch
Package: FlowSorted.Blood.450k
Commit: 4c41c843bb47753d4148a226c95ce1de28e4e927
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-04-25 10:34:08 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_17 branch
Package: FlowSorted.Blood.450k
Commit: f2eacbfe44e7fe7fcaf490de3bfc59959729a841
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:57:59 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
Package: FlowSorted.Blood.450k
Commit: 01e99c4a845527f4ed73ea8d6f228b12db624f88
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-01 10:57:59 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
Package: FlowSorted.Blood.450k
Commit: b0238875283f64bdc080f3a4fd560d749bc0b761
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:11:40 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_15 branch
Package: FlowSorted.Blood.450k
Commit: 35441914d49cbad5f33dbbb2eb4f16ff7417ba30
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2022-04-26 17:11:40 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
Package: FlowSorted.Blood.450k
Commit: a7f7eda5303682791477d6a7e6018c51205cf1e8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-11-21 21:06:10 -0500
Commit message:

 Pass serialized S4 instances thru updateObject()
Package: FlowSorted.Blood.450k
Commit: 9581ddaba86eefc94a83aba50892272918e06739
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 12:04:57 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
Package: FlowSorted.Blood.450k
Commit: 04de9e50bbacc85a679383e021e4b10352eebafe
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2021-10-26 12:04:57 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
Package: FlowSorted.Blood.450k
Commit: 3c85392dd7bb1b5d27832ea4525dbbeae15d9c83
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:43:51 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
Package: FlowSorted.Blood.450k
Commit: 33947d8350baaa3cfac6bf04972bf1f66e870fe7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-19 11:43:51 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
Package: FlowSorted.Blood.450k
Commit: 509ba5366b3c902f54d77374b4ddd7d9effb329c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:05:36 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_12 branch
Package: FlowSorted.Blood.450k
Commit: 9e8c9856e75e38c87e778544603cda4c7a7422de
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-10-27 10:05:36 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch
Package: FlowSorted.Blood.450k
Commit: b0d0265190133893c5fdfd170f2f3706168bad62
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:22:59 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_11 branch
Package: FlowSorted.Blood.450k
Commit: 6843e3c78d84c76b9f41cc86048b2d0c73bf939a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2020-04-27 15:22:59 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
Package: FlowSorted.Blood.450k
Commit: 8dadd6933ab73c8c04971afacfa6a27b981b5648
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:37:02 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
Package: FlowSorted.Blood.450k
Commit: cf0557679af58a1eb898aaa0867de597f248e1a1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-10-29 13:29:41 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
Package: FlowSorted.Blood.450k
Commit: ac63378a43959c210ee8274fec8a27b60a28006d
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 12:06:19 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_9 branch
Package: FlowSorted.Blood.450k
Commit: a54dd5c0bb64bc6392ac9bae95e95b3eec6eba90
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-05-02 11:56:36 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch
Package: FlowSorted.Blood.450k
Commit: 0bec9d4391a9cb1c45da5f28b10214c27eb89d0e
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:38:33 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
Package: FlowSorted.Blood.450k
Commit: 5f7654ec10567cb684bcbb4fe5e3ac2c84dfe099
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:36:23 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
Package: FlowSorted.Blood.450k
Commit: ee0d81bd8a181f5e4b4c5355e7f12746e14d722d
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:34:47 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
Package: FlowSorted.Blood.450k
Commit: 51d59d2a2c0cd390328dd81f2bf2ab7cc3f0ad72
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-04-30 10:31:28 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
Package: FlowSorted.Blood.450k
Commit: eea5ea2f86a449cd6e99335a88e0f4ec4f20414e
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 12:09:07 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
Package: FlowSorted.Blood.450k
Commit: 71cc98469bb98f3b6573a90a74de2fcc676f1400
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2017-10-30 11:58:26 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
Package: FlowSorted.Blood.450k
Commit: ca630b6f12f8cde6656957a2d6612e81800c4941
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2017-08-16 18:52:51 +0000
Commit message:

 Committing experiment data for FlowSorted.Blood.450k
Package: igvShiny
Commit: e997145d1e9f9df292181de99599a9f76375f71a
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2026-09-10 17:26:38 +0200
Commit message:

 Pre-flight reference genome compatibility checking (#180)

Related: #179\n\nAdds offline reference compatibility checks for local BED, bedGraph, VCF, BAM, CRAM, and Bioconductor tracks, including canonical and custom genomes.
Package: scrapbook
Commit: 819482c4f77cd5867ade55ee29f5a9a61b1f83dd
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-11 01:23:18 +1000
Commit message:

 Switched to 10X PBMCs to demonstrate the PCA blocking.

Apparently the concept of heterogeneity within cell lines is too confusing for
certain people, so perhaps some diverse cell types are more palatable.
Package: scrapbook
Commit: 5347d51aca0651cb36405eb53604d5aa44336882
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-11 00:28:27 +1000
Commit message:

 Assorted clean-ups.

- Use consistent naming for the motivation section.
- More compact data inspection for the 10X QC section.
- Visualize the pancreas data prior to batch-correction.
Package: CLAMP
Commit: 59e236cba548e0c28580d09382ce6a3e4d5cccbc
Author: msubirana <mb2subi@gmail.com>
Date: 2026-09-10 09:22:39 -0600
Commit message:

 Bump to 0.99.7: add log2 control and align population variance
Package: topdownr
Commit: 34ae55e2b85e21bb4ff1d016b2066f7684833e92
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2026-09-10 13:32:06 +0200
Commit message:

 docs: re-roxygenize with roxygen2 8.1.0
Package: topdownr
Commit: 60594fe9144a0b9f652774c59ce9f19d7634c637
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2026-09-10 13:31:38 +0200
Commit message:

 fix: import subject from IRanges
Package: topdownr
Commit: 477056bd59e1c7a0eb6f52f118838a8bf509346b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2026-09-10 13:30:28 +0200
Commit message:

 refactor: use .data in ggplot to avoid NSE NOTE
Package: topdownr
Commit: c3dbd4e9b808d55ab20cd7edb154b9432380d3d0
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2026-09-10 11:10:02 +0200
Commit message:

 fix: handle column-less/name-less input for .groupByLabels
Package: topdownr
Commit: 6ef8072a648d0db0ead9d5aa75b17e5c559c41ae
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2026-09-09 11:52:40 +0200
Commit message:

 chore: add newline at eof
Package: methylclock
Commit: cb06285e79b2f88aac92d7ddb3aabeb5c2fca8d9
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-09-10 13:16:10 +0200
Commit message:

 Resolve data resources without the local mirror, version 1.99.1

R CMD build failed on any machine without the development data mirror (r-universe, the Bioconductor builders): the resource resolver stopped
at the first coefficient load because the manifest only existed in the mirror and the local backend aborted instead of falling through.

The manifest now ships with the package in inst/extdata (a configured mirror still takes precedence), the local backend declines instead of
stopping so the chain reaches ExperimentHub, cell-type reference panels fall back to their ExperimentHub copy (EH6083), and file resources such as the AltumAge HDF5 bundle gain an ExperimentHub backend (EH10476).
ExperimentHub moves from Suggests to Imports accordingly.
Package: epimutacions
Commit: c1ba7966ba2083e55eb3bdbcd3b98b0735115053
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-09-10 11:28:38 +0200
Commit message:

 Fix CITATION encoding and minor BiocCheck notes

- inst/CITATION: use bibentry() with ASCII-escaped (\uXXXX) author names so
  utils::readCitationFile() no longer warns about non-ASCII input without a
  declared encoding.
- vignette: give every code chunk a label.
- plot_epimutations(): use vapply()/seq_len() instead of sapply()/1:n.
Package: epimutacions
Commit: c8e3f4a434edca8347a3d16400677d544005c749
Author: dpelegri <43083225+dpelegri@users.noreply.github.com>
Date: 2026-09-09 12:55:34 +0200
Commit message:

 Reduce dependency footprint

Remove the unused 'ensembldb' dependency and move optional
annotation/visualization packages that are already used conditionally via
requireNamespace() from Imports to Suggests (Homo.sapiens, Gviz, rtracklayer,
AnnotationHub, ExperimentHub, the UCSC TxDb packages, the Illumina
manifest/annotation packages, reshape2, purrr, ggrepel, gridExtra).

Qualify ExperimentHub::ExperimentHub() and AnnotationHub::query() and drop the
corresponding NAMESPACE imports. Imports go from 39 to 20 packages.
Package: MetaboDynamics
Commit: afc8c73dfc286d24980860efececa7ec09b4a495
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-09-10 11:38:09 +0200
Commit message:

 version bump
Package: MetaboDynamics
Commit: fb56d53648dbd89fc3403a082745cabfebbe12e2
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-09-10 11:36:56 +0200
Commit message:

 edits vignette guide to prior setting
Package: MetaboDynamics
Commit: 091a8beebc29120fcd5673588e6a5376eff80aa4
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-09-10 10:43:10 +0200
Commit message:

 revision of guide to prior setting
Package: MetaboDynamics
Commit: 6ac85d38a023e0fa930fd9098feea1b1d9cca595
Author: Katja Danielzik <katja.danielzik@stud.uni-due.de>
Date: 2026-09-08 13:49:35 +0200
Commit message:

 revised Guide to prior setting
Package: exploreSE
Commit: 350a67d128ba6f0e6fe1af6a0a55253790c66be6
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-09-10 11:08:47 +0200
Commit message:

 visual adjustments on readme
Package: exploreSE
Commit: 1fc68a5d07f155db3bcc3b8dc6a38a55d9f5c4a6
Author: jaspitzer <jasspitzer135@gmail.com>
Date: 2026-09-10 11:01:05 +0200
Commit message:

 visual fixed to the vignette
Package: exploreSE
Commit: 94c17c377de2d3fc2ce3330a88b16a06ce26cc9c
Author: Jasper Spitzer <97746217+jaspitzer@users.noreply.github.com>
Date: 2026-09-04 11:41:42 +0200
Commit message:

 readme adjustments
Package: SingleR
Commit: 36f72d9d0bdc27b95ed553d907edc39e1b069cc1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-10 18:03:20 +1000
Commit message:

 Updated GHA versions in the check workflow.
Package: SingleR
Commit: 8712212530a86c7069d911f5c2c85be435126342
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-09-10 18:01:56 +1000
Commit message:

 Vignette now automatically redirects to the book.

This reduces duplication of documentation; just read the book.
Package: compcodeR
Commit: 61dcdc49d2a309c5c72fbd6e175aada1a8cd0e5b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-09-10 10:12:44 +0200
Commit message:

 Update Roxygen
Package: compcodeR
Commit: ea091d5c6b15dd4313c0d4f4dd6ccdd553ca6201
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-09-10 10:12:10 +0200
Commit message:

 Add missing documentation for codefile argument
Package: compcodeR
Commit: 4f518388da40dc5fe11baf5536c02d79d6e5232c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-09-10 10:10:58 +0200
Commit message:

 Bump version
Package: compcodeR
Commit: ae3d4949078f9bf85e85e4c05d2a4d4dc11712d9
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-09-10 10:10:32 +0200
Commit message:

 Switch modeest dependency to statip
Package: compcodeR
Commit: 929687236ee37ca12903799c8911fdebef967022
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-28 19:34:59 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: compcodeR
Commit: 1701eb354cbe8997f4a4bedf7d45f8436a1412f7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-04 21:04:58 +0200
Commit message:

 Try to set version constraints for pak
Package: compcodeR
Commit: 8c9152e338cef203ccf6ed01514e163b75d6928f
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-04 20:53:52 +0200
Commit message:

 Try to specify BH version explicitly
Package: compcodeR
Commit: 35a25ad139be11047b9577d55e2dd446fa74a7c9
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-04 20:44:50 +0200
Commit message:

 Install EBSeq manually on Linux GHA runners
Package: seqCAT
Commit: d548fc63b92165954cb82f56a30900cd001a7f00
Author: Erik Fasterius <erik.fasterius@outlook.com>
Date: 2026-09-10 08:58:10 +0200
Commit message:

 Increment version to `1.35.1`
Package: seqCAT
Commit: 961811d83fefec1e12238742d57549433fdd0b1f
Author: Erik Fasterius <erik.fasterius@outlook.com>
Date: 2026-09-10 08:56:30 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: seqCAT
Commit: 92922196c902cf2630439f205d0663b3ad85c5c6
Author: Erik Fasterius <erik.fasterius@outlook.com>
Date: 2026-09-10 08:48:51 +0200
Commit message:

 Fix issue with new `GenomicRanges::as.data.frame`

Fix an issue introduced in version `1.64.4` of `GenomcRanges` and its
`as.data.frame` function, used in `R/filter_variants.R`. Previous
behaviour was to use the input's names be default, while the new does
not, and requires explicitly adding `row.names = names(gr)` to achieve
the same behaviour
Package: polyICSFlow
Commit: a6b6e7e13e82ce64452478f2dd4d9df0a1d52caf
Author: Lisa Loksø Dietz <lisa.dietz@live.dk>
Date: 2026-09-10 09:01:24 +0200
Commit message:

 fixed LaTeX Error: Unicode character error
Package: SpectraStash
Commit: a31acfc39ad0ec5a107d709b17445751dbfed6d2
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-09-10 07:37:07 +0200
Commit message:

 Merge pull request #13 from rformassspectrometry/jomain

tests: complete unit test coverage
Package: SpectraStash
Commit: 4e53ca212712e41f6a64ec784da4c99c66d849a7
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-09-09 16:49:25 +0200
Commit message:

 tests: complete unit test coverage
Package: SpectraStash
Commit: 5567a5bfd31ba8e5eeb4044b473aee1333a60ce1
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-09-07 10:22:41 +0200
Commit message:

 Merge pull request #12 from rformassspectrometry/jomain

README: add Bioc badge
Package: SpectraStash
Commit: 66eabaccbec41244f73aaa9fbf8eeb3a3d6a1c87
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-09-07 08:12:07 +0200
Commit message:

 README: add Bioc badge
Package: MAGAR
Commit: 84edbb2d6f52af186ea167bed388f8cd2bf64c9c
Author: Michael Scherer <michael.scherer@dkfz.de>
Date: 2026-09-10 10:11:48 +0200
Commit message:

 Added UpSetR
Package: igblastr
Commit: 641437e4f3301af477699c7d83ce308bc87f5554
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-09-09 22:24:08 -0700
Commit message:

 igblastr 1.3.21

o Enable automatic intdata generation in:

    install_IMGT_germline_db("", "Macaca_mulatta")

  and in:

    install_IMGT_germline_db("", "Mus_musculus", tcr.db=TRUE)

o compute_V_gene_delineations() argument 'fwrcdr_widths' now can be an
  integer matrix with dimnames in addition to a named integer vector.
  See '?compute_V_gene_delineations' for the details.

o Rename predefined vector 'IMGT_FWRCDR_WIDTHS' to
  'IMGT_DEFAULT_FWRCDR_WIDTHS'.

o Export predefined matrix 'IMGT_MOUSE_FWRCDR_WIDTHS'.
 </pre>
    </div>
  
    

      Package: HiCaptuRe

      Commit: aff341ff0b0e21b97e7e9d635dea339321b30824

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-09 18:07:28 +0200

      Commit message:


	  
		
 typo and version bump
 

    

  
    

      Package: SingleR

      Commit: 53edadf2ffdc7e9daea07d4103f9fd1517591982

      Author:  Julien Roux <julien.roux@unibas.ch> 

      Date: 2026-09-10 06:26:32 +0200

      Commit message:


	  
		
 Bugfix to pass along assay.type.ref to trainSingleR  (#306) 

    

  
    

      Package: ggsc

      Commit: 62fcd982ede45f5afac30702974d454dbd2f65bf

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-10 10:31:17 +0800

      Commit message:


	  
		
 biocinit
 

    

  
    

      Package: ggsc

      Commit: b3ef19c029be85bbd27b98d74d3c7f70a0de118f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-10 10:29:53 +0800

      Commit message:


	  
		
 compatible with new S4Vectors
 

    

  
    

      Package: ggsc

      Commit: 20db3b5d13621652a76e29324578bdcd1f6b96b8

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-05-17 17:03:29 +0800

      Commit message:


	  
		
 compatible with Seurat V5
 

    

  
    

      Package: ggsc

      Commit: dce838ec0114c0eefc98dd7ef078505ca4588258

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-29 12:18:51 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: ggsc

      Commit: 5d0b8f1833a3196a68dc4c80a307971f31201c6d

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-29 12:18:44 +0800

      Commit message:


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

    

  
    

      Package: ggsc

      Commit: 804ef229305a2133f78f01de23e14eead563b0c3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 17:16:44 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: DuckDBArray

      Commit: f138676f1bf0dfa5f6a02cefa4b4b96794dbd726

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-09-09 15:19:15 -0700

      Commit message:


	  
		
 fix: prevent %*%/crossprod temp-table name collisions under a seeded RNG (0.99.9)

For the body, if you want one:

%*%/crossprod's vector-multiply helpers named their left_join(..., copy =
TRUE) temp table via dbplyr::unique_table_name(), which draws its "random"
suffix from R's global RNG rather than an independent source. Under a
caller-seeded RNG (needed for reproducible iterative-solver results, since
irlba also draws its starting vector from the global RNG), repeated calls
could regenerate the same name and collide with a still-live temp table,
since none of these helpers ever drop theirs.
 

    

  
    

      Package: rBLAST

      Commit: f46522f38a27b91e58569189c27d046315e64dee

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-09 15:40:12 -0500

      Commit message:


	  
		
 cleanup for BioC.
 

    

  
    

      Package: TPP

      Commit: 93369bedffd208919b62215f0ebf4ccdfe2754c6

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 20:06:58 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: TPP

      Commit: 78834be1630170d238828efdf684e7f85d83fabb

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 20:03:47 +0200

      Commit message:


	  
		
 Remove obsolete inline comments from NAMESPACE
 

    

  
    

      Package: TPP

      Commit: 100fdf22abaf18aecce0fd2a6a3864dfe92f47fd

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 20:01:31 +0200

      Commit message:


	  
		
 Resolve R CMD check code-analysis NOTES

- Move startup message from .onLoad to .onAttach and qualify capture.output with utils.
- Declare tidyverse and ggplot2
non-standard evaluation variables in their owning scopes to eliminate
undefined global variable and function NOTES.
 

    

  
    

      Package: TPP

      Commit: dbc7f87f5e2ddcb49c028363d0a4de6bfee07fe7

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 19:51:39 +0200

      Commit message:


	  
		
 Fix missing Rd cross-reference anchors

Qualify external links to brewer.pal and squeezeVar with their
owning packages, and render the internal AICc helper as code to
prevent missing cross-reference NOTE messages.
 

    

  
    

      Package: TPP

      Commit: 980be216645af8bd97fb615768bf369908c36155

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 19:46:29 +0200

      Commit message:


	  
		
 Fix invalid package documentation alias

Remove the legacy package docType annotation and suppress roxygen's invalid default `-package` alias while retaining the valid
`TPP-package` alias. This prevents the Bioconductor Rd metadata NOTE.
 

    

  
    

      Package: TPP

      Commit: 06d5ae122d08c91d96414f93466f4524b8ff25af

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 19:38:05 +0200

      Commit message:


	  
		
 Fix roxygen markup

Use valid \describe blocks and double-quoted code literals so devtools::document() parses the @details sections correctly.
 

    

  
    

      Package: TPP

      Commit: 2e9c30b77093f709038f58c4187bc98160495dd0

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 19:19:06 +0200

      Commit message:


	  
		
 Fix NEWS version headers for R CMD check parsing
 

    

  
    

      Package: DegCre

      Commit: cac427e13deef557c594076629ff7ab55a587ddb

      Author:  brianSroberts <146755772+brianSroberts@users.noreply.github.com> 

      Date: 2026-09-09 18:05:25 +0000

      Commit message:


	  
		
 Fix S4 coercion error in plotPairsArches
 

    

  
    

      Package: TPP

      Commit: fc0d2544f5595ace3981c12b1202201a7374846a

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 18:53:12 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: TPP

      Commit: 62743b7b7538e86cbee67c111f6c0af2cc41e6f8

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-09 18:48:04 +0200

      Commit message:


	  
		
 Replace methods::is() with inherits() and remove the unused mefa dependency
 

    

  
    

      Package: igblastr

      Commit: c47354f8fa8ed964ad9905f84c74a0d0f40bba64

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-09-09 09:42:15 -0700

      Commit message:


	  
		
 Add print_gapped_V_alleles() to display a set of gapped V allele sequences
where the sequences are colored and split by FWR/CDR regions.

Also rename:
- IMGT_FWRCDR_ENDS to IMGT_FWRCDR_WIDTHS;
- Argument 'fwrcdr_ends' of functions compute_V_gene_delineations() and
  install_custom_germline_db() to 'fwrcdr_widths'.
 

    

  
    

      Package: MSstatsShiny

      Commit: 7ab020bd6d09e650906154a3b5f3314d1f6a0236

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-09-09 12:30:29 -0400

      Commit message:


	  
		
 Update package version to 1.15.8

Bump version number from 1.15.7 to 1.15.8. 

    

  
    

      Package: MSstatsShiny

      Commit: 4e98438d627a58835b6c49c00b10ce91cbb9c563

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2026-09-08 17:45:52 -0400

      Commit message:


	  
		
 chore(tmt): Adjust TMT documentation (#230) 

    

  
    

      Package: cellmig

      Commit: 0a47e6f63a987892777a250f1dac4ee4c341c6a0

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-09 18:07:07 +0200

      Commit message:


	  
		
 offset -> offset_group
 

    

  
    

      Package: cellmig

      Commit: 30fbd4f3b500ea2a4d14ad205c1cf61128136d52

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-09 18:06:45 +0200

      Commit message:


	  
		
 bump
 

    

  
    

      Package: polyICSFlow

      Commit: db827a0d363663bf2152fd59a6d29d89bccf51e8

      Author:  Lisa Loksø Dietz <lisa.dietz@live.dk> 

      Date: 2026-09-09 15:59:29 +0200

      Commit message:


	  
		
 Remove CytoExploreR dependency
 

    

  
    

      Package: epimutacions

      Commit: 3ef7edc5ed74496b3aad0060eb1face646d1b092

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-09-09 12:21:13 +0200

      Commit message:


	  
		
 Fix plot_epimutations numeric coercion and make vignette annotation resilient

- epi_plot.R: coerce melted 'value' back to numeric so plot_epimutations()
  no longer fails with 'non-numeric argument to binary operator'.
- vignette: wrap annotate_epimutations() in tryCatch and gate the annotation
  tables with eval=ann_ok so a transient Ensembl/biomaRt outage does not
  break the vignette build.
- LICENSE: use valid DCF stub (full text kept in LICENSE.md).
- add_ensemble_regulatory: use \describe instead of \itemize (lost braces).
 

    

  
    

      Package: CSOA

      Commit: b2b8792e8d81a456b87dd2ba7cfba8786af57946

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-09-09 17:39:09 +0800

      Commit message:


	  
		
 Bumped version
 

    

  
    

      Package: CSOA

      Commit: d572356f14efdf92b4a7d6ded9da46568b54991d

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-09-09 17:38:35 +0800

      Commit message:


	  
		
 Added adjustRanks parameter
 

    

  
    

      Package: BiocBookDemo

      Commit: 48c333add63a333481095dcbc3fc7d6475539b45

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-08 13:33:32 +0200

      Commit message:


	  
		
 bump to 1.11.2
 

    

  
    

      Package: BiocBookDemo

      Commit: 0881c2454e06a82ca2bb9e39bda6f57f49779547

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-09-08 13:33:18 +0200

      Commit message:


	  
		
 fix: disable pdf
 

    

  
    

      Package: igvShiny

      Commit: 1dae97626c1a2a686e0a5516ca29d28d2d4d6292

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-09 09:55:19 +0200

      Commit message:


	  
		
 ci: add User-Agent to check-asset-urls.sh to avoid 403 on bot-blocking servers
 

    

  
    

      Package: methylclock

      Commit: 788b0a9804d05a7b731e97081ab574a24a507526

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-09-09 09:52:19 +0200

      Commit message:


	  
		
 Expand the README: overview, quick start, and the clock catalogue
 

    

  
    

      Package: igvShiny

      Commit: 187c7bf5fcf4750b5fb5a7fef37c77b48e917f3f

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-09 09:45:49 +0200

      Commit message:


	  
		
 chore(demo): pin Connect Cloud manifest to 34e2413
 

    

  
    

      Package: igvShiny

      Commit: 34e2413d63ac7d442e80cbaa250da0b44bb5baac

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-09 09:45:25 +0200

      Commit message:


	  
		
 fix: align demo tumor.bam to GRCh38 for clean local stream rendering
 

    

  
    

      Package: edgeR

      Commit: 91462a8839312470fc9f24e52d30a9f5a27ce0d7

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-09 17:39:49 +1000

      Commit message:


	  
		
 edgeR 4.99.5
- catchSalmonWithGencode() removed in favor of catchSalmonGene().
- catchKallisto() now imputes missing effective lengths.
- catchSalmonGene() now returns max tx length for each gene.
 

    

  
    

      Package: methylclockData

      Commit: 4787fc57de0ccf74b9e21bdb89c8d1e0eaba16df

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-09-09 08:12:52 +0200

      Commit message:


	  
		
  in the coefGarma ExperimentHub id EH10518 and bump to 1.21.4

The hubs team added the coefGarma resource to ExperimentHub devel on 2026-09-04 as EH10518 (49 methylclockData records in total). The get_coefGarma() accessor now retrieves that id and its example is runnable.
 

    

  
    

      Package: methylclock

      Commit: 091d97f1969930f913a05a7b7701fd58756d089f

      Author:  dpelegri <43083225+dpelegri@users.noreply.github.com> 

      Date: 2026-09-09 09:25:15 +0200

      Commit message:


	  
		
 methylclock 2.0: rewrite on BigDataStatMeth, version 1.99.0 for devel

Complete rewrite of the package. Each clock is now a declarative entry in a registry, so adding one is a single registration rather than edits
across the code base. 44 clocks (age, gestational, mitotic, causal and trait scores; EPICv2-native Garma included), computed by engines that
share one pipeline.

Computation and storage go through BigDataStatMeth: results live in HDF5, beta matrices larger than memory are read out-of-core in C++, and
the linear algebra runs batched on the HDF5 backend. Configurable imputation (mean, reference, none, KNN in C++), cell-type deconvolution,
canonical IEAA/EEAA (parameters from patent EP 3 494 210 B1, verified against Horvath's online calculator), QC reports, a plotting suite and
a rewritten vignette with per-clock references. The public API is methylclock(), with DNAmAge() and DNAmGA() kept as wrappers.

Coefficient data come from methylclockData >= 1.21.4 via ExperimentHub, with a Zenodo fallback (10.5281/zenodo.21840402 and .22069904).
 

    

  
    

      Package: edgeR

      Commit: 9f20334c5feb45e6d3bdd14517f7e3471d0bb4e3

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-09 17:24:30 +1000

      Commit message:


	  
		
 edgeR 4.99.5 (step one)
- Delete catchSalmonWithGencode.R
- Rename catchSalmonWithGencode.Rd to catchSalmonGene.Rd
 

    

  
    

      Package: igvShiny

      Commit: 235b419dfbf9229e1e41232a1425eb6c57d30936

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-09 08:52:56 +0200

      Commit message:


	  
		
 docs: update sample BAM URL in track-options vignette

Closes #116
Closes #126
Closes #112
Closes #143
Closes #174
 

    

  
    

      Package: clustSIGNAL

      Commit: a1fa57cfdc01f9b63f19f131489ba3e8578e112a

      Author:  ppan0697 <pratibha.panwar@sydney.edu.au> 

      Date: 2026-09-09 13:28:01 +1000

      Commit message:


	  
		
 Updated ReadME and made minor changes to the package.

Merge branch 'main' into devel
 

    

  
    

      Package: clustSIGNAL

      Commit: 17c2e5e3b3f7bd7ea2a7375ef666fe80e6131aee

      Author:  ppan0697 <pratibha.panwar@sydney.edu.au> 

      Date: 2026-09-09 13:11:51 +1000

      Commit message:


	  
		
 ReadMe description edited and minor edits to the package.
 

    

  
    

      Package: SpotSweeper

      Commit: 7717432f8ad9ed0bdec51b0f637917e6ac6887a3

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2026-09-08 18:19:06 -0400

      Commit message:


	  
		
 Fix CI: resilient BiocCheck install, fresh cache, single pkgdown deploy

- Install BiocCheck in the Run BiocCheck step if the continue-on-error
  dependency pass failed to install it (Windows failure mode).
- Bump cache-version to cache-v2 to discard a Windows library cache
  holding a broken AnnotationHub install.
- Disable the pkgdown build/deploy in the check workflow; the dedicated
  pkgdown workflow owns the gh-pages deployment, and deploying from both
  raced and failed with git exit 128.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 

    

  
    

      Package: CNVRanger

      Commit: a159c05ac20157f3de30c7b80e9aea6415d7ccd1

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2026-09-08 18:10:39 -0400

      Commit message:


	  
		
 populationRanges: update man page for RO mode
 

    

  
    

      Package: MotifPeeker

      Commit: 50b0c74ba6e179c6a288a6d447fdc402733298f4

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2026-09-08 22:18:33 +0100

      Commit message:


	  
		
 Use ghcr.io bioc-meme container for Ubuntu CI
 

    

  
    

      Package: SpotSweeper

      Commit: 839c204d08990f1460c05e1fa2322b660bcc5e85

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2026-09-08 17:52:55 -0400

      Commit message:


	  
		
 Fix Bioconductor 3.24 Linux CI environment
 

    

  
    

      Package: SpotSweeper

      Commit: 7e70d421a7dc0b9c8e1b2d9fa96a54ca85e59f69

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2026-09-08 17:47:23 -0400

      Commit message:


	  
		
 Merge Bioconductor devel and fix local outlier scoring
 

    

  
    

      Package: SpotSweeper

      Commit: 17d64d66899c79beb7281fb7207c75f50d391f8f

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-10-22 10:02:14 -0400

      Commit message:


	  
		
 Add Seurat compatibility to flagVisiumOutliers function
 

    

  
    

      Package: SpotSweeper

      Commit: d62d27d370a66ed27b5efd08565bf9c931e9efd7

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-10-22 09:20:08 -0400

      Commit message:


	  
		
 Fix coordinate column detection for non-Visium Seurat spatial data
 

    

  
    

      Package: SpotSweeper

      Commit: d07a2b2aee5e01e2b3b3c74861f774da29576fe6

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 12:06:12 -0400

      Commit message:


	  
		
 Remove BiocCheck output folder
 

    

  
    

      Package: SpotSweeper

      Commit: 8cdfcb1faf9415878f84d35979aa378fdde1cbe3

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 10:28:24 -0400

      Commit message:


	  
		
 Fix BiocCheck errors: reduce package size and add runnable examples
 

    

  
    

      Package: SpotSweeper

      Commit: ac761b8b35bfd50412447357484fdfb1454be7e7

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 00:32:31 -0400

      Commit message:


	  
		
 Update localOutliers test to remove hard-coded outlier counts
 

    

  
    

      Package: SpotSweeper

      Commit: 8e5827af4323d98a64f2aee1b6d8f0d7a1c3c38d

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 00:29:05 -0400

      Commit message:


	  
		
 Fix localOutliers to preserve log-transformed columns in output
 

    

  
    

      Package: SpotSweeper

      Commit: 15f493bc24398667e0fbd77b66356b6f22f7e419

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 00:11:16 -0400

      Commit message:


	  
		
 Add S4Vectors dependency and fix DataFrame compatibility
 

    

  
    

      Package: SpotSweeper

      Commit: 447ffd46f3d0aebe56e53a61f29a41037e5fcb86

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-12 00:06:09 -0400

      Commit message:


	  
		
 Fix DataFrame compatibility in setMetadata function
 

    

  
    

      Package: SpotSweeper

      Commit: c59c1da89cf732f07f6d6cb84110b4b20cb90455

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:51:23 -0400

      Commit message:


	  
		
 Remove BiocCheck artifacts
 

    

  
    

      Package: SpotSweeper

      Commit: 558dae52bb157be7cb259be8e656cb2739b94feb

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:50:14 -0400

      Commit message:


	  
		
 Merge Seurat compatibility and flexible coordinates features
 

    

  
    

      Package: SpotSweeper

      Commit: c154660569be00ea3a1226b61d590b5a2f5cc662

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:48:53 -0400

      Commit message:


	  
		
 Clean up DESCRIPTION and add documentation for compatibility functions
 

    

  
    

      Package: SpotSweeper

      Commit: 4bba4b66e0c6836186a9055b5188c82a19362a2f

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:40:04 -0400

      Commit message:


	  
		
 Fix DESCRIPTION file format
 

    

  
    

      Package: SpotSweeper

      Commit: 85a0f8141c088d839fff0887c0dde4d6818e26fc

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:35:28 -0400

      Commit message:


	  
		
 Update version to 1.5.0 for Bioconductor devel
 

    

  
    

      Package: SpotSweeper

      Commit: 3ce5ab5ad0060ed791b2aecef1a9a6d06b26e167

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:29:42 -0400

      Commit message:


	  
		
 Update documentation for v1.3.4 features

- Updated NEWS.md with Seurat compatibility and flexible coordinates
- Added focal spot bug fix documentation
- Added Seurat to Suggests in DESCRIPTION
- Comprehensive documentation of all new features and improvements
 

    

  
    

      Package: SpotSweeper

      Commit: ca9bea279809b255cd5d2f1ff3ad3956b5318e02

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:25:11 -0400

      Commit message:


	  
		
 Add flexible coordinate system to localOutliers

- New 'coords' parameter allows custom coordinates for neighborhood detection
- Default behavior unchanged (uses spatial coordinates)
- Supports PCA, UMAP, or any coordinate system for neighbor finding
- Added comprehensive validation and examples
- Enables outlier detection in reduced-dimension spaces
 

    

  
    

      Package: SpotSweeper

      Commit: a6c42cecb001c98fe5ce6ca69d2073fc08cd0e5e

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:18:34 -0400

      Commit message:


	  
		
 Fix focal spot inclusion in localOutliers z-score calculation

Remove focal spot from neighborhood when calculating modified z-scores
to prevent circular logic and bias. Now uses neighbors-only for
unbiased outlier detection.
 

    

  
    

      Package: SpotSweeper

      Commit: 98e7d1a9c9d671b76af5a95a999dc3c7c91de14c

      Author:  Michael Totty <mictott@gmail.com> 

      Date: 2025-09-11 23:12:23 -0400

      Commit message:


	  
		
 Add Seurat compatibility layer v1.3.4

- New compatibility functions for Seurat spatial objects
- Updated localOutliers to work with both SpatialExperiment and Seurat
- Added comprehensive test suite
- Maintains existing SpatialFeatureExperiment support
 

    

  
    

      Package: microbiome

      Commit: d1a308ba4e7f21d99da499c60e26ae0de0b55b14

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-09-09 00:18:11 +0300

      Commit message:


	  
		
 devel README
 

    

  
    

      Package: microbiome

      Commit: e7011d6b050f5f7360ee8843a176932f00be4a7c

      Author:  Leo Lahti <leo.lahti@iki.fi> 

      Date: 2026-09-08 23:44:55 +0300

      Commit message:


	  
		
 Merge pull request #229 from microbiome/devel

Devel 

    

  
    

      Package: microbiome

      Commit: 2dafe8e954d585096e882ff311f7ad9e9dfb9d01

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-09-08 23:42:58 +0300

      Commit message:


	  
		
 conflicts ok
 

    

  
    

      Package: microbiome

      Commit: 0e8a90bbdcbe3973a97aa9c934b73e3f65e0f9bd

      Author:  Leo Lahti <leo.lahti@iki.fi> 

      Date: 2026-09-08 22:52:04 +0300

      Commit message:


	  
		
 Merge pull request #230 from sabujcb/fix/bioccheck-metadata

Fix BiocCheck metadata and citation warnings 

    

  
    

      Package: microbiome

      Commit: fe699f5442bba50bf8a1c0e3c5ffea2e6791b1b4

      Author:  Sabuj Chandra Bhowmick <sabuj606@gmail.com> 

      Date: 2026-09-08 22:35:10 +0300

      Commit message:


	  
		
 Restore minimum R version to 4.5.0
 

    

  
    

      Package: microbiome

      Commit: 06635ae766c69f57e26f0552653ccb2951cab275

      Author:  Sabuj Chandra Bhowmick <sabuj606@gmail.com> 

      Date: 2026-09-03 17:33:50 +0300

      Commit message:


	  
		
 Fix BiocCheck metadata and citation warnings
 

    

  
    

      Package: microbiome

      Commit: 08323b4ff10d809845f6053804403190001e57ad

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-11 01:18:55 +0300

      Commit message:


	  
		
 Address the BiocCheck coding practice notes

Signal conditions. Ten stop() and warning() calls built their message
with paste(), which BiocCheck flags because the parts are then separated
by spaces that the author did not ask for. All were also written as
multi-line string literals, so the message carried the source
indentation into the user's console:

    Warning: Of the given OTU removal list,  12 % (n= 3 ) match the
    data.
            Removing these.

They now pass their parts to stop()/warning() directly, which
concatenates without separators, and the text is a single line.

The integer-abundance warning in transform() was additionally flagged as
a redundant signal, because the phrase "transformation errors" trips the
check that looks for error and warning wording inside a condition
message. Reworded.

Verbose output. The thirteen if (verbose) print() calls in
aggregate_taxa() are progress reporting, so they are message() calls
now. They go to stderr rather than stdout, and lose the [1] and the
quotes that print() puts around a string.

Assignment. Eight uses of = as assignment converted to <-.

Indentation. Leading whitespace in R/ normalised to multiples of four,
and whitespace-only lines emptied. Applied by a script that parses each
file before and after and refuses the file if any string constant would
change, since a multi-line string literal is the one place where leading
whitespace is load-bearing. No file was refused, and git diff -w confirms
the only non-whitespace changes are the ones described above.

Not done, and why:

  - the indentation note counts man/ and vignettes/ as well as R/. Of
    the 507 lines, only 78 are in R/. Most of the rest are in the Rd
    files, which roxygen generates, so they cannot be fixed at the source
  - the seven suppressWarnings/suppressMessages calls are deliberate.
    quiet() exists to suppress; the rest silence known warnings from
    dplyr and ggplot2 internals. Removing them would make the plotting
    functions noisy to no end, and BiocCheck only says to avoid them
    "if possible"
  - the 31 functions over 50 lines are a note, not a rule. Splitting
    them is a behavioural refactor rather than a formatting pass, and
    doing it as part of a release that is otherwise green would be a
    large unreviewable diff. Worth doing deliberately, on its own

build.sh now takes R from the environment, so the same script can check
against another R:  R=$HOME/bin/R-devel/bin/R sh build.sh

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: fff9fe9f083e2341ff74c262e22d19d1f4809671

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-11 00:57:17 +0300

      Commit message:


	  
		
 Add a TreeSummarizedExperiment vignette

The TreeSE support shipped in this cycle was documented only in NEWS and
the README. This adds a vignette that walks a TreeSummarizedExperiment
through the operations the package is normally used for: the accessors,
assay selection, transformations, the alpha diversity and dominance
indices, core and prevalence, subsetting, plotting and the time series
helpers. Every example is one the test suite already checks against the
equivalent phyloseq result.

It also documents the two ways the TreeSE path differs from the phyloseq
one, and closes with the functions that are phyloseq only and their mia
equivalents.

Masking. Attaching mia pulls in IRanges and Biostrings, which export a
transform() and a coverage() that mask ours. Neither errors on a
microbiome object, so a bare transform(tse, "compositional") silently
returns an object with no new assay. The vignette says so up front and
qualifies both calls throughout, as the tests already do.

.Rbuildignore. The new vignette did not make it into the tarball at
first. The entry meant to drop knitr's generated .R files was written as
the glob vignettes/*.R, but these entries are Perl regexps matched
case-insensitively, so it read as "vignettes", any number of slashes,
any character, then r or R. That matched vignettes/tr... and excluded
the vignette source. vignettes/vignette.Rmd was spared only by its
second letter. Rewritten as ^vignettes/.*\.R$, which excludes
vignettes/main.R as intended and nothing else.

Also added a sessionInfo section to the introductory vignette, which
clears a BiocCheck note, and a pointer from it to the new vignette.

R CMD check is Status: OK. BiocCheck is at 0 errors and 17 notes, down
from 18.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: 15f335ed403e7e310403c65b96d1cff0c8d5ce84

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-10 23:56:18 +0300

      Commit message:


	  
		
 Clear the remaining R CMD check note and BiocCheck class-check warning

R CMD check is now Status: OK, with no notes, warnings or errors.

Rd markup. checkRd raised 53 "Lost braces in \itemize" complaints across
eight man pages, all from \item{name}{description} written inside
\itemize, where the braces are silently dropped. Fixed at the roxygen
source in three ways, according to what each block is:

  - in @return, the \itemize wrapper is removed. \value renders
    \item{}{} directly
  - in prose, \itemize becomes \describe, which is the list type that
    takes a term and a description
  - in @references, the empty-tag \item{}{Livina et al. ...} form
    becomes a plain \item, since there is no term to render

Class membership. Replaced seven class(x) == / is(x) == comparisons with
is(x, "class"), which BiocCheck asks for and which also handles
subclasses:

  - is.phyloseq() compared length(x) == 1 && is(x) == "phyloseq". Since
    R 4.3 a length > 1 condition in && is an error, so this would have
    errored rather than returned FALSE for any input whose class
    hierarchy has more than one entry
  - map_levels() guarded a taxonomyTable check the same way
  - the two try() error checks in potential_analysis() and transform(),
    and the loess check in plot_regression(), followed the same pattern
  - add_refseq() and psmelt2() used class(x) != "phyloseq"

Also bumped the R dependency from 3.6.0 to 4.5.0, as BiocCheck asks.

BiocCheck is down to 1 warning from 2. The remaining one is the
even-y version rule, which this machine applies because it has
BiocVersion 3.21 installed; odd y is correct on devel.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: a8407605aa93b39bc1a55fdc3459c8de4777e511

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-10 22:09:44 +0300

      Commit message:


	  
		
 Clean the R CMD check warning and note, and fix build.sh

R CMD check now reports 1 NOTE, down from 1 WARNING and 2 NOTEs.

  - declare methods in Imports and import as() and is() from it. The
    warning about an undeclared '::' import came from the methods::as()
    call added to R/se_utils.R with the SummarizedExperiment support
  - ignore .claude when building, so the tarball no longer carries a
    hidden directory

The remaining note is pre-existing: checkRd flags "Lost braces in
\itemize" in a dozen Rd files whose roxygen blocks use \itemize where
\describe or a plain \value item list is meant.

build.sh had gone stale. It called R 4.3.2, which is no longer the
version in use here, and named the tarball as 1.31.4, four versions
back, so every step after build silently ran against a file that was not
there. The R version is now a variable and the tarball name is read from
DESCRIPTION, so only the former needs touching from here on. R CMD
BiocCheck no longer exists either; BiocCheck is now called as a function.

BiocCheck reports 0 errors, 2 warnings and 19 notes. Both warnings are
pre-existing or environmental:

  - the even-y version warning comes from this machine having
    BiocVersion 3.21 installed, so the release rule is applied to a devel
    version number. Odd y is correct on devel
  - class(x) != "phyloseq" instead of !is(x, "phyloseq") in seven files,
    none of them touched by the recent work

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: 5214e682f0de4b06a8701f3c4000c777a4b930d3

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-10 12:47:24 +0300

      Commit message:


	  
		
 Regenerate DESCRIPTION and NAMESPACE with roxygen2 8.1.0

Moves the package to roxygen2 8. No documentation content changes: the
man pages are byte-identical, and NAMESPACE exports and imports the same
symbols as before. Only the generated formatting differs.

  - roxygen 8 records itself as Config/roxygen2/version rather than
    RoxygenNote
  - importFrom directives are now written as one multi-symbol block per
    package instead of one line per symbol

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: 928470eb753180561059dfc37457de33720493e4

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-10 12:43:20 +0300

      Commit message:


	  
		
 Add a one-time deprecation notice for phyloseq input

Passing a phyloseq object to the package now emits a message
recommending the (Tree)SummarizedExperiment framework and mia, which is
where method development takes place. The notice is shown once per
session and can be silenced with
options(microbiome.phyloseq_deprecation = FALSE).

Once per session rather than once per call: the accessors call each
other freely (alpha -> richness -> abundances and so on), so a per-call
message would produce dozens of repeats for a single user-level call.
.reset_phyloseq_deprecation() brings it back within a session, for
tests, examples and vignettes.

The hooks sit in the accessors and internal helpers that every path goes
through (abundances, meta, taxa, the se_utils helpers) plus the
phyloseq-only functions that bypass them (map_levels, psmelt2,
tax_tibble, add_besthit, add_refseq). All 16 top-level entry points
checked fire exactly once for phyloseq input and stay silent for
TreeSummarizedExperiment. Bare otu_table and tax_table objects pass
silently, since the gate is is.phyloseq().

README and NEWS gain the migration guidance: the recommendation to move
to the methods described in the Orchestrating Microbiome Analysis (OMA)
book, which functions accept TreeSummarizedExperiment, that the
taxonomy-table functions remain phyloseq only, and that transform()
stores its result as a named assay.

Version bumped to 1.35.1.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: 6b7169e52d4c3eecd90c0e1c3105ed655224d506

      Author:  antagomir <leo.lahti@iki.fi> 

      Date: 2026-08-09 01:25:12 +0300

      Commit message:


	  
		
 Add TreeSummarizedExperiment support via the microbiome accessors

Teach abundances(), meta() and taxa() about SummarizedExperiment-derived
objects, then convert the functions that reach past them into phyloseq
internals. 48 functions now return identical results for a phyloseq
object and the equivalent TreeSummarizedExperiment.

Accessors and helpers:

  - abundances() gains assay.type, defaulting to the counts assay when
    present and otherwise the first assay
  - meta() returns colData; taxa() returns rownames
  - new internal helpers in R/se_utils.R for the counts, subsetting and
    metadata/abundance writeback that previously went through phyloseq

transform() stores its result as a new named assay for
SummarizedExperiment input, leaving the original assays untouched, and
gains a name argument to control that assay name. This follows the mia
transformAssay convention, so the result is read back with
abundances(x, assay.type = name) rather than abundances(x). Internal
callers were switched to the backend-neutral abundances(x, transform =)
form, which never round-trips through the object.

Taxonomy-table dependent functions (aggregate_taxa, plot_composition,
map_levels, psmelt2, the tibble utilities and the read_* family) are
unchanged and remain phyloseq only.

SummarizedExperiment, TreeSummarizedExperiment and mia are in Suggests;
all calls are :: qualified so the phyloseq path is untouched when they
are absent. NAMESPACE needs no changes.

Incidental fixes to pre-existing bugs found while converting, all
independent of the backend:

  - low_abundance() assigned names from colnames() of a phyloseq object,
    which is NULL, silently returning an unnamed vector
  - collapse_replicates() dropped meta(x)[, replicate_fields] to a vector
    for a single field, so apply() failed and the one-field case errored
  - summarize_phyloseq() recomputed the margin sums a dozen times; the
    abundance matrix is now taken once

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: microbiome

      Commit: c11f17c7dc8acbdddd2b8ee398b059af5552ed6f

      Author:  Leo Lahti <leo.lahti@iki.fi> 

      Date: 2025-08-19 19:48:11 +0300

      Commit message:


	  
		
 Merge pull request #226 from raivo-otus/master

Quick fix for rclr transformation  

    

  
    

      Package: microbiome

      Commit: 8b025547f24c16e5fe9a6370488fee2e9c920c1b

      Author:  raivo-otus <hindstrom.rasmus@gmail.com> 

      Date: 2025-08-19 13:15:57 +0300

      Commit message:


	  
		
 Update docs to reflect explicit addition of rclr transformation
 

    

  
    

      Package: microbiome

      Commit: cd8d22fb3612630c2de08f545bf84f1896889f9d

      Author:  raivo-otus <hindstrom.rasmus@gmail.com> 

      Date: 2025-08-19 13:14:45 +0300

      Commit message:


	  
		
 Update contributer
 

    

  
    

      Package: microbiome

      Commit: 44926a2c7f629662a786c88a1d91ba00c548df4a

      Author:  raivo-otus <hindstrom.rasmus@gmail.com> 

      Date: 2025-08-19 13:07:07 +0300

      Commit message:


	  
		
 version number bump
 

    

  
    

      Package: microbiome

      Commit: 972abf5a6f5f1a4bf7210ee98b789a143b334252

      Author:  raivo-otus <hindstrom.rasmus@gmail.com> 

      Date: 2025-08-19 13:06:55 +0300

      Commit message:


	  
		
 tabs to spaces
 

    

  
    

      Package: microbiome

      Commit: 4ac07348a3a6efe483bab0887b86c1f5bef41dcd

      Author:  raivo-otus <hindstrom.rasmus@gmail.com> 

      Date: 2025-08-19 08:55:35 +0300

      Commit message:


	  
		
 Quick fix for rclr transformation
 

    

  
    

      Package: igvShiny

      Commit: c3dd82bfd47e6db7b1727a5b7a391820b27ebff1

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-08 23:08:59 +0200

      Commit message:


	  
		
 chore: re-pin manifest.json to master squash commit 0708283
 

    

  
    

      Package: igvShiny

      Commit: 0708283e4c19510b3eb0eb1fbc96e1b21f9f60be

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-08 23:06:54 +0200

      Commit message:


	  
		
 feat: stream local BAM in showcase demo and update local data demo (#177)

- Add BAM (Local File Stream) button to inst/showcase/igvShinyDemo.R using loadBamTrackFromLocalFile() with extdata/tumor.bam
- Update inst/demos/local-data.R with loadBamTrackFromLocalFile() file streaming alongside in-memory readGAlignments
- Add shinytest2 integration test in test-shinyApp.R asserting title="tumor.bam"
- Update demo/posit-connect README, app.R comments, and re-pin manifest.json
- Add NEWS.md entry 

    

  
    

      Package: rBLAST

      Commit: 40dadc1bf677b8f2c069e9df099fc96ed5f515e3

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 14:13:25 -0500

      Commit message:


	  
		
 BioC Release Candidate.
 

    

  
    

      Package: rBLAST

      Commit: c296807f69d26addefa4a3040e388323d0d5768c

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 14:13:12 -0500

      Commit message:


	  
		
 Fixed name.
 

    

  
    

      Package: rBLAST

      Commit: 0b36819300243256563947b4144a0834ba0c85c6

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 14:06:55 -0500

      Commit message:


	  
		
 Added a TOC.
 

    

  
    

      Package: rBLAST

      Commit: d96757676eb918de4af64c975639dc9d8920edb3

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 14:00:53 -0500

      Commit message:


	  
		
 fixed path normalization for windows.
 

    

  
    

      Package: rBLAST

      Commit: 04f1c994e71ea5a61c45b61ef730178a6019b658

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 13:30:21 -0500

      Commit message:


	  
		
 fixed executable detection.
 

    

  
    

      Package: rBLAST

      Commit: dc29199a387a73848db164d227db9eaf2b333d3c

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 13:23:21 -0500

      Commit message:


	  
		
 Fixed issues with missing executables.
 

    

  
    

      Package: rBLAST

      Commit: 169454f67d31d7ef7940bd5bf18be4121628225f

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 12:59:58 -0500

      Commit message:


	  
		
 added more guards for uninstalled BLAST.
 

    

  
    

      Package: DESeq2

      Commit: 9e885b581380291797f2777145c395f50aaaa72b

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-09-08 14:55:04 -0400

      Commit message:


	  
		
 another url fix
 

    

  
    

      Package: DESeq2

      Commit: 7f6493b81088939495429ddf23e93263ff9696a1

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-09-08 14:54:14 -0400

      Commit message:


	  
		
 fix url in DESeq2.cpp comment
 

    

  
    

      Package: rBLAST

      Commit: 7a2f455ba1b029834f06b4d5a838a2a4b4eaf9a1

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 11:57:13 -0500

      Commit message:


	  
		
 Added date.
 

    

  
    

      Package: rBLAST

      Commit: 6840924f72d6a647dda5d3d00852720a8a19ef63

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 11:50:05 -0500

      Commit message:


	  
		
 Release candidate.
 

    

  
    

      Package: rBLAST

      Commit: 708c867e9c471013af80abaa1c258cb22eb93ca2

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 11:43:45 -0500

      Commit message:


	  
		
 Updated NEWS.
 

    

  
    

      Package: rBLAST

      Commit: bad78e86bc55b61cfdac06d0279cacb6d096b7eb

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 11:41:20 -0500

      Commit message:


	  
		
 Improved documentation.
 

    

  
    

      Package: rBLAST

      Commit: c42151626c80f90eb4ea59f7fbed1627aeb0c665

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 11:40:58 -0500

      Commit message:


	  
		
 moved.
 

    

  
    

      Package: rBLAST

      Commit: 29f11ac0bf2734026ac2b8961b33e913674a25bb

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 09:39:00 -0500

      Commit message:


	  
		
 Added checks if sequences are written without an error.
 

    

  
    

      Package: rBLAST

      Commit: 28b562e790a97042f60aee613d963f6921a35a0b

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-08 09:38:25 -0500

      Commit message:


	  
		
 Added tests.
 

    

  
    

      Package: rBLAST

      Commit: 283721bf5e2d8617a5df6db0c279d59d3e95611d

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2026-09-03 09:26:11 -0500

      Commit message:


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

    

  
    

      Package: rBLAST

      Commit: 9cb5287309776457794902f84e448649a772c1d2

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2025-10-07 13:43:11 -0500

      Commit message:


	  
		
 Added a note on how slow the -remote option is.
 

    

  
    

      Package: rBLAST

      Commit: a4c57292a551bbc3a2d34884912ca691bd7ba295

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2025-07-03 10:50:47 -0500

      Commit message:


	  
		
 Added more fields to example query.
 

    

  
    

      Package: rBLAST

      Commit: d6ad9adc8cdfc31deef1e991572484d1387e2229

      Author:  mhahsler <michael@hahsler.net> 

      Date: 2025-07-03 10:47:39 -0500

      Commit message:


	  
		
 TYPO
 

    

  
    

      Package: igvShiny

      Commit: 81ec6e2f8cee96fb2fc4c5f594b323f5b8c44452

      Author:  Arkadiusz Gładki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-08 18:22:55 +0200

      Commit message:


	  
		
 chore: re-pin manifest.json to master squash commit 66c7437
 

    

  
    

      Package: igvShiny

      Commit: 66c7437a5c5e90f464e2edb4f6da1b5c836f02e0

      Author:  Arek Gladki <41166437+gladkia@users.noreply.github.com> 

      Date: 2026-09-08 18:20:39 +0200

      Commit message:


	  
		
 feat: stream local BAM and CRAM files via HTTP 206 Range requests (#175)

* feat: stream local BAM and CRAM files via HTTP 206 Range requests (#174)

Add native HTTP 206 Partial Content range request support to Shiny
via session$registerDataObj() and .serveFileWithHttpRange(). This enables
viewing multi-gigabyte BAM and CRAM alignment tracks directly from disk
without running out of browser memory (V8 ArrayBuffer OOM) or loading
entire files into R memory.

- Add serveLocalFile() and loadBamTrackFromLocalFile()
- Route loadCramTrackFromLocalData() through serveLocalFile()
- Delegate character file paths in loadBamTrackFromLocalData()
- Normalize 'index' to 'indexURL' in startup track sanitizer
- Add unit tests for HTTP 206 Range serving and session dataobj
- Add custom-genome-bam demo and Posit Connect Cloud dev wrapper

* chore: bump version to 1.9.44 and add NEWS entry

* chore: re-pin manifest.json to commit 9664880 containing custom-genome-bam demo

* fix: address CodeRabbit review and pkgdown index topic (#174)

- Add @keywords utils to serveLocalFile so pkgdown includes it in reference
- Forward displayMode parameter in loadBamTrackFromLocalFile and delegate from loadBamTrackFromLocalData
- Add roxygen @examples for loadBamTrackFromLocalFile
- Support RFC 7233 suffix ranges (bytes=-N), multiple/malformed range fallback to 200 OK, and full-file serving
- Make temporary manifest creation in bump-pin.sh atomic on same filesystem
- Add unit tests for suffix, multiple, and malformed ranges and displayMode forwarding 

    

  
    

      Package: Damsel

      Commit: be93cec0583220420f3c640a7f03d15a322a895b

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:02:55 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_23 branch
 

    

  
    

      Package: Damsel

      Commit: c148934abb67195a2113ab512c324c2f41bd77ce

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2026-04-28 09:02:55 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_23 branch
 

    

  
    

      Package: Damsel

      Commit: 9142f23f39644dc8d0b12c7fb6ec29a5bd537d2f

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 11:29:38 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

    

  
    

      Package: Damsel

      Commit: 12e5320b0e44c3d42c42b9b0df18d27dbaea1025

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-10-29 11:29:38 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: Damsel

      Commit: 52bf23cc0b13e42bb5036343695a1c07785a797f

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-04-15 13:33:48 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
 

    

  
    

      Package: Damsel

      Commit: be2753accd538853b933b4813b8cdba17e607d4d

      Author:  A Wokaty <andres.wokaty@sph.cuny.edu> 

      Date: 2025-04-15 13:33:48 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
 

    

  
    

      Package: Damsel

      Commit: b4361078ec3a3bd154c360f03960bced6bb1b4e0

      Author:  J Wokaty <jennifer.wokaty@sph.cuny.edu> 

      Date: 2024-10-29 11:30:17 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_20 branch
 

    

  
    

      Package: Damsel

      Commit: 897c5bc1c9c40c046265faa7e389ea5d88d3492b

      Author:  J Wokaty <jennifer.wokaty@sph.cuny.edu> 

      Date: 2024-10-29 11:30:17 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_20 branch
 

    

  
    

      Package: Damsel

      Commit: 8c79e15af1c93976241aebd465b8d86bde10afbb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-04 13:46:34 +1000

      Commit message:


	  
		
 version update devel
 

    

  
    

      Package: Damsel

      Commit: 608c44c6da5261c894f44fa9975b95f63839d910

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-04 13:45:33 +1000

      Commit message:


	  
		
 greater functionality of design matrix - optional replicates or have own design
 

    

  
    

      Package: Damsel

      Commit: 6b11b4dc35f1ce15c728851a6f2ae4d2c764f9e6

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 12:12:45 +1000

      Commit message:


	  
		
 devel version update
 

    

  
    

      Package: Damsel

      Commit: fc9cda796d25446c3816c9f6b1b97ba6be28892a

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 12:02:17 +1000

      Commit message:


	  
		
 reflect additional plots and other changes
 

    

  
    

      Package: Damsel

      Commit: 971adcc67a4d3fdac8ae10f5061969d50dfa5bc9

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 12:01:50 +1000

      Commit message:


	  
		
 new quality control plots
 

    

  
    

      Package: Damsel

      Commit: af0914857ed0569cdc4cba423f9296f01834487b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 12:01:01 +1000

      Commit message:


	  
		
 update plot
 

    

  
    

      Package: Damsel

      Commit: aa02f530abe8f76266475a2e84e530756305cc94

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 12:00:35 +1000

      Commit message:


	  
		
 add hierachical clustering to heatmap
 

    

  
    

      Package: Damsel

      Commit: de0816662b8b5bfdbe4eb6f337050ca71ad19ed5

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 11:59:53 +1000

      Commit message:


	  
		
 add hierachical clustering to heatmap
 

    

  
    

      Package: Damsel

      Commit: 78e4c63d78c31f8561ae1448b2f369a23024e5a3

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-10-01 11:58:42 +1000

      Commit message:


	  
		
 fix function names in documentation
 

    

  
    

      Package: Damsel

      Commit: 8301ab2ef00db2008edeb97c93cc665132ed4fac

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-08-28 11:57:12 +1000

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: Damsel

      Commit: 1109c0eeda3735b2e908700b4519d6c74432a3f1

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-08-28 11:56:26 +1000

      Commit message:


	  
		
 bug fix: factor problem
 

    

  
    

      Package: Damsel

      Commit: 91475d2168f1897d6856b4eb4ea963a139cc0581

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-08-23 12:23:38 +1000

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: Damsel

      Commit: f91253f71974e7e08bb23cebdf62d3adae04fc7b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-08-23 12:22:27 +1000

      Commit message:


	  
		
 bug fix: seqnames factor, and windows multiple cores
 

    

  
    

      Package: Damsel

      Commit: 3d4cb64c0f06191e50202b59b714d2e9311afc83

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2024-04-30 11:56:05 -0400

      Commit message:


	  
		
 bump x.y.z version to odd y following creation of RELEASE_3_19 branch
 

    

  
    

      Package: Damsel

      Commit: 7aa60c89c86d12075a2a7da17f021ccb941e768f

      Author:  J Wokaty <jwokaty@users.noreply.github.com> 

      Date: 2024-04-30 11:56:05 -0400

      Commit message:


	  
		
 bump x.y.z version to even y prior to creation of RELEASE_3_19 branch
 

    

  
    

      Package: Damsel

      Commit: 753f76d09e92466c672bec5855d5c5deb5e30258

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-16 14:58:22 +1000

      Commit message:


	  
		
 fix indent
 

    

  
    

      Package: Damsel

      Commit: 47b5a2d228a8a50ec225800f2d812f56b0faa0d1

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-16 14:45:09 +1000

      Commit message:


	  
		
 version update
 

    

  
    

      Package: Damsel

      Commit: 8ca77909df7bd4c6527c9ba6de31aab11dcda6ad

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-16 14:44:39 +1000

      Commit message:


	  
		
 change seqnames with seqlevelsStyle for some cases, fix consequences
 

    

  
    

      Package: Damsel

      Commit: 15f132a7d9b54bd7bee1910659038522fca487da

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-16 14:40:55 +1000

      Commit message:


	  
		
 add makeDGE checks, fix documentation, change p-value threshold to 0.05
 

    

  
    

      Package: Damsel

      Commit: 75219adcfbfe8459766a35b9a8fba31130f09735

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-08 12:04:03 +1000

      Commit message:


	  
		
 fix column order
 

    

  
    

      Package: Damsel

      Commit: 6f99b5814c100a3165eaf06071af091d12024ad0

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-08 11:51:45 +1000

      Commit message:


	  
		
 fixed column order for as_granges - v0.99.3
 

    

  
    

      Package: Damsel

      Commit: e474d20596aa09ae8c7628312bcebe70c8d788aa

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 16:27:45 +1100

      Commit message:


	  
		
 set regions as df
 

    

  
    

      Package: Damsel

      Commit: 304e610f2602b33fa1662b2e8e949edf95d7adcd

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 15:42:49 +1100

      Commit message:


	  
		
 update to 0.99.2
 

    

  
    

      Package: Damsel

      Commit: e17eac92e8d4a1470998fbf67e6be2ff6251aeae

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 15:40:40 +1100

      Commit message:


	  
		
 update for bioc review
 

    

  
    

      Package: Damsel

      Commit: 7d2dc1ee8d4a607a6915897a5b2349e110f27f45

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 15:40:18 +1100

      Commit message:


	  
		
 added Rplots to gitignore
 

    

  
    

      Package: Damsel

      Commit: 0fb1696ce0ace8dec6f0f479ff3eac2d22438e8f

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 15:39:58 +1100

      Commit message:


	  
		
 use biocstyle, added orcid
 

    

  
    

      Package: Damsel

      Commit: 5113e1d242ce270c5df8938657cb69b0fa10162a

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-04-05 15:39:24 +1100

      Commit message:


	  
		
 bioc review edits - removed old code, new fn for help in plotting counts and dm, replaced some loops with apply, inherits instead of class
 

    

  
    

      Package: Damsel

      Commit: 8b822d847d58a4ae8cf67e75cb387f0ce6a85aad

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-22 14:01:40 +1100

      Commit message:


	  
		
 update version with tarball size fix
 

    

  
    

      Package: Damsel

      Commit: 41cc56b72ec0cc6697b4ba33ec1e3c2c4f6fac59

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-22 14:00:28 +1100

      Commit message:


	  
		
 changed fixtures to be smaller so that tarball is <5MB
 

    

  
    

      Package: Damsel

      Commit: 291679e0da7521b12df4ab5fa56a55e012e90886

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-21 11:11:42 +1100

      Commit message:


	  
		
 update Damsel installation
 

    

  
    

      Package: Damsel

      Commit: 78c2199c25d031fd38acf851874abcca830174cf

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 17:04:13 +1100

      Commit message:


	  
		
 added file showing how I made the testthat fixtures
 

    

  
    

      Package: Damsel

      Commit: b4195517fd14363db6363a7417abf079fb967d9d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 17:03:54 +1100

      Commit message:


	  
		
 updated data documentation and extdata data info
 

    

  
    

      Package: Damsel

      Commit: 86f3fa3d46940ab8d400caa91e116b5c9ac30913

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 15:38:45 +1100

      Commit message:


	  
		
 add gitignore files
 

    

  
    

      Package: Damsel

      Commit: 94ae05e3e52eb1e537612cfb29cf660b275e729b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 15:38:33 +1100

      Commit message:


	  
		
 remove testhat/fixtures from gitignore
 

    

  
    

      Package: Damsel

      Commit: 458dfac26f399d001da49e1bfa6a0ba9c7922764

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 15:38:15 +1100

      Commit message:


	  
		
 update
 

    

  
    

      Package: Damsel

      Commit: fea75a1f39e56d1a0c5ea2544f94a5c39733f138

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 15:38:07 +1100

      Commit message:


	  
		
 update to tests
 

    

  
    

      Package: Damsel

      Commit: 81ee4c10967685900740c4cb2b4760f4535172ca

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 14:42:17 +1100

      Commit message:


	  
		
 added raw example bams
 

    

  
    

      Package: Damsel

      Commit: 568098ef51bf7f261b4c771206fa4f8ac967e06d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 14:37:37 +1100

      Commit message:


	  
		
 removed inst extdata
 

    

  
    

      Package: Damsel

      Commit: e4ea44934612af6f9a8e06b6868709688eac604d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-06 12:47:03 +1100

      Commit message:


	  
		
 update gitignore
 

    

  
    

      Package: Damsel

      Commit: 53a258ddcea0f10835e37220d3e5102d9c43c2ce

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 22:31:58 +1100

      Commit message:


	  
		
 expanded readme
 

    

  
    

      Package: Damsel

      Commit: 71fa0c385814a83c747721d86370d297f5792a63

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 16:59:06 +1100

      Commit message:


	  
		
 try
 

    

  
    

      Package: Damsel

      Commit: 7f2f39df2e101139f9c2a7234785ce2fdaa211cb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 15:21:12 +1100

      Commit message:


	  
		
 simplify to just match all **/.DS_Store
 

    

  
    

      Package: Damsel

      Commit: d91678f561bf7505664a5c1555ffe08a117d2880

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 15:19:52 +1100

      Commit message:


	  
		
 remove .DS_Store files
 

    

  
    

      Package: Damsel

      Commit: 2800327f71406e5ef2faccdeb1e35442f8e4bc44

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 13:58:21 +1100

      Commit message:


	  
		
 update
 

    

  
    

      Package: Damsel

      Commit: 77ddfb77a6fa231497fa828dd0ef682280e9b045

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 10:37:50 +1100

      Commit message:


	  
		
 added files to .gitignore
 

    

  
    

      Package: Damsel

      Commit: ffd011dbb72e300845deb7db05942cacf0d14ea7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-05 10:32:41 +1100

      Commit message:


	  
		
 fixed authors
 

    

  
    

      Package: Damsel

      Commit: 2bfe15f1e3235dc5abc83eb0220c392d53c6f33b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 23:08:08 +1100

      Commit message:


	  
		
 authors update
 

    

  
    

      Package: Damsel

      Commit: c5a92b6030e61c56932e6b990d68ae263f05e1f3

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 23:05:35 +1100

      Commit message:


	  
		
 stop git track
 

    

  
    

      Package: Damsel

      Commit: 3d124f20f4eda3ab9bc821273f622378c1ab224a

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 22:39:32 +1100

      Commit message:


	  
		
 fix vignette
 

    

  
    

      Package: Damsel

      Commit: a277cd1607ee9252472bd6b6942ac07022694897

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 22:35:23 +1100

      Commit message:


	  
		
 v0.99.0
 

    

  
    

      Package: Damsel

      Commit: d25fbc9f88b41b39d6851fc317cecbf4b0124b95

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 18:19:20 +1100

      Commit message:


	  
		
 update v 0.8 - changed function names
 

    

  
    

      Package: Damsel

      Commit: 5768c0f8d350c1d365af2d755e5ba6def124fbb1

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 16:38:42 +1100

      Commit message:


	  
		
 fixed data
 

    

  
    

      Package: Damsel

      Commit: 9d36dee052ec2a60e0bca4193bd928aaac114893

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 16:38:25 +1100

      Commit message:


	  
		
 fixed position for sites
 

    

  
    

      Package: Damsel

      Commit: 48fb8a26cfbbe4bbb1b88b8dee5ed40bfa123cbb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 16:37:42 +1100

      Commit message:


	  
		
 update documentation
 

    

  
    

      Package: Damsel

      Commit: 9192c9748ba3f91e128500247a071333bfdce917

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-04 16:35:30 +1100

      Commit message:


	  
		
 minor update
 

    

  
    

      Package: Damsel

      Commit: 3738421b05ba28602a343a18adc1f2eee4c6f622

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-01 17:33:47 +1100

      Commit message:


	  
		
 deprecated edgeR_plot_mds and edgeR_plot results - incorporated results plot into dm results fn
 

    

  
    

      Package: Damsel

      Commit: 39e809771ee9c4af572a9906f6ee05e18b290689

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-01 17:10:49 +1100

      Commit message:


	  
		
 updates to function names
 

    

  
    

      Package: Damsel

      Commit: 811bf1f4b451735df2650b81f9289293ad56855a

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-03-01 17:04:13 +1100

      Commit message:


	  
		
 v 0.7.1
 

    

  
    

      Package: Damsel

      Commit: 21ece62512641fdb03580b166c05f1a274e018be

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 13:31:42 +1100

      Commit message:


	  
		
 set indent to 4, added bugreports and url
 

    

  
    

      Package: Damsel

      Commit: caeef4208e37e1da21feb9d17ba64ca967d8d6f2

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:59:12 +1100

      Commit message:


	  
		
 update
 

    

  
    

      Package: Damsel

      Commit: c275497dc5ac0bdb6e6454f32513af204d8e64e1

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:58:44 +1100

      Commit message:


	  
		
 dros_counts
 

    

  
    

      Package: Damsel

      Commit: 62376d012cf6fb5e728f147f76e2f732f073635e

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:58:19 +1100

      Commit message:


	  
		
 update to v0.7
 

    

  
    

      Package: Damsel

      Commit: ef4a654bed0ab57831b4756c9b9a8c34b0a9fc67

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:56:48 +1100

      Commit message:


	  
		
 update to v0.7
 

    

  
    

      Package: Damsel

      Commit: 31842f5adce54aaf6d60b5db05087d7a0441647e

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:55:49 +1100

      Commit message:


	  
		
 updated example code to use new gene fn and TxDb
 

    

  
    

      Package: Damsel

      Commit: d9b014a9562630b135b198b9ddc8f8ed1bd9561c

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-29 11:50:35 +1100

      Commit message:


	  
		
 new genes fn and deprecated old get biomart genes
 

    

  
    

      Package: Damsel

      Commit: 9ff8b3d16cff8bb197f5ef5b4573a9430ec8edc9

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-27 11:09:43 +1100

      Commit message:


	  
		
 sped up tests by not running them through every previous step
 

    

  
    

      Package: Damsel

      Commit: 7d8ad3b2f5176bfb04de7d8d18ed7091c077404b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:19:23 +1100

      Commit message:


	  
		
 plot man updates
 

    

  
    

      Package: Damsel

      Commit: e10b9507012a095dddcb3fcc00a60947dd6b1e86

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:18:55 +1100

      Commit message:


	  
		
 fixed id check
 

    

  
    

      Package: Damsel

      Commit: b0fb2db1f1cae049a072d17e472949a0a1908b67

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:14:50 +1100

      Commit message:


	  
		
 set levels for meth status
 

    

  
    

      Package: Damsel

      Commit: 0d83cb3b45fd79891ce2dc10b7a6b0fa1b0308f7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:14:12 +1100

      Commit message:


	  
		
 set colours for 2 or 3 replicates
 

    

  
    

      Package: Damsel

      Commit: db6866f0cf9a0357c12ca69d6eb078dcce7dc34e

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:08:35 +1100

      Commit message:


	  
		
 minor param update
 

    

  
    

      Package: Damsel

      Commit: 423fb2db2571964611d883fc761344999cb6be6c

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:07:32 +1100

      Commit message:


	  
		
 minor peaks update
 

    

  
    

      Package: Damsel

      Commit: 0d69b0ab2a93173038f0057011a63fcc9add22d3

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:06:34 +1100

      Commit message:


	  
		
 gene ontology update
 

    

  
    

      Package: Damsel

      Commit: a2450e4de73a9a833dcddc1b756f2f51fc5d2683

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:06:11 +1100

      Commit message:


	  
		
 minor update to documentation
 

    

  
    

      Package: Damsel

      Commit: 1b3d618805239ff7dbbbf1df50a6605cd1955d7b

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:05:37 +1100

      Commit message:


	  
		
 update
 

    

  
    

      Package: Damsel

      Commit: 6e3dc24026b4a3d5aa1770b20d627d77be5bc77f

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:05:29 +1100

      Commit message:


	  
		
 reworked gene ontology results to the useful outputs, added plotting fn
 

    

  
    

      Package: Damsel

      Commit: 808fee6c6620ce65ad92332b81f29fa98a90d4c7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-21 16:04:58 +1100

      Commit message:


	  
		
 remove -1 from de results
 

    

  
    

      Package: Damsel

      Commit: b814182b64126ece1fb22922bba4e1cfa12102c7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-09 13:11:19 +1100

      Commit message:


	  
		
 added new peak fn, and fixed ordering of old aggregate_peaks
 

    

  
    

      Package: Damsel

      Commit: cf00203a7c0623e6032c229cfb3fa2e447676f37

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-09 13:10:13 +1100

      Commit message:


	  
		
 fixed helper function
 

    

  
    

      Package: Damsel

      Commit: 1b5d07e52fc6d4cd76ae4c961d855cbcee31bef3

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-05 17:39:25 +1100

      Commit message:


	  
		
 updated to be case insensitive - dam/Dam and .bam/BAM
 

    

  
    

      Package: Damsel

      Commit: 992f0300fb2b867be1091e7652a48dfe2bee72cb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-05 17:25:09 +1100

      Commit message:


	  
		
 fixed process bams so it can handle samples that are paired and single end in the same folder
 

    

  
    

      Package: Damsel

      Commit: 7ddfeb829da6782e7d18827b311bae5b26225dd2

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-02-05 16:15:29 +1100

      Commit message:


	  
		
 allow for files to have .bam or .BAM
 

    

  
    

      Package: Damsel

      Commit: a51c9995ff7cc79eb3df6c00438de1b633ced478

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-25 11:44:22 +1100

      Commit message:


	  
		
 df
 

    

  
    

      Package: Damsel

      Commit: 82e885a98b6ca8041f45fe53291a6cfb9d6a77dd

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:47:30 +1100

      Commit message:


	  
		
 set indent to 4
 

    

  
    

      Package: Damsel

      Commit: 105cdedb41b0fa7fcdcc9aae6f15931e06c6b74c

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:46:49 +1100

      Commit message:


	  
		
 set indent to 4
 

    

  
    

      Package: Damsel

      Commit: 0ee89bcfef22c9e39a0be690d109c0f82deb1a81

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:45:42 +1100

      Commit message:


	  
		
 use names instead of index for column order
 

    

  
    

      Package: Damsel

      Commit: 0d45532ff5f91220279f408b76d442a927d5c0ac

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:27:47 +1100

      Commit message:


	  
		
 df
 

    

  
    

      Package: Damsel

      Commit: f1b05bc72e93ca9c8b34eeef33d1078a4eca94c0

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:24:33 +1100

      Commit message:


	  
		
 df
 

    

  
    

      Package: Damsel

      Commit: 8dd428e77126a41c7156b2e4014d38eee87d784f

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 16:21:27 +1100

      Commit message:


	  
		
 ensure df - also indent of 4
 

    

  
    

      Package: Damsel

      Commit: b02191632781dbe4ceb23ca2e650f596fb72dc1e

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 11:14:04 +1100

      Commit message:


	  
		
 test
 

    

  
    

      Package: Damsel

      Commit: da4f6d9ea5fe57b4ac4d1f9567cd7c74606a0df9

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-24 11:06:36 +1100

      Commit message:


	  
		
 how to install
 

    

  
    

      Package: Damsel

      Commit: 28c049cdd0ee8c2a90cbe1bce592b3a44e75d84d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-23 11:51:45 +1100

      Commit message:


	  
		
 removed process_bams_old as dependency exomeCopy has been deprecated - Damsel v0.6.0
 

    

  
    

      Package: Damsel

      Commit: 72c317e55a812c8c8fed0aaa0c4b233f6f55589d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-18 10:04:38 +1100

      Commit message:


	  
		
 Merge branch 'main' of github.com:Oshlack/Damsel
 

    

  
    

      Package: Damsel

      Commit: a99079e5080cefbbab2c24a5471e9767ff0c89d4

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-18 10:03:21 +1100

      Commit message:


	  
		
 new peak functions - not exported yet
 

    

  
    

      Package: Damsel

      Commit: 119f137a42a864684f702497b588c090e692b424

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-18 10:03:02 +1100

      Commit message:


	  
		
 v 0.5.0 - removed region file
 

    

  
    

      Package: Damsel

      Commit: ae3680ba4fa8f7c219f7c9a563391f32f8f1ccb5

      Author:  Andrew Lonsdale <andrew.lonsdale@lonsbio.com.au> 

      Date: 2024-01-17 10:34:46 +1100

      Commit message:


	  
		
 Add citation heading to README
 

    

  
    

      Package: Damsel

      Commit: 2611ee55d5e5d4a5d94dae21c7bc8df5cd3ad3ad

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-12 16:48:27 +1100

      Commit message:


	  
		
 tidied up code
 

    

  
    

      Package: Damsel

      Commit: b85c2de7cca380f2d12656615f770ba4e9d9b4d9

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-12 16:48:05 +1100

      Commit message:


	  
		
 removed regions file
 

    

  
    

      Package: Damsel

      Commit: 3bc1da8d8c454f4f492790dc2559de851e23801d

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-12 16:44:56 +1100

      Commit message:


	  
		
 expanded, removed lazydata as per bioconductor
 

    

  
    

      Package: Damsel

      Commit: fd6c653ae895538ac2ef1b4bbc1902cbda88d7b6

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-11 18:56:14 +1100

      Commit message:


	  
		
 removed unnecessary code - simplified and added helper functions
 

    

  
    

      Package: Damsel

      Commit: 237d4e5d6cc8866e35d7deb51ed13691a727c9ae

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-11 18:54:31 +1100

      Commit message:


	  
		
 broke up annotate_genes into smaller function, slightly more efficient code - removed unncessary code
 

    

  
    

      Package: Damsel

      Commit: 7c7e54049aef87d614575a1cc887ef9ced3535f5

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-11 18:52:39 +1100

      Commit message:


	  
		
 removed add_de from export
 

    

  
    

      Package: Damsel

      Commit: 3a3afa560a1759ba0df362713d5cb562522b43c4

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-11 16:22:31 +1100

      Commit message:


	  
		
 add examples
 

    

  
    

      Package: Damsel

      Commit: 9fe06f832fa896d49b6fcc9e310167bafb8c84fb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-08 12:11:44 +1100

      Commit message:


	  
		
 create helper fns
 

    

  
    

      Package: Damsel

      Commit: cf1cdae34d0140676abcc4031568463aa17b1c37

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-08 12:11:24 +1100

      Commit message:


	  
		
 minor code tidying
 

    

  
    

      Package: Damsel

      Commit: 0a53850828e072649ba6541dc3c6108f71bb2388

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-08 10:56:24 +1100

      Commit message:


	  
		
 redid fn
 

    

  
    

      Package: Damsel

      Commit: 887766fe8d84dd41ac7b0f7064b2934d238482eb

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-08 09:45:08 +1100

      Commit message:


	  
		
 minor update - code formatting
 

    

  
    

      Package: Damsel

      Commit: 660d3808e360b38441c0c8071ef71e5ff2ca90d4

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-03 11:22:21 +1100

      Commit message:


	  
		
 replaced 1:n() with seq_len as per bioconductor guidelines
 

    

  
    

      Package: Damsel

      Commit: 1218f56f8803f4255ea4a631e9c74f8c0e076458

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-03 10:19:15 +1100

      Commit message:


	  
		
 update arguments
 

    

  
    

      Package: Damsel

      Commit: 9b862044ce90f85c76d4d982be6c64017ff5bfe7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2024-01-03 10:01:38 +1100

      Commit message:


	  
		
 update arguments
 

    

  
    

      Package: Damsel

      Commit: 33119b56e69100e11f9624d902ed1dcff0a60095

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-30 08:48:21 +1100

      Commit message:


	  
		
 readded new version but with suggests
 

    

  
    

      Package: Damsel

      Commit: a3c5961da271c4d5463929bf055fddffa02a3653

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-29 11:42:30 +1100

      Commit message:


	  
		
 readd old process bams so hopefully user can work around
 

    

  
    

      Package: Damsel

      Commit: 38bc7ec72fe21d6e4276ec7667c035f4246d3846

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-27 11:26:20 +1100

      Commit message:


	  
		
 update v4.0
 

    

  
    

      Package: Damsel

      Commit: 2c96228001ec8bff8231084f2fb8aeb5e4053fca

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-27 11:25:30 +1100

      Commit message:


	  
		
 fixed binding note, .data$
 

    

  
    

      Package: Damsel

      Commit: f09c60c5f6c0ac8071e7a1458a8bf3897142354f

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-24 14:55:50 +1100

      Commit message:


	  
		
 fixed bug - will now plot a region without any exons
 

    

  
    

      Package: Damsel

      Commit: 812cb5ff234bd5ed1e07ae8c49dc745b0bc3b15f

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-24 14:55:17 +1100

      Commit message:


	  
		
 tidied up y axis so less cluttered
 

    

  
    

      Package: Damsel

      Commit: 0d02ec6e8e31aaf60a1e47f65357b9a9f4a40277

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-24 09:10:49 +1100

      Commit message:


	  
		
 fix filter
 

    

  
    

      Package: Damsel

      Commit: 32dc29a84d5770f3d45da1b591489158231668e2

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-23 16:53:19 +1100

      Commit message:


	  
		
 remove non-significant tiny peaks
 

    

  
    

      Package: Damsel

      Commit: d9829cac6cbffedb57bf6329fb902a0fee47e977

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-22 17:35:21 +1100

      Commit message:


	  
		
 update to 0.4.0 - with new ranking, counts etc
 

    

  
    

      Package: Damsel

      Commit: f8ca7f004ce4d62a50a0bd20f18892c452e535e7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-22 17:35:00 +1100

      Commit message:


	  
		
 update details on ranking
 

    

  
    

      Package: Damsel

      Commit: 06c19d975ae8f59781b062281d3fe7def651d042

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-22 17:34:18 +1100

      Commit message:


	  
		
 minor update
 

    

  
    

      Package: Damsel

      Commit: 17ffbc83ef7d2d86d766a472c7ac13fe0509a170

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-21 09:40:34 +1100

      Commit message:


	  
		
 minor updates to reflect changes
 

    

  
    

      Package: Damsel

      Commit: 02a9088799b979ae98e06fe7b88297d1f0fca7a7

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-21 09:39:27 +1100

      Commit message:


	  
		
 combined arguments into 1 - it then identifies if it's a bsgenome or a fasta file
 

    

  
    

      Package: Damsel

      Commit: e63074ecbc9cdb6bab25a8117ad42076eaa7b245

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-21 09:38:46 +1100

      Commit message:


	  
		
 added parameter to filter out excessively large regions from analysis - not very useful results wise
 

    

  
    

      Package: Damsel

      Commit: afe980e0bad92ca5dbf12df3209ab4197fcded35

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-21 09:34:17 +1100

      Commit message:


	  
		
 Major update, using featureCounts to get data instead of exomeCopy - believe more accurate and also allows for separation of paired end vs non paired end bams
 

    

  
    

      Package: Damsel

      Commit: a0330d594fa2e4f4c975e0c49641257868c33495

      Author:  Caitlin Page <caitlin.page@petermac.org> 

      Date: 2023-11-16 10:20:25 +1100

      Commit message:


	  
		
 update - v0.3.1
 

    

  
    

      Package: canceR

      Commit: 063e3203ab9af11e5fe80260210c7e21cfe28990

      Author:  kmezhoud <kmezhoud@gmail.com> 

      Date: 2026-09-08 16:03:50 +0100

      Commit message:


	  
		
 \usage without \alias in Rd file 'dialogSpecificMut.Rd'
 

    

  
    

      Package: MAGAR

      Commit: 4186d360b75652d6ccb825c45bd13b37bc028c72

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-09-08 18:59:37 +0200

      Commit message:


	  
		
 Added link to de.NBI survey
 

    

  
    

      Package: MAGAR

      Commit: c97e731ee9943572e8662254514da95b6f66761b

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-09-08 18:57:10 +0200

      Commit message:


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

    

  
    

      Package: MAGAR

      Commit: 5930fc0b93a854fdcfa0a78190fe58968d2da636

      Author:  Michael Scherer <michael.scherer@dkfz.de> 

      Date: 2026-09-08 18:56:44 +0200

      Commit message:


	  
		
 Removed UpSetR
 

    

  
    

      Package: consICA

      Commit: f0ed2665ed0886f9799ba21d0146906493e7ea94

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-09-08 16:36:08 +0200

      Commit message:


	  
		
 [R][consICA] reproducible seed via BiocParallel RNGseed + bump 2.11.2
 

    

  
    

      Package: consICA

      Commit: d8b3d44214c134957230f13fc5db6196aa2251ed

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-07-28 14:47:50 +0200

      Commit message:


	  
		
 [tests] add seed test for reproducibility
 

    

  
    

      Package: consICA

      Commit: 925d17a512d8998caf012946c07deb419c76c9ab

      Author:  Maryna Chepeleva <maryna.chepeleva@gmail.com> 

      Date: 2026-07-28 14:46:24 +0200

      Commit message:


	  
		
 [R][consICA] add seed param for reproducible parallel calculations
 

    

  
    

      Package: universalmotif

      Commit: d72a77eadc9ff8c9c4fc5b8d32d02ec84548a567

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-08 13:33:14 +0100

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: universalmotif

      Commit: 62b686d0543967b9db0810df28cb0ef95eca5436

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-08 13:32:58 +0100

      Commit message:


	  
		
 docs: record recent bug fixes in NEWS
 

    

  
    

      Package: universalmotif

      Commit: 9313772a0504e08d94a73710465fedb089c4d7cd

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-08 12:59:41 +0100

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: universalmotif

      Commit: 6d9558dbce6eaf6432f1f43a3ee683f1901e21f7

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-08 12:58:57 +0100

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/master'
 

    

  
    

      Package: universalmotif

      Commit: 7b44b80ca0898a775be525c9359a5a04dc34b11b

      Author:  Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com> 

      Date: 2026-09-08 12:14:25 +0100

      Commit message:


	  
		
 Merge pull request #33 from snystrom/master

Correct contributor name 

    

  
    

      Package: universalmotif

      Commit: 7088a1d75024a449df9b9dcfd64d57d15b2b021c

      Author:  Sabrina Nystrom <snystrom@users.noreply.github.com> 

      Date: 2026-09-07 20:42:17 -0700

      Commit message:


	  
		
 Correct contributor name.
 

    

  
    

      Package: universalmotif

      Commit: c9444c65f2a0be5821a4dba9b23893882d44a103

      Author:  bjmt <benjmtremblay@gmail.com> 

      Date: 2026-09-05 09:07:53 +0100

      Commit message:


	  
		
 fix: correct motif scanning and validation edge cases
 

    

  
    

      Package: cellmig

      Commit: 1aaaacc148d17dbd15a1d3ed2a8be6a5188cf72c

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-08 13:52:23 +0200

      Commit message:


	  
		
 int [x] array [x]
 

    

  
    

      Package: cellmig

      Commit: 0fb1d1d126f39792d04475c648f0a7039f9b0b59

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-08 13:51:58 +0200

      Commit message:


	  
		
 updated citation file
 

    

  
    

      Package: cellmig

      Commit: 522f2ccf5b746726ae930d3271fbcefda0f8c49a

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-09-08 13:51:47 +0200

      Commit message:


	  
		
 bump
 

    

  
    

      Package: HiCaptuRe

      Commit: 168e2c34d629627ae10b3d07df6b7f9d7c419083

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-08 12:05:31 +0200

      Commit message:


	  
		
 Correct S4 transformation to tibble
Update some notes with seq_len and typos correction
Version bump
 

    

  
    

      Package: lcmsPlot

      Commit: 5e974f55c7caa78180fb5655657e2f44599d25aa

      Author:  Ossama Edbali <ossedb@gmail.com> 

      Date: 2026-09-07 13:18:20 +0100

      Commit message:


	  
		
 feat(compound-discoverer): support filtering on the Checked column

Compound Discoverer's per-compound Checked box is how analysts curate a
result set by hand, but there was no way to act on it from lcmsPlot.
`compounds_query` can now reference a `checked` column, so a curated
selection can be plotted with `lp_compound_discoverer(compounds_query =
"checked")`.
 

    

  
    

      Package: PostChicago

      Commit: bf45d2c20553f5c89648058e3f31db169aa5bb01

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-08 10:46:23 +0200

      Commit message:


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

    

  
    

      Package: PostChicago

      Commit: f9b79ce6db58dc39cd369b6a5b0b4aa550cecea7

      Author:  Angelika Feldmann <angelika.feldmann@dkfz-heidelberg.de> 

      Date: 2026-09-06 17:27:56 +0200

      Commit message:


	  
		
 Add files via upload 

    

  
    

      Package: PostChicago

      Commit: 5adfbc872ef577d4905808844b178ef084efd1cd

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:26:32 +0200

      Commit message:


	  
		
 Delete NEWS.md 

    

  
    

      Package: PostChicago

      Commit: f87dd938d3fc44a8ea1b2e43c660f8842499bb63

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:26:23 +0200

      Commit message:


	  
		
 Delete NAMESPACE 

    

  
    

      Package: PostChicago

      Commit: 84d168954d634a16ee8278825492ed756a2ab26f

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:26:15 +0200

      Commit message:


	  
		
 Delete DESCRIPTION 

    

  
    

      Package: PostChicago

      Commit: 35bc29e74a2d1a4da3a8ced86144c9cac4e01b10

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:26:05 +0200

      Commit message:


	  
		
 Delete vignettes directory 

    

  
    

      Package: PostChicago

      Commit: 5bfd2c6684c450f67f1c540363c88b392317ce62

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:25:55 +0200

      Commit message:


	  
		
 Delete man directory 

    

  
    

      Package: PostChicago

      Commit: fa80cad9a88dfb10ccf3983dcb5e684b40422f32

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:25:46 +0200

      Commit message:


	  
		
 Delete inst/extdata directory 

    

  
    

      Package: PostChicago

      Commit: 1b9cec80c21e9078339a31eaf955f143fcdca699

      Author:  Angelika Feldmann <angifeldmann@gmail.com> 

      Date: 2026-09-06 17:25:28 +0200

      Commit message:


	  
		
 Delete R directory 

    

  
    

      Package: LipidTrend

      Commit: 49294b2a653ca85ef4d3108533fa0173ed89aa30

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:36:05 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: fec0fa74948e33bdaeab898803c3064b1b360a91

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:35:47 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: 13c4963f0008344915953709f55fed46836109d0

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:35:29 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: 7264deacf392d02c2e986ae27d87ac2b61f71941

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:35:05 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: 0a29f384421ec5e96cac09aecf8ab88e46eee6fe

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:34:38 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: 56586100f31c549ff1a655952a115301a6008cdd

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:34:11 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: LipidTrend

      Commit: 7aecd64f417d3d20d01e16fd689ef2e4317b5a49

      Author:  hcliu <hcliu@localhost.localdomain> 

      Date: 2026-09-08 16:33:37 +0800

      Commit message:


	  
		
 Add files via upload
 

    

  
    

      Package: UCell

      Commit: f778e091f19e28d3d05bde134663fd6b2f938267

      Author:  Massimo Andreatta <massimo.andreatta@unil.ch> 

      Date: 2026-09-08 10:12:39 +0200

      Commit message:


	  
		
 Add tests. Default to SerialParam()
 

    

  
    

      Package: UCell

      Commit: 08209e4cedc97fb2510029ae1c3bb8b7c09e6f1c

      Author:  Benjamin Demaille <benjamin.demaille@icloud.com> 

      Date: 2026-08-30 22:58:02 +0200

      Commit message:


	  
		
 Accept any matrix-like input, not a fixed list of classes

ScoreSignatures_UCell() and StoreRankings_UCell() gate their input on an
explicit class list (matrix, dgCMatrix, data.frame) and reject everything
else with "Unrecognized input format." That list has fallen behind the
ecosystem: a DelayedMatrix (DelayedArray/HDF5Array), an HDF5Matrix, a
BPCells IterableMatrix or even a dense dgeMatrix is refused.

The refusal is not a real limitation. calculate_Uscore() already begins by
coercing anything that is not a dgCMatrix, so the engine handles these
inputs; only the gate rejects them. Test the capability instead: accept any
object with a length-2 dim().

Two supporting changes:

- Coerce via as(x, "dgCMatrix") when a method exists, falling back to the
  previous dense route otherwise. Out-of-core backends implement the sparse
  coercion directly, so admitting them no longer implies materializing a
  dense intermediate first. Results are unchanged for existing input types.
- A Seurat object now gets a pointed error naming AddModuleScore_UCell()
  (or LayerData()) rather than the generic "Unrecognized input format".

UCell has no test directory today, so this adds the minimal testthat
scaffolding along with the cases for the change; happy to drop it if you
would rather keep the package without tests. Against master those tests
report 2 failures and 2 errors; with this change all 13 pass.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: alabaster.mae

      Commit: dc576429ed7cfdabc252cef189da051e237cfc55

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-08 17:32:44 +1000

      Commit message:


	  
		
 Streamlined the README by referencing the BioC landing page.
 

    

  
    

      Package: alabaster.files

      Commit: 53a145b9c94fb6f692343f3f4a97a5fa596cef4c

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-08 17:30:28 +1000

      Commit message:


	  
		
 Streamlined the README by referencing the BioC landing page.
 

    

  
    

      Package: epiSeeker

      Commit: d85262c1264782751db2c8a1182ea26117817e2a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-08 10:34:51 +0800

      Commit message:


	  
		
 fixed r check
 

    

  
    

      Package: epiSeeker

      Commit: af8d8805c3d25a53a76bb5e15e209340b81b9714

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 23:00:56 +0800

      Commit message:


	  
		
 Merge pull request #4 from MingLi-929/devel

fix: preserve tag matrix window order 

    

  
    

      Package: epiSeeker

      Commit: 465a5778c9601574a0f4f712341b62fb576e85c8

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 22:46:27 +0800

      Commit message:


	  
		
 Remove unused utils::data import

utils::data is only ever called fully-qualified (utils::data(...) in R/GEO.R),
so the import is dead. Dropping it for consistency with ChIPseeker and to
avoid the BiocGenerics::data conflict once BiocGenerics exports data as a
generic.
 

    

  
    

      Package: epiSeeker

      Commit: 54a0aa4b5aeeeb3fbbe729adbed6beab8fd60863

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 22:41:15 +0800

      Commit message:


	  
		
 migrate documentation build to roxygen2 8.1.0

Regenerate Rd pages and NAMESPACE with roxygen2 8.1.0 (previously
8.0.0). 8.1.0 requires @aliases to be a single logical line, so the
csAnno class @aliases is collapsed onto one line.

NAMESPACE is semantically identical to before: the exported API
(unexport of functions/methods/classes) and the importFrom set are
unchanged; only the formatting of importFrom directives differs.

R CMD check: no new errors or warnings. The remaining WARNINGs are
pre-existing (upsetplot generics codoc mismatch) or environment-related
(vignette build skipped, non-ASCII data), not introduced here.
Add the build artifacts (epiSeeker.Rcheck/, epiSeeker*.tar.gz) to
.gitignore.
 

    

  
    

      Package: epiSeeker

      Commit: ab6f05062211b1ac965f8fbfcffee902c39d26fc

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 22:33:49 +0800

      Commit message:


	  
		
 fix getNearestFeatureIndicesAndDistances overlap="all" bug

Port the bug fix from ChIPseeker (YuLab-SMU/ChIPseeker#267): in
getNearestFeatureIndicesAndDistances(), the findOverlaps() +
distanceToTSS <- 0 block ran unconditionally at the end of the
!ignoreOverlap block, silently overriding the overlap=="all" result
with the overlap=="TSS" behaviour. Wrap the TSS handling in an else
branch so overlap="all" returns the true distance to the TSS.

Also carry over the equivalent seq2gene() refactor (merge the promoter
and flanking-gene extraction into one condition; no behaviour change).

Verified: for a peak spanning the TSS, overlap="TSS" gives distance 0
and overlap="all" now gives -20 (previously both gave 0).
 

    

  
    

      Package: epiSeeker

      Commit: 87be6ee97daa524acb9b049ad15a2fed2aa6bde0

      Author:  mingli <mingli@minglideMacBook-Pro.local> 

      Date: 2026-09-06 20:53:32 +0800

      Commit message:


	  
		
 fix: preserve tag matrix window order
 

    

  
    

      Package: ChIPseeker

      Commit: d67bc47df8ba121607cd6313b8def40cf8973238

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-08 10:18:27 +0800

      Commit message:


	  
		
 fixed r check
 

    

  
    

      Package: ChIPseeker

      Commit: dc6d55af9c27979a81aba99e9ec89a83ec398478

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 23:05:41 +0800

      Commit message:


	  
		
 Merge pull request #270 from MingLi-929/devel

fix: preserve tag matrix window order

Resolve conflict between PR #267 (docs/@noRd on tagMatrix.R) and PR #270:
keep the PR #270 code fix (idx.list indexed by chr.idx so window order is
preserved, and idx.list maintained through the binning filter + final
reorder) while retaining PR #267's documentation/@noRd changes.

Fix for issue #236: getTagMatrix window order was determined by chromosome
factor order (do.call("c", idx.list)) instead of the chr.idx order used
when building the tag matrix, so windows could be reordered incorrectly.

Regression test (test-getTagMatrix.R) passes: 22 tests, 0 failures.
 

    

  
    

      Package: ChIPseeker

      Commit: 866e4d7e55703e90aacd8f3aae5e8ea8612adb77

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 16:51:37 +0800

      Commit message:


	  
		
 Remove unused utils::data import

utils::data is only ever called fully-qualified (utils::data(...) in R/GEO.R),
so the import is dead. Newer BiocGenerics exports data as a generic, so
importing both triggers the load warning:
  replacing previous import 'BiocGenerics::data' by 'utils::data'

Addresses #269.
 

    

  
    

      Package: ChIPseeker

      Commit: 78c6f7fb046d770ffd228270cd6a0e3416026b12

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 16:42:10 +0800

      Commit message:


	  
		
 Merge pull request #267 from haibol2016/devel

update documentation and fix one bug 

    

  
    

      Package: ChIPseeker

      Commit: 7f218f9444b5f308d4e9d127b42a966e6806e940

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-09-07 16:28:53 +0800

      Commit message:


	  
		
 Merge ChIPseeker PR #267 (docs + getNearestFeatureIndicesAndDistances bug fix)

Integrate haibol2016's contribution (github.com/YuLab-SMU/ChIPseeker/pull/267):

* Fix a real bug in getNearestFeatureIndicesAndDistances(): the
  overlap=="all" result was silently overridden by the overlap=="TSS"
  branch because findOverlaps()+distanceToTSS<-0 ran unconditionally
  at the end of the !ignoreOverlap block. Wrapped the TSS handling in
  an else branch so overlap="all" now returns the true distance-to-TSS.
  Verified with a head-to-head R test (all vs TSS gave identical 0 for a
  peak spanning the TSS before; "all" now gives -20).

* Rewrite/extend roxygen documentation for nearly every function (the
  bulk of the PR: +3400/-750 lines across 22 R files).

* Simplify redundant logic in seq2gene() (promoter + flanking-gene
  extraction merged into one equivalent condition; no behavior change).

* Add @noRd to ~58 internal (non-exported) helper functions and the
  S4 setMethod doc blocks, so roxygen no longer emits man pages for
  them (methods remain exported/registered and documented via the
  generic/class pages).

* Fix documentation issues surfaced by regenerating with roxygen2 8.1.0:
  - csAnno class @aliases must be a single line
  - removed duplicated @export/@importFrom on getTagMatrix
  - escaped bare '%' that broke Rd parsing (e.g. ylab "Percentage(%)")
  - replaced '±' with ASCII '+/-'
  - cross-ref \link[GenomicRanges]{subset} -> \link[base]{subset}
  - stripped trailing whitespace throughout the modified R files

* Regenerate man/*.Rd and NAMESPACE via devtools::document(); NAMESPACE
  is semantically identical to before (reformatted by roxygen 8.1.0).

R CMD check: 0 errors, 0 Rd/code/namespace warnings. The only 2
remaining WARNINGs are vignette-related and arise solely because the
check was run with --no-build-vignettes (BiocStyle not installed).
 

    

  
    

      Package: ChIPseeker

      Commit: ccd4b949a64bf348bb33d636530066cf95cca8e7

      Author:  mingli <mingli@minglideMacBook-Pro.local> 

      Date: 2026-09-06 20:53:32 +0800

      Commit message:


	  
		
 fix: preserve tag matrix window order
 

    

  
    

      Package: ChIPseeker

      Commit: c1f4a507f22679776fe4e184032461360dc3da3f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2026-04-29 11:31:56 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: AlphaMissenseR

      Commit: 05995a078e297461d257cf2a0fca52f38866de48

      Author:  Martin Morgan <mtmorgan.xyz@gmail.com> 

      Date: 2026-09-07 18:55:14 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: AlphaMissenseR

      Commit: f2638c81d2063a57c1646a076d9ee48ef64df65b

      Author:  Martin Morgan <mtmorgan.xyz@gmail.com> 

      Date: 2026-09-07 18:54:46 -0400

      Commit message:


	  
		
 update roxygen to 8.1.0
 

    

  
    

      Package: AlphaMissenseR

      Commit: d74ed63578cea2b8d419d5cf5ccb4a782fa2bd41

      Author:  Martin Morgan <mtmorgan.xyz@gmail.com> 

      Date: 2026-09-07 18:53:39 -0400

      Commit message:


	  
		
 avoid duckdb message about secrets and extensions location breaking unit test
 

    

  
    

      Package: TPP

      Commit: 84f37ada2ed0252ec09feeb2f568191be1d49e3d

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-07 21:20:55 +0200

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: TPP

      Commit: 3a7da9454c8d4259f1e5910dfd7eba8eddaf0fca

      Author:  Dorothee Childs <childs@embl.de> 

      Date: 2026-09-07 20:28:41 +0200

      Commit message:


	  
		
 Replace deprecated biobroom ExpressionSet tidying with internal helper
 

    

  
    

      Package: MetaboDynamics

      Commit: 2ac1f214bc52ca77f7253fc80154c17434f6128a

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-09-07 15:43:27 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: 02daa5cc0d7e5a768d639dad2fe5d3c5ece0bf6b

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-09-07 15:42:54 +0200

      Commit message:


	  
		
 stan files updates to new rstan version
 

    

  
    

      Package: MetaboDynamics

      Commit: abf678df71b52f76e7e04a9b11019ff2d3669ed8

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-09-07 15:42:42 +0200

      Commit message:


	  
		
 stan files updates to new rstan version
 

    

  
    

      Package: terapadog

      Commit: 0aaebe9b0a33adfe34efb2f0ec502faa2ff1dbd3

      Author:  gionmattia <gionmattia@gmail.com> 

      Date: 2026-09-07 13:24:29 +0100

      Commit message:


	  
		
 v_bump
 

    

  
    

      Package: terapadog

      Commit: 3ee4c690f60ab80ec0d3c7a36944ecaedd5918dc

      Author:  gionmattia <gionmattia@gmail.com> 

      Date: 2026-09-07 13:11:09 +0100

      Commit message:


	  
		
 polished_viz
 

    

  
    

      Package: HiCaptuRe

      Commit: 2d2ea13005c4b6fa22a59641fc19e4a3baa8f120

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-07 11:42:49 +0200

      Commit message:


	  
		
 update package and version bump
 

    

  
    

      Package: HiCaptuRe

      Commit: fa67a8764c4e77f6e6877b3006d1e0d0fe4da421

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-07 11:34:06 +0200

      Commit message:


	  
		
 vignette update
 

    

  
    

      Package: HiCaptuRe

      Commit: f8a716d80a9ce08c8226743d30970d93ee9c88a1

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-07 11:28:11 +0200

      Commit message:


	  
		
 typo
 

    

  
    

      Package: HiCaptuRe

      Commit: 2c627ab017a8546b5a57c787b0f86206752e4d7e

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-07 11:26:16 +0200

      Commit message:


	  
		
 update export_interactions doc
 

    

  
    

      Package: HiCaptuRe

      Commit: 0832dcd0b585b282b920a7e1f75c882f6760e7b1

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-09-07 11:21:19 +0200

      Commit message:


	  
		
 biginteract for UCSC added to export_interactions
 

    

  
    

      Package: HiCaptuRe

      Commit: 2177954a5a1e16052d9eaa899b83ba581b19ce38

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-08-24 14:00:37 +0200

      Commit message:


	  
		
 seqmonk process_function corrected
 

    

  
    

      Package: HiCaptuRe

      Commit: 3bf615eb65cf36ec3971336f1164f69726343dfb

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-08-24 12:57:06 +0200

      Commit message:


	  
		
 typo in washUold naming
 

    

  
    

      Package: HiCaptuRe

      Commit: 81850312944445f51f5018725aeff3230d27a1df

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2026-08-20 10:51:44 +0200

      Commit message:


	  
		
 unname Granges and interactions to avoid error in unique
 

    

  
    

      Package: ramr

      Commit: ea196b25946812c0d6b5a4f3bb017cbb28b91823

      Author:  Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no> 

      Date: 2026-09-07 11:34:57 +0200

      Commit message:


	  
		
 +doi
 

    

  
    

      Package: SpectraStash

      Commit: 2af246bd85c3c5b992fc2b36c681773e4fd8c2aa

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2026-09-07 07:49:01 +0200

      Commit message:


	  
		
 docs: add logo
 

    

  
    

      Package: growkar

      Commit: 6c1fa596975dd272f5d593c6c235f8fc6ded4348

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-09-07 11:46:56 +1000

      Commit message:


	  
		
 Fix vignette chunk guards that fail when the vignette is tangled

R CMD build weaves and tangles each vignette. Tangling does not evaluate
chunk code, so `eval = has_graphics`, whose flag was assigned in the setup
chunk, could not be resolved and the build reported

  Error in eval(x, envir = envir) : object 'has_graphics' not found

once per guarded chunk. Write the ggplot2 availability check inline in the
chunk options instead, so it resolves in both the woven and the tangled
pass, and drop the now unused flag from the setup chunk.

Bump to 0.99.4 so the change propagates on the Bioconductor build system.
 

    

  
    

      Package: growkar

      Commit: 1fbc71ed9c1b98c6b6547190e4fb6d033cae3b3e

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-08-24 12:20:04 +1000

      Commit message:


	  
		
 Re-render README with rmarkdown, not knitr

The previous commit regenerated README.md with knitr::knit(), which copies
non-chunk content through verbatim. That left the YAML header in the output,
which GitHub renders as a front-matter table at the top of the page, and it
hard-wrapped the text instead of honouring pandoc_args: --wrap=none.

Re-render through rmarkdown::render() so pandoc consumes the header, and
restore the original 1344x960 figures that the same bad render had rewritten
at 672x480. The plots themselves are unchanged.

 

    

  
    

      Package: growkar

      Commit: 2d8f7a44ba78e0320c2b629fb1b7ab4a37de2772

      Author:  Pooja Sethiya <poojasethiya24@gmail.com> 

      Date: 2026-08-24 12:09:34 +1000

      Commit message:


	  
		
 re-using available functionality implemented
 

    

  
    

      Package: HiCPotts

      Commit: 5d3f5d02a29a7a0c9a6b51d55dd2adbb8acf54d0

      Author:  Itunu <hitunes4@gmail.com> 

      Date: 2026-09-06 18:44:43 +0100

      Commit message:


	  
		
 Update HiCPotts to 1.3.1 and remove accuracy evidence file
 

    

  
    

      Package: HiCPotts

      Commit: 18875d8c7fc6eaf3145e9633494fbe07b2b23265

      Author:  Itunu <hitunes4@gmail.com> 

      Date: 2026-09-06 18:39:18 +0100

      Commit message:


	  
		
 Update HiCPotts to 1.3.1
 

    

  
    

      Package: SynMut

      Commit: 29d76e9e5d56c9cb3305722168578041f42a2069

      Author:  Haogao Gu <koohoko@gmail.com> 

      Date: 2026-09-05 21:12:07 -0400

      Commit message:


	  
		
 Bundle vignette flowchart for offline builds
 

    

  
    

      Package: edgeR

      Commit: db4e697f7a4badcc70ee3d7024412b14dca86706

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-06 22:22:19 +1000

      Commit message:


	  
		
 Update catchSalmonWithGencode() to catchSalmonGene() in NEWS.Rd
 

    

  
    

      Package: edgeR

      Commit: 1efc79ef4eca3b82789d00847b2f5732f84aaf1a

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2026-09-06 21:49:42 +1000

      Commit message:


	  
		
 edgeR 4.99.4
- New function catchSalmonGene(), similar to catchSalmonWithGencode() but can accept gene annotation as data.frame as well.
- New argument 'remove.version.numbers' for splitGencodeTxNames().
 

    

  
    

      Package: OmniAgeR

      Commit: 4f8684052b0d48885c0e437d8e3028e69616aa54

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-09-06 16:11:58 +0800

      Commit message:


	  
		
 Update sample data document update
 

    

  
    

      Package: OmniAgeRData

      Commit: bccd4a05027d8e4666d5af41ce59bc15433b443c

      Author:  Zhaozhen Du <duzhaozhen@inspur.com> 

      Date: 2026-09-06 16:08:07 +0800

      Commit message:


	  
		
 Complete data package documentation updates
 

    

  
    

      Package: scp

      Commit: ef4428653931d45604042a8df44c979a6464b192

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-09-06 09:27:52 +0200

      Commit message:


	  
		
 aggreagateFeaturesOverAssays() is now defunct
 

    

  
    

      Package: scp

      Commit: a657fc087d544f5908492107585a99e6537036b0

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-08-28 13:44:16 +0200

      Commit message:


	  
		
 fix link syntax
 

    

  
    

      Package: scp

      Commit: 9a84afce689fd68863d5bb45780d57687b3dbe8d

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-07-23 13:19:30 +0200

      Commit message:


	  
		
 rm old workflow
 

    

  
    

      Package: scp

      Commit: 5b02b3d2a25b3b977abb8c3764e1f4638df4da71

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-07-23 13:18:14 +0200

      Commit message:


	  
		
 add ref in readme
 

    

  
    

      Package: scp

      Commit: 29c722630d68ff3fed88c8f56002d12b1d3adf65

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-07-23 13:13:14 +0200

      Commit message:


	  
		
 Merge branch 'devel'
 

    

  
    

      Package: scp

      Commit: 5a3e230dfbd85ade1d20962a833dc1d62e88efbd

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-06 21:26:43 +0200

      Commit message:


	  
		
 use other workflow
 

    

  
    

      Package: scp

      Commit: 617bc8f43af8eec58c72f092facff1d799f8d5c5

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-06 20:46:20 +0200

      Commit message:


	  
		
 ignore RELEASE branches
 

    

  
    

      Package: scp

      Commit: 103f459998e472ce070923a18cfe5ee3fe789bb6

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2026-04-06 20:34:05 +0200

      Commit message:


	  
		
 update gha
 

    

  
    

      Package: alabaster.base

      Commit: 6b6157efc1d7dd429b2495f2f60f0d1ca692042f

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-06 12:39:18 +1000

      Commit message:


	  
		
 Generalize search for alabaster.string to all XStringSet objects.
 

    

  
    

      Package: alabaster.string

      Commit: e0c54c8f50a41e7f21155b473b0840404eac10bb

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-06 12:38:19 +1000

      Commit message:


	  
		
 Bumped version and date, streamlined README, fixed license.
 

    

  
    

      Package: alabaster.string

      Commit: b83bd38f9b5092f54d0db7ed9c925c2f918b3593

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2026-09-06 12:37:15 +1000

      Commit message:


	  
		
 Officially deprecate all functions for stageObject/loadObject.

Also fixed docs to reference the package name when linking external functions.
 

    

  
    

      Package: tidybulk

      Commit: fa381063a6c959cff52eafd4cb759cc11cb95c2f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-06 11:51:27 +1000

      Commit message:


	  
		
 Merge pull request #347 from tidyomics/dispersion_estimation

Dispersion estimation 

    

  
    

      Package: tidybulk

      Commit: 7002727d0453f89f65c629f3e8082d582f76761d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-06 06:25:40 +1000

      Commit message:


	  
		
 Merge branch 'master' into dispersion_estimation 

    

  
    

      Package: tidybulk

      Commit: 7f34e9d2fd5691f4b79e3250060c81c970cea437

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-06 06:24:56 +1000

      Commit message:


	  
		
 Merge pull request #348 from tidyomics/fix/granges-as-tibble-ci

Fix aggregate_duplicates GRanges CI failure on Bioconductor devel 

    

  
    

      Package: tidybulk

      Commit: 126e970f6a5dd61eccd74981fea77b32d6e19256

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:59:49 +1000

      Commit message:


	  
		
 Update documentation for differential abundance methods to clarify usage of `formula_dispersion` and remove deprecated parameters. Adjust examples and descriptions for consistency across methods.
 

    

  
    

      Package: tidybulk

      Commit: 1d5af8f700f9bb7b60abf5dd904fae83ea3242ed

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:31:01 +1000

      Commit message:


	  
		
 Enhance glmmTMBcore function to utilize fixed edgeR phi for dispersion estimation, ensuring consistent parameter handling across gene models.
 

    

  
    

      Package: tidybulk

      Commit: 2d7ad84c5179fe20b3ffdd20ce1c34a69594c09f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:26:13 +1000

      Commit message:


	  
		
 Add informative messages for dispersion calculations.
 

    

  
    

      Package: tidybulk

      Commit: ad2b8fe02bbdc304d82bd72f1b87d8410d163ab1

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:22:07 +1000

      Commit message:


	  
		
 Merge branch 'dispersion_estimation' of https://github.com/tidyomics/tidybulk into dispersion_estimation
 

    

  
    

      Package: tidybulk

      Commit: e66e2d54a0ccba197f29a20645f9c4431b1eb1e7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:22:05 +1000

      Commit message:


	  
		
 Update estimate_dispersion to enforce fixed-effects formula usage and improve error handling.
 

    

  
    

      Package: tidybulk

      Commit: 0de28a01b606eba715160903ed813af075a85041

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:06:08 +1000

      Commit message:


	  
		
 Fix aggregate_duplicates GRanges conversion on Bioconductor devel.

as_tibble() on GRanges now hits broken S4Vectors List dispatch; convert via as.data.frame() first so ubuntu CI passes.

Co-authored-by: Cursor <cursoragent@cursor.com>
 

    

  
    

      Package: tidybulk

      Commit: 49e1c03466125170ff4fe07e23ee5625b271fcae

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-05 14:04:45 +1000

      Commit message:


	  
		
 Merge branch 'master' into dispersion_estimation 

    

  
    

      Package: tidybulk

      Commit: 47e46bd68df7f019faad0a8420739708d3bad270

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-02 19:28:47 +0930

      Commit message:


	  
		
 add dependencies
 

    

  
    

      Package: tidybulk

      Commit: b568a4b8d1607a7e4059156457414ce2fa85baa7

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-02 18:16:43 +0930

      Commit message:


	  
		
 Refactor glmmSeq to estimate tagwise dispersion keeping the random effects as fix effects.
 

    

  
    

      Package: tidybulk

      Commit: f77671fd9400c8594caa72d8772c7b68bfbdeb2b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-01 13:27:01 +0930

      Commit message:


	  
		
 update dev directory
 

    

  
    

      Package: tidybulk

      Commit: 1b5767948e048fc3d852edbbf9de71223c8b3606

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-09-01 13:26:40 +0930

      Commit message:


	  
		
 Reeplace deprecated edgeR::calcNormFactors() with edgeR::normLibSizes() across scaling and differential abundance methods, and document changes in NEWS.rd.
 

    

  
    

      Package: tidybulk

      Commit: b7d302d826033d469632d6a7bde2ec7d8d8be0be

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-31 13:25:55 +0930

      Commit message:


	  
		
 add check for identify abundant
 

    

  
    

      Package: tidybulk

      Commit: ed4e85e6fbd904399e9e446574204ee26be8b447

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-08-24 17:26:28 +0930

      Commit message:


	  
		
 Enhance estimate_dispersion function to include trended dispersion and update documentation. The function now writes three columns: tagwise dispersion (dispersion_shrinked), trended dispersion (dispersion_trended), and effective degrees of freedom to rowData. Adjusted tests to reflect these changes.
 

    

  
  


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