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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: h5mread
Commit: 6ead8d5cee6fe373aca041d0e1b6b18f6a196641
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-21 06:30:37 -0800
Commit message:

 h5mread 1.3.1: Add example of how to use an H5File with the rhdf5 package
Package: MetaProViz
Commit: b8ff4f3c048f8bd7678ae66fdf9e844b609da94d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 13:04:04 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/MetaProViz into devel
Package: MetaProViz
Commit: a09a5e805c7e0f9291695b7505f562a13360cc3f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:59 +0100
Commit message:

 Bump version: 3.99.26 → 3.99.27
Package: MetaProViz
Commit: 9f40e2ed40107cd92409b8308c248aaec9710fef
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:30 +0100
Commit message:

 Revert "Merge branch 'bioc-submission' into devel"

This reverts commit c2bbb6f3395209c0832a684b617c8b693393de57, reversing
changes made to 314373acda1efeae23cdc66dd33e9c28028a5e08.
Package: MetaProViz
Commit: c2bbb6f3395209c0832a684b617c8b693393de57
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:16 +0100
Commit message:

 Merge branch 'bioc-submission' into devel
Package: MetaProViz
Commit: 314373acda1efeae23cdc66dd33e9c28028a5e08
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:10:45 +0100
Commit message:

 license update in `DESCRIPTION`: GPLv3 → BSD 3-clause
Package: MetaProViz
Commit: fa7e1b729f9b2ff444aa8fc14b512a6db8e9e27f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 15:24:15 +0100
Commit message:

 Bump version: 3.99.25 → 3.99.26
Package: MetaProViz
Commit: ca98fa8e405ffde44cd993e5502d245b528b81de
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 15:24:03 +0100
Commit message:

 license update: GPLv3 → BSD 3-clause
Package: MetaProViz
Commit: aea083231c0cc15255b211bfc5d5b2d5dcc4d478
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 14:41:39 +0000
Commit message:

 handling BioC NOTE: not using paste in conditional statements
Package: MetaProViz
Commit: 57bcb6933fbed3fc30a6d42304581a2f8f4d6c90
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 14:25:53 +0100
Commit message:

 Bump version: 3.99.24 → 3.99.25
Package: MetaProViz
Commit: f30899cfaa71272da069c567de3228354f4488e8
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 13:46:57 +0000
Commit message:

 NA handling for metabolites without assigned pathways
Package: MetaProViz
Commit: c51796fc82d9a38a2e361775349d375a70006dfb
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 13:30:31 +0000
Commit message:

 added and fixed VizVolcano plotting in case of nrow(Inputvolcano) = 0
Package: MetaProViz
Commit: b17e8a14ebdfd1012402ea5ea7d5fe0bbefbdf60
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 11:33:49 +0000
Commit message:

 changed block eval to TRUE
Package: MetaProViz
Commit: 45c856914833fa1ec982ae65fdaa94c55d2fb705
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 11:01:30 +0000
Commit message:

 disabled upset_plot plotting
Package: MetaProViz
Commit: 0ca71e3e401470ff60edd58ac4004ea3bcb1cf36
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:38:56 +0000
Commit message:

 wrapped second viz_upset in tryCatch block
Package: MetaProViz
Commit: 826e55e8bf2b6aa98fba489f90d2a1a71fa8907d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:12:58 +0000
Commit message:

 enabled block eval and fixed data load
Package: MetaProViz
Commit: fdb661ae4f6197a9352c3c62b04ca6b725c31a13
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:12:09 +0000
Commit message:

 wrapped viz_upset in tryCatch
Package: MetaProViz
Commit: 66571d97c9c4198a7d583cf99cd9a605bc822db1
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-19 17:23:13 +0000
Commit message:

 added variable declaration in VizVolcano and reordered denominator-numerator naming
Package: MetaProViz
Commit: 33c3f170d7ce5bff1562010e21e27a2c1341af76
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 19:34:35 +0100
Commit message:

 well, the bioc container's tag is `latest`
Package: MetaProViz
Commit: d8981cb060eb33b099eded4ff3d7d8e5221c17b7
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 19:27:03 +0100
Commit message:

 pkgdown action: run on `bionconductor:release` container + added some custom pkg installation steps, not sure all necessary
Package: MetaProViz
Commit: 20872ced418e739b94b2d2964dfcdfc38d2e1d47
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:37:49 +0100
Commit message:

 Merge branch 'devel'
Package: MetaProViz
Commit: 8fdde5a79b1d1e2b0074c98d32add69a4347327f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:37:41 +0100
Commit message:

 Bump version: 3.99.23 → 3.99.24
Package: MetaProViz
Commit: bcb268f17c8d5576d89762c63ad9868bae0686a1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:57 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 288559a266402cbb427f91599f5ab1638c28d68b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:46 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 352057fc69e53430665d953b42800af92333d63f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:38 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: d5306d9fd0024870695ff8f632e1190d561b6e17
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 16:52:37 +0000
Commit message:

 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
Package: MetaProViz
Commit: aa92f1da7d8fee5e74fd433989877849dbcffb8d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 16:51:22 +0000
Commit message:

 mca_core example issue
Package: MetaProViz
Commit: b41b5779c8c6038483a3fdac97c461a5c2ca0a08
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 15:19:12 +0000
Commit message:

 make_gene_metab_set folder and subfolder handling logic for different input combinations
Package: MetaProViz
Commit: 72c9bda388b0821234d084cbf951ec8d52364b67
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:44:22 +0100
Commit message:

 added claude notes & instructions
Package: MetaProViz
Commit: db17bad8d3984a8d895f28a792f33c1e66c5eff8
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:25:42 +0000
Commit message:

 typo
Package: MetaProViz
Commit: 3560f1b63f59815e0ee5a2f65b4ca419af2f99ef
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:21:48 +0100
Commit message:

 Bump version: 3.99.22 → 3.99.23
Package: MetaProViz
Commit: 11430b0e67f7220ec1c9cfd90a36eb6e973cd690
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:21:37 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: f2595c9d4324fcf0c0a95bb780ddf626e1b4371d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:18:42 +0000
Commit message:

 fixed ALL other missing magrittr function in roxygen strings and added double colon magrittr:: calls
Package: MetaProViz
Commit: 584c02a0da778aefae293c4fc668bcfd034ce491
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:04:11 +0000
Commit message:

 fixed missing magrittr function in roxygen strind and added double colon magrittr:: call
Package: MetaProViz
Commit: 444f241d66b63fd2a246b992145b5144035ae89d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:49:26 +0000
Commit message:

 fix viz_volcano() metadata_info bool check logic
Package: MetaProViz
Commit: 3da8ae5b6aa67bbd22693b04615f32168ea0ac1c
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:38:21 +0000
Commit message:

 fixing logical values stored as stirings in ORA
Package: MetaProViz
Commit: 57f0156cc3a995f1394958bae787da39cd466077
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:31:05 +0000
Commit message:

 simplify ORA top/bottom logical check
Package: MetaProViz
Commit: 8a1e8793ff7ce591f6a5a936da46d63266bb99e2
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:21:54 +0000
Commit message:

 Fix ORA top/bottom logical check
Package: MetaProViz
Commit: 5bab062598b2326ce76b4276537005e15d60bfff
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:12:54 +0000
Commit message:

 Fix ORA case_when
Package: MetaProViz
Commit: 73fcf3ac3da99980effd554e3c8212ea91533f9e
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:06:13 +0000
Commit message:

 Fix processing() outlier merge pipe
Package: MetaProViz
Commit: 92153d5a2e4391e6f19b83a9bafd27ebf702bdfd
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 12:59:38 +0000
Commit message:

 fixed missing pipe assignment
Package: MetaProViz
Commit: 97345461653d8bbeaa36b3ef778a874908d2553d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 11:18:33 +0000
Commit message:

 fixed processing() error, non-connected pipe
Package: MetaProViz
Commit: c61dffc6e0118f2795e0f3bb8221452895719d75
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 10:53:26 +0000
Commit message:

 fixed featurefilt check of processing() call
Package: MetaProViz
Commit: e83fcb4ee4abe011c9192dfc665106803b0bb067
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:56:07 +0100
Commit message:

 Bump version: 3.99.21 → 3.99.22
Package: MetaProViz
Commit: 11f0f9be9ce84e3122dd54f760727ed30be5877a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:56:02 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 305cc6e9be53e6fa4748fc64021a83f5f039c6cf
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:55:47 +0100
Commit message:

 long lines in docstring examples
Package: MetaProViz
Commit: f14719f28b7b15d37048e071386f6c0bac667707
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 18:13:55 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: c958f8487a4178e91478f6aae35d03d22d93edc2
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:33 +0100
Commit message:

 Bump version: 3.99.20 → 3.99.21
Package: MetaProViz
Commit: 75a6c40cf08f4069a175e8bf53faf2db538be254
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-04 12:57:45 +0100
Commit message:

 Bump version: 3.99.19 → 3.99.20
Package: MetaProViz
Commit: 75fbbe72c6259099344422d282c28bc41b077857
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:20 +0100
Commit message:

 enabled doctests of small infrastructure functions
Package: MetaProViz
Commit: edf96d6e0431f4ce4116bc3a7ccdb16cbacd4bd5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:45:48 +0100
Commit message:

 Bump version: 3.99.18 → 3.99.19
Package: MetaProViz
Commit: d677f0505b4af3372fa00af173e7c9c34a5ccc63
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:41:43 +0100
Commit message:

 `RefactPK`: various formatting
Package: MetaProViz
Commit: d9f851523fe6045e13883fea3ab9f4b84211a19d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:33:10 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 63520e216a359d11d24f643de6a58b5a29f6895d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:30:39 +0100
Commit message:

 `MetabClustAn`: indentations & line breaks
Package: MetaProViz
Commit: 1f3350abfcf6b2549647f5a4c7028bd6608ab00c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:20:29 +0100
Commit message:

 long messages: breaking them by `paste0` + also send them to the log
Package: MetaProViz
Commit: 768becae3c1fcd5d7431fd3c24f91aad92f9938b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:09:29 +0100
Commit message:

 spacing around `else if`
Package: MetaProViz
Commit: de817bcb351c47318a2f0a39ad7bc5553a261c3e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:04:51 +0100
Commit message:

 use `%<>%` pipe
Package: MetaProViz
Commit: 4bbf0398284b3494b0546683b677ca10774590bd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:49:56 +0100
Commit message:

 indentation
Package: MetaProViz
Commit: 650a748651135506dbf3e0fa1392316013308347
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:48:24 +0100
Commit message:

 break lines of `mutate(case_when(...))` expressions
Package: MetaProViz
Commit: eae4c158a0db1d4d720e1cbc7460af9b5129c8b1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:25:05 +0100
Commit message:

 spaces around `<-` operators
Package: MetaProViz
Commit: 13d1dbd56c903306334ba2b259060ad7e2530c67
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:22:32 +0100
Commit message:

 break long lines at boolean operators
Package: MetaProViz
Commit: 24880f68a6f973f599387fceaa406e45e3e396db
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:44:59 +0100
Commit message:

 indentation
Package: MetaProViz
Commit: 114c204a9c5eca676ce1557c13e6eba8f3424d48
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:28:20 +0100
Commit message:

 formatting of comments
Package: MetaProViz
Commit: 9d63ff5c820e26a2edb5d11d4a9cdeffe46c31d7
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:08:42 +0100
Commit message:

 inconsistent spacing around `==`
Package: MetaProViz
Commit: c803ba2feebce234d24726e6a9b956e3b7fa7223
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:05:01 +0100
Commit message:

 inconsistent spacing around pipes
Package: MetaProViz
Commit: 828917147163fb141b4f2cab49c6c68b38c7d340
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 22:57:17 +0100
Commit message:

 inconsistent spacing around commas
Package: MetaProViz
Commit: 5a5925775b25416c35372098e3ee99e83ccbe6b8
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:59:29 +0100
Commit message:

 inconsistent spacing around `=`
Package: MetaProViz
Commit: 66c08ed31770a53fc66a88347928ddb4b316546c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:51:13 +0100
Commit message:

 break long conditionals at boolean operators
Package: MetaProViz
Commit: a5c261f1779b20a5318c714f5111459288e32bf6
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:41:22 +0100
Commit message:

 fixed indentation and `else if` → `if` issues introduced by claude + further manual cleanup of messy code
Package: MetaProViz
Commit: 84a218bc3ae25c7eb1ec6d06c226a18e310e2e3a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 19:24:18 +0100
Commit message:

 manually fixed some ugly checks for parameter presence in list arguments
Package: MetaProViz
Commit: 53b01674015e89f129ed91fb13b49ba56df8eedd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 18:51:31 +0100
Commit message:

 cleaned up redundant ` == TRUE` and ` == FALSE` expressions in boolean conditions
Package: MetaProViz
Commit: af8f221934a8bb0e05d9467739917be2dea33df3
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 16:20:33 +0100
Commit message:

 formatting: fixed indentation of verbs within pipes
Package: MetaProViz
Commit: 02b00288804d53cd1400cb14550cec9286aa8451
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 15:45:42 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 2c74212028d2505f49d3686f6f1e6bcc06992701
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 15:22:56 +0100
Commit message:

 code formatting: break long argument lists
Package: ORFik
Commit: 7b43c67a171ffa1f2d83347d21d256e54e5eed9e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 12:05:35 +0100
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 4d4f7205f30fc97b24a975b5cc2a72f287bf619c
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 12:05:22 +0100
Commit message:

 added more docs and fixed examples
Package: ORFik
Commit: 07d7500a9337930825c9efc4806f366bb0cfa1ec
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:47:23 +0100
Commit message:

 bump version
Package: ORFik
Commit: 41de42bb1973575ccfb4ce07141fb36ae84096ce
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:46:45 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/ORFik into devel
Package: ORFik
Commit: de0c0812e3666fb5b7a04bc293bf7b94bc0cc372
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:46:22 +0100
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 6a9536af0dae1d366fbf97522ad81a5458893e35
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 15:25:28 +0100
Commit message:

 Improved widthPerGroup + more tests
Package: ORFik
Commit: dd30b0f51120b61f4526b189c7fde9c6c96a49a8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 14:22:13 +0100
Commit message:

 New speedups for grl getter / setters
Package: ORFik
Commit: 42552d875dd044da79999c65cb65157fa38c0d76
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 12:34:53 +0100
Commit message:

 Massive speedups for grl getters
Package: ORFik
Commit: 9e5a2dd6b873226833605057015f7a34dfd4e41f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-13 15:32:12 +0100
Commit message:

 Added makeGRangesFromDataFrameFast
Package: ORFik
Commit: 79daa480d581c1bdb49588fe4411d50087b45e90
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-11 13:04:18 +0100
Commit message:

 Improved go plotting
Package: ORFik
Commit: 1b734addd2f4ebf436b52152fb23544df158ecb8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-11 12:40:46 +0100
Commit message:

 Added GOrilla plot similar to clusterProfiler
Package: ORFik
Commit: 2698a4478a748d791ed263b1781142a04bb07b73
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-05 22:27:50 +0100
Commit message:

 Small fix DEG plot
Package: ORFik
Commit: b1342cdc1dc3a6111b4a45d9247d730f49add6ff
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-05 22:00:04 +0100
Commit message:

 Now save optimized ranges in qs, not sure why this was not here yet for some reason, also improved DEG plotting
Package: ORFik
Commit: ba005cda1930270218f90d99cdd442207fc369a2
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-29 16:06:41 +0100
Commit message:

 Added working example to collapse function
Package: ORFik
Commit: ef3a4ec306e7046c6fb63bb0168068bb5ca75cca
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-29 13:40:53 +0100
Commit message:

 Improved collapsing
Package: ORFik
Commit: d7589e56cf30f9a28b60dd71c7d9d84810ea76b3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-21 15:08:21 +0200
Commit message:

 Added some checks for gorilla copy function
Package: ORFik
Commit: f70a41dfde60a1cd4cb04930598ced5786298f85
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-21 14:26:39 +0200
Commit message:

 Added gorilla copy local function
Package: ORFik
Commit: 2df5a890e08f53c7293c126d846387b409242df6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-13 23:49:16 +0200
Commit message:

 Improved bed12
Package: ORFik
Commit: 1ceed998c59d3dbccdf3e158c0965969bb77322a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-08 14:21:57 +0200
Commit message:

 Fixed bug categorize_and_filter_ORFs
Package: ORFik
Commit: 5f83a8831720e84de21d6213718cd58601a9105a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-26 12:59:34 +0200
Commit message:

 Improved coveragePerTiling
Package: ORFik
Commit: 15bcdfa3e517dad811b1d8cfe2db1eb35f791012
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-25 15:34:14 +0200
Commit message:

 Massive speed up for countOverlaps on covRle
Package: ORFik
Commit: e538aa99fa7d0751df264a2701d088f1244beaf7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-24 13:47:04 +0200
Commit message:

 STAR added more checks on trim inputs
Package: ORFik
Commit: 66739dcf0dcb7e52974fd00d7a132367b9940c86
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 14:40:13 +0200
Commit message:

 Improved docs
Package: BioNAR
Commit: 5e908e7e135a2f2829f2525dc1a6473debcffb02
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2025-11-21 10:40:16 +0000
Commit message:

 convert Entrez to characters for annotation
Package: LimROTS
Commit: 4c0a6dc1ccbd980bd5cfbc5aa5f6e470588536cf
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-11-21 10:53:49 +0200
Commit message:

 Core functions reimplemented and refactored
Package: crisprDesign
Commit: a739727c863c807fdbf8a43430b1db9979b7870d
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 23:38:16 -0500
Commit message:

 Adapted to new crisprScore paradigm
Package: crisprScore
Commit: c805e178225327be206352ef0612db4aaa555762
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 17:04:11 -0500
Commit message:

 Added note re. RS3 tracer
Package: crisprScore
Commit: b5d8888e3b2a2e4c3331b9af131d974e5de852a9
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 17:02:50 -0500
Commit message:

 Ready to push
Package: crisprScore
Commit: 22dd03ce20b4af2aa6def2123cf02450376bcb03
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 16:11:19 -0500
Commit message:

 Ready to write vignette
Package: crisprScore
Commit: 0e3c216773bff006df2a0a82434cad3c808f301e
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 15:49:36 -0500
Commit message:

 Conda env arguments added
Package: crisprScore
Commit: 2643bc2f9d9176a7d08654e0d1cb05745eb9de68
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 23:43:42 -0500
Commit message:

 Updated basilisk
Package: crisprScore
Commit: b358c1b0760b2ffbe9b77093305fa8753782a4b8
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 23:43:11 -0500
Commit message:

 Fixed enpamgb score
Package: crisprScore
Commit: ba76282360b8f89a31814c6255faa9fb02802ad3
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 21:00:27 -0500
Commit message:

 Removed azimuth
Package: crisprScore
Commit: 02b4c566f9b640ce8e522279c3ba2b0331b723b6
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 20:59:07 -0500
Commit message:

 Fixed DeepHF and RuleSet3 scores
Package: crisprScore
Commit: 2b69581ac85d2e66366e287a2b187c570ef913f3
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 16:59:09 -0500
Commit message:

 Removed python2-based scores
Package: InPAS
Commit: f16f6421b703190599d63d52962399215c221772
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-20 21:24:51 -0500
Commit message:

 remove plyranges::filter.

Merge branch 'RELEASE_3_22' into devel

# Conflicts:
#	DESCRIPTION
Package: InPAS
Commit: 5e70ec51c0ad3f244d6a29856c4f1447c722a9de
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-20 21:19:47 -0500
Commit message:

 remove plyranges::filter
Package: SparseArray
Commit: 612972d0bbabaa7e08bec016be514a5aa126573a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-20 16:00:03 -0800
Commit message:

 SparseArray 1.11.4: Refactor subassignment with a "short" right vector

Refactor SparseArray:::.subassign_SVT_with_short_Rvector().
This is the workhorse behind subassignment of an SVT_SparseArray object
with a "short" vector on the right e.g.
    svt[i, j, k] <- 0
or
    svt[i, j, k] <- c(4, 0, -1, 1)
where each of i, j, k is either missing or a vector of subscripts.

The new implementation is simpler, cleaner, faster.
Package: BiocCheck
Commit: 318b33b6e2fbd88e72a45d7932bef59c4ea885c6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:55:37 -0500
Commit message:

 version bump 1.47.5
Package: BiocCheck
Commit: 4de856b280f8e1f0d94854f2ebf508b162c87a46
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:55:33 -0500
Commit message:

 update docs to explain use NULL and FALSE for dot-options
Package: BiocCheck
Commit: 41b0bb7b11a642f20c3086b2c31ab8163326ad32
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:35:01 -0500
Commit message:

 version bump 1.47.4
Package: BiocCheck
Commit: 9cc228ae50c149c18c8bf214e3a578fad13e07cf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:34:46 -0500
Commit message:

 installation should be done when install is NULL or TRUE
Package: BiocCheck
Commit: 40e1f9eb400a8de7cf620c058e9e492a24dbdce7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:25:32 -0500
Commit message:

 explicitly check for TRUE for !is.null options
Package: BiocCheck
Commit: 5c5e27ebaa0390d22f5052e2b5df1746c76b9e8e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:25:08 -0500
Commit message:

 check for NULL or FALSE in negative options e.g. no-check-deprecated
Package: BiocCheck
Commit: b3d9eb6e017174ade5ac3a42c972e5d5fd413969
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 15:27:31 -0500
Commit message:

 version bump 1.47.3
Package: BiocCheck
Commit: 89101051d2eaddf76888f5d2827489d8a699610b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 15:26:09 -0500
Commit message:

 use .BiocCheck consistently
 </pre>
    </div>
  
    

      Package: BiocCheck

      Commit: 0972766e50eb4a863f65366766d6f8765c8dc186

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:25:50 -0500

      Commit message:


	  
		
 remove example from param dots and move to dot-options section
 

    

  
    

      Package: BiocCheck

      Commit: 06719a429eb8baf598bd1d9b68249bfeecd0cb09

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:24:58 -0500

      Commit message:


	  
		
 use md for R CMD build cmd
 

    

  
    

      Package: BiocCheck

      Commit: 94b6f7350abaafb1e41b99e2a66b7ef335fbe18b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:24:26 -0500

      Commit message:


	  
		
 add skip installation section in docs
 

    

  
    

      Package: BiocCheck

      Commit: 1445420e8c735eee8556d47cfe62b14669c86a0c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:23:32 -0500

      Commit message:


	  
		
 document dot-options value options, TRUE, NULL, other
 

    

  
    

      Package: CATALYST

      Commit: a1cad2251f4c1d34617daf11f03c32e9f2405b74

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 20:04:37 +0100

      Commit message:


	  
		
 fix #204 on devel
 

    

  
    

      Package: CATALYST

      Commit: 4f0aaa011d1818561f66d4acd7f7b26dd65988dd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:42:54 +0100

      Commit message:


	  
		
 fix typo; plz work now :(
 

    

  
    

      Package: CATALYST

      Commit: 7fafa8537fbbd2449283e6c4a705dde1a4f879ad

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:07:24 +0100

      Commit message:


	  
		
 add final line?
 

    

  
    

      Package: CATALYST

      Commit: 39eb277d6ffd48b194b858762e889eb10573c4fc

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:05:13 +0100

      Commit message:


	  
		
 fix R CMD warning
 

    

  
    

      Package: CATALYST

      Commit: 3c44e1cdb32f546105226a95285d8915d28dec0d

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 18:26:20 +0100

      Commit message:


	  
		
 add code comms
 

    

  
    

      Package: CATALYST

      Commit: 0db8f7f01c6bb9a38aa455d73bd39c07a886e0ec

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 18:21:40 +0100

      Commit message:


	  
		
 fix CITATION
 

    

  
    

      Package: CATALYST

      Commit: 5acbc7109eea062ac983391201a64a4eb6555728

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 17:05:13 +0100

      Commit message:


	  
		
 add CITATION
 

    

  
    

      Package: CATALYST

      Commit: 6890b94f038940a0c34fdd0c5f9b0a5204c7262d

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 17:00:26 +0100

      Commit message:


	  
		
 plotSpillmat fix (#204)
 

    

  
    

      Package: CATALYST

      Commit: f9e5c3e60f6cd09bbf3e39d54f2e17322ea0f0ca

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 08:10:23 +0100

      Commit message:


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

    

  
    

      Package: CATALYST

      Commit: 57f08a51c4e5cd57023cc7b8b67dbc79b47537bb

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-05 22:30:55 +0200

      Commit message:


	  
		
 update GHA
 

    

  
    

      Package: CATALYST

      Commit: eb014a23bb4d76532b403ff6c99ff86388872705

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-05 22:30:13 +0200

      Commit message:


	  
		
 fix #424 on devel
 

    

  
    

      Package: CATALYST

      Commit: 6a1220abf5e154419fbb8d4a5d2ffcb40eef3839

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-09-21 11:54:11 +0200

      Commit message:


	  
		
 update roxygen & GHA
 

    

  
    

      Package: BiocCheck

      Commit: be1d6943badb02b0bb7283a10815c15e07349542

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:36:28 -0500

      Commit message:


	  
		
 version bump 1.47.2
 

    

  
    

      Package: BiocCheck

      Commit: dcc254b30b2dd24b55367cf4cbe467ac7dc4f423

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:35:45 -0500

      Commit message:


	  
		
 replace installAndLoad with .tryInstallwLoad
 

    

  
    

      Package: BiocCheck

      Commit: 6751e2804290e5c2bf297456e7a0e08386f128a4

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:19:58 -0500

      Commit message:


	  
		
 version bump RoxyenNote
 

    

  
    

      Package: BiocCheck

      Commit: 4bdfa8ae6282d9351dc6facecee54aea7b41d998

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:19:45 -0500

      Commit message:


	  
		
 add installation section to vignette
 

    

  
    

      Package: BiocCheck

      Commit: 234e47cbcaddb3e15d08c51b275891fd22008f6b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-19 18:46:16 -0500

      Commit message:


	  
		
 add install dot option and document
 

    

  
    

      Package: BiocCheck

      Commit: 202c10d46eac9cbd3f38c810b923967b13d0a9f6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:37:35 -0500

      Commit message:


	  
		
 version bump 1.47.1
 

    

  
    

      Package: BiocCheck

      Commit: 5236447bf2226b63529884b3dacf9fb7a3e5c06f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:35:36 -0500

      Commit message:


	  
		
 minor update spacing
 

    

  
    

      Package: BiocCheck

      Commit: 8b552fd0ccee61ea43bed743afa73bb642345f1a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:35:27 -0500

      Commit message:


	  
		
 use default package size in checkPackageSize call
 

    

  
    

      Package: BiocCheck

      Commit: ffa4adb76f8d3ceb88a4052a335ea93d135f6d89

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 12:19:44 -0500

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: BiocCheck

      Commit: 3a19c8f6f50115e0c5f7b1cffc5a194d41c23972

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-10-31 12:32:53 -0400

      Commit message:


	  
		
 change size requirement in vignette
 

    

  
    

      Package: BiocCheck

      Commit: 12e28a8b2f6494ba9ab66f45927dd6425ae3e7f1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-10-31 12:29:41 -0400

      Commit message:


	  
		
 update package size requirement
 

    

  
    

      Package: BiocCheck

      Commit: 43eff7706c29bfd92f7a1f0c7c35ba1a69530853

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-10-31 12:35:51 -0400

      Commit message:


	  
		
 remove Martin from PR template
 

    

  
    

      Package: hypeR

      Commit: 3913d70bd0cc13aad54a5b1d2076f15b7541f7d9

      Author:  Andrew Chen <andrewdchen@berkeley.edu> 

      Date: 2025-11-20 13:55:40 -0500

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 

    

  
    

      Package: hypeR

      Commit: e407bf13a3dcd26b3f526b24c8ade03f595ca496

      Author:  tetomonti <9437983+tetomonti@users.noreply.github.com> 

      Date: 2025-08-12 09:40:00 -0400

      Commit message:


	  
		
 Update DESCRIPTION: changed the mainainer 

    

  
    

      Package: hypeR

      Commit: 9fdbb1ff2a442ef17399388754371b4e79261ea1

      Author:  Andrew Chen <31497311+andrewdchen@users.noreply.github.com> 

      Date: 2025-06-03 12:22:10 -0400

      Commit message:


	  
		
 Update hyp_dots.R

Fixing FDR scale plotting 

    

  
    

      Package: hypeR

      Commit: b496f10d330fe813ef7dbfa9ade307b22e7b4e0f

      Author:  Andrew Chen <andrewdchen@berkeley.edu> 

      Date: 2025-06-03 09:14:50 -0400

      Commit message:


	  
		
 Update README msigdb examples
 

    

  
    

      Package: hypeR

      Commit: 5fbf99e471522dd6dc826c65ddb4cc208a14de8c

      Author:  Andrew Chen <andrewdchen@berkeley.edu> 

      Date: 2025-06-02 18:35:38 -0400

      Commit message:


	  
		
 msigdb updates
 

    

  
    

      Package: hypeR

      Commit: 410930d8ceed5def261a8d13672ce7c529408566

      Author:  Andrew Chen <31497311+andrewdchen@users.noreply.github.com> 

      Date: 2025-06-02 14:45:04 -0400

      Commit message:


	  
		
 Update build.yml

The bioconductor container did not have the R version necessary for the latest versions of the packages. 
The actions checkout also was old. 

    

  
    

      Package: hypeR

      Commit: 8d0ac2d6b4917a5fc7cbaa4aaad9080d91599b3d

      Author:  Andrew Chen <31497311+andrewdchen@users.noreply.github.com> 

      Date: 2025-05-14 12:38:35 -0400

      Commit message:


	  
		
 Merge pull request #59 from Kupac/bugfix/rename-species-function

Align with msigdbr 

    

  
    

      Package: hypeR

      Commit: 1382c8c47139f70f310df10ee2f0320a33ac4259

      Author:  László Kupcsik <koopac@gmail.com> 

      Date: 2025-04-28 20:50:08 +0200

      Commit message:


	  
		
 Align with msigdbr

Probably the function was renamed upstream
 

    

  
    

      Package: hypeR

      Commit: fe96a7b82bdf09419aa671e41486fb4db782b1c3

      Author:  anfederico <anfederico@users.noreply.github.com> 

      Date: 2023-10-25 23:09:02 -0400

      Commit message:


	  
		
 Merge pull request #55 from montilab/devel

Sync 

    

  
    

      Package: hypeR

      Commit: ef8f2ec080688219ee15f23d8faad62214aa40a7

      Author:  anfederico <anfederico@users.noreply.github.com> 

      Date: 2023-10-25 22:49:07 -0400

      Commit message:


	  
		
 Bump
 

    

  
    

      Package: nullranges

      Commit: ffc311bfd0a76329e7059a9ffa82f5aa56ff3dc0

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

      Date: 2025-11-20 13:19:43 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: nullranges

      Commit: 31d0aa489215e3110a6b129e05fb9533d15f3b34

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

      Date: 2025-11-20 13:19:07 -0500

      Commit message:


	  
		
 add matchitToMatched
 

    

  
    

      Package: nullranges

      Commit: 46ab992dc43ddc55f5d5fd00ac8dce4616398c14

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

      Date: 2025-11-20 09:38:12 -0500

      Commit message:


	  
		
 skip test no mariner
 

    

  
    

      Package: OSTA.data

      Commit: 65c3bbaf645d69cbdacec05775fbc4623a7311f4

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-11-20 17:04:15 +0100

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: OSTA.data

      Commit: 573063e50a846268834a7ea084d7df306bb00fb5

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-11-20 17:03:01 +0100

      Commit message:


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

    

  
    

      Package: OSTA.data

      Commit: dea9c4361366498ac954ff56c2abb46f8df36f62

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-11-20 17:00:56 +0100

      Commit message:


	  
		
 update to OSTA.data after vhd cell seg reader update
 

    

  
    

      Package: BioNAR

      Commit: 30958a755f695297cf54b75de5db16543dd0c326

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2025-11-20 15:56:46 +0000

      Commit message:


	  
		
 fix error in the membership assignment to the vertices
 

    

  
    

      Package: BioNAR

      Commit: a126c06add486b3814c85bdd67fcc7713b998814

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2025-11-20 14:41:33 +0000

      Commit message:


	  
		
 fix discrepancy between cluster names and cl in enrichment results
 

    

  
    

      Package: BiocPkgDash

      Commit: c49ed9799a3c6864f0832c62aaaa6bdd89632c25

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 10:44:03 -0500

      Commit message:


	  
		
 version bump 0.99.38
 

    

  
    

      Package: Pirat

      Commit: ad69e4a852b599e728adc3692dd60a9c9c1a47a2

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-19 19:05:34 +0100

      Commit message:


	  
		
 Python -> 3.10
 

    

  
    

      Package: MotifPeeker

      Commit: d02958ecbc866cb3ec37533abd6aa7028d9f235f

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-11-20 12:15:08 +0000

      Commit message:


	  
		
 Merge pull request #11 from neurogenomics/revision_changes

Revision changes 

    

  
    

      Package: MotifPeeker

      Commit: aa5c4c949b41b092871b77a44a1c58aa6e5d0a4a

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-11-20 12:13:39 +0000

      Commit message:


	  
		
 Merge branch 'master' into revision_changes 

    

  
    

      Package: MotifPeeker

      Commit: 4db6e62d6208ac90a21e9f885533c57db95254f0

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

      Date: 2025-11-20 12:13:01 +0000

      Commit message:


	  
		
 Update example report links
 

    

  
    

      Package: MotifPeeker

      Commit: a4a5d0df5c40cdd1057d3aa85329799bb90c3a19

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

      Date: 2025-11-06 14:37:52 +0000

      Commit message:


	  
		
 Add check emoji for reference dataset
 

    

  
    

      Package: MotifPeeker

      Commit: a3c63edaea6fc089af3c099ab2bcce535b3a1bd3

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

      Date: 2025-11-06 14:33:19 +0000

      Commit message:


	  
		
 Bootstrap implementation clean-up
 

    

  
    

      Package: MotifPeeker

      Commit: 7eff3a5e195b9f8b810c0e900b9add30a1aa27ea

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

      Date: 2025-11-05 13:49:28 +0000

      Commit message:


	  
		
 Bootstrap motif-summit distances
 

    

  
    

      Package: MotifPeeker

      Commit: 77e92954b57ab6cf8d0f3feff39c2d7f4aab6bb6

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

      Date: 2025-11-04 12:01:10 +0000

      Commit message:


	  
		
 Rework motif-summit distances

- Reword description
- Remove plot by peak count
 

    

  
    

      Package: MotifPeeker

      Commit: 3835dabc69a8f949bec238eba8672c1fbd58f549

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

      Date: 2025-11-03 10:35:35 +0000

      Commit message:


	  
		
 Remove all references to the old `workers` parameter

Closes #8
 

    

  
    

      Package: MotifPeeker

      Commit: 1627a06f5774d1b182975180a5b99b2bfdf2c710

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

      Date: 2025-09-15 11:46:06 +0100

      Commit message:


	  
		
 Tabulate input datasets sub-section
 

    

  
    

      Package: MotifPeeker

      Commit: b3f1bfc8d10a134605f523f5e31d6c93feafa7b2

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

      Date: 2025-08-29 13:20:06 +0100

      Commit message:


	  
		
 Add support for directly importing mouse genome builds

Also enhance documentation for importing genome builds
 

    

  
    

      Package: MotifPeeker

      Commit: 5457c57f0d4802fb8286208efb8cc77abfa369a8

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

      Date: 2025-10-29 11:33:15 -0400

      Commit message:


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

    

  
    

      Package: MotifPeeker

      Commit: 0f087957afa07d6231026afb53dea7b12778323f

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

      Date: 2025-08-31 17:06:40 +0100

      Commit message:


	  
		
 Use Bioc devel for Mac GA runner
 

    

  
    

      Package: MotifPeeker

      Commit: 46bcd05bc9ba7b61cab18cc6cf0a0ab1a578fc1c

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

      Date: 2025-08-29 14:43:21 +0100

      Commit message:


	  
		
 Motif file import enchancements

- Accept universalmotif objects
- Improve documentation
 

    

  
    

      Package: MotifPeeker

      Commit: 6caca7eb159f84ef963e4638b465b265ff879ebd

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

      Date: 2025-08-29 13:20:06 +0100

      Commit message:


	  
		
 Add support for directly importing mouse genome builds

Also enhance documentation for importing genome builds
 

    

  
    

      Package: MotifPeeker

      Commit: 48057f34fc6bba983258c65a60af3a983740971c

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

      Date: 2025-08-29 11:54:05 +0100

      Commit message:


	  
		
 Add changes for v1.1.3
 

    

  
    

      Package: stPipe

      Commit: 4830cb839910fd2912352bd4aad7ca68dbc97275

      Author:  YangXuuu <xuyang1121wws@gmail.com> 

      Date: 2025-11-20 16:26:43 +1100

      Commit message:


	  
		
 Fix testthat bug.
 

    

  
    

      Package: clusterProfiler

      Commit: fffb636bc60983fcbc8002c964bcc1234acd7827

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-20 11:22:51 +0800

      Commit message:


	  
		
 use quarto
 

    

  
    

      Package: clusterProfiler

      Commit: d04999dfab613ca85bf18f3b1ff5f394202d139d

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-20 09:42:46 +0800

      Commit message:


	  
		
 update kegg data
 

    

  
    

      Package: enrichplot

      Commit: c0a81b43a451c1f3408c8d56ad19a41d7e10115f

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-20 11:13:06 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: enrichplot

      Commit: d206f04f9993cf346632f83ac461ddfadc31d12d

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-18 17:15:13 +0800

      Commit message:


	  
		
 typo
 

    

  
    

      Package: enrichplot

      Commit: 9be1185be4deadaea7d93aae0cf27dbbffc07120

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-18 15:43:32 +0800

      Commit message:


	  
		
 bug fixed in heatplot
 

    

  
    

      Package: enrichplot

      Commit: 936851a7d1b2a39f3ab607034c366bd559a8eba6

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-18 09:45:37 +0800

      Commit message:


	  
		
 import %<+%
 

    

  
    

      Package: enrichplot

      Commit: 8ea589f465a6872d5f6bd56957f43dac7953ce66

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-16 00:28:12 +0800

      Commit message:


	  
		
 #334
 

    

  
    

      Package: enrichplot

      Commit: 258d6f23064e24ac4b38049afbef9694007575a4

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-11 17:38:50 +0800

      Commit message:


	  
		
 cleanup code
 

    

  
    

      Package: enrichplot

      Commit: c14600d10e7ebceec8fb89128cb381137e3cd657

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-11 17:37:08 +0800

      Commit message:


	  
		
 change set_enrichplot_color default parameter
 

    

  
    

      Package: enrichplot

      Commit: 52ffb6d38e00349f28c348541a5e53c9310f80fa

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-11 17:28:50 +0800

      Commit message:


	  
		
 use quarto
 

    

  
    

      Package: enrichplot

      Commit: 24982878a93ae7ae57f5f949469aafdadf0e7f46

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-11 10:12:13 +0800

      Commit message:


	  
		
 fixed bug
 

    

  
    

      Package: enrichplot

      Commit: 4589d0130447596ea60fd7266bc4ee2ba01567a4

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-05 17:04:04 +0800

      Commit message:


	  
		
 cnetplot color
 

    

  
    

      Package: enrichplot

      Commit: 5b2b5b9a8a498d38757c39f46a025ee95a1c3545

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 17:00:59 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: igblastr

      Commit: 734951bb2d26b6361a7382d28f1bee9422d80d63

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

      Date: 2025-11-19 14:07:58 -0800

      Commit message:


	  
		
 igblastr 1.1.2: Add CITATION file
 

    

  
    

      Package: igblastr

      Commit: ad10003e35cfe7e52e8888e0e43d3fe0e01e2873

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

      Date: 2025-11-19 13:17:51 -0800

      Commit message:


	  
		
 add "devel" row in BioC_version/Status table in README.md
 

    

  
    

      Package: SparseArray

      Commit: 201be11aec498e90e70c56e23ef747329408714b

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

      Date: 2025-11-19 11:57:48 -0800

      Commit message:


	  
		
 no tabs in R code
 

    

  
    

      Package: SparseArray

      Commit: 7e631cc61018aab33999b7396e0b6e832f76c25e

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

      Date: 2025-11-19 11:37:43 -0800

      Commit message:


	  
		
 SparseArray 1.11.3

Subassignment of an SVT_SparseArray object with a right value that is
also an SVT_SparseArray object is finally supported. For example this
allows things like

    x[3:6, , 1] <- y
    x[ , 11:15, 1] <- x[ , 1:5, 3]

(where 'x' and 'y' are both SVT_SparseArray objects) to operate
natively on the sparse representation and therefore to be very fast
and very memory-efficient.
 

    

  
    

      Package: GSVA

      Commit: c8b568163e91b6b37b19cf491e8870723b845732

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-19 20:25:35 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: fbe9979c417baa18f6e81642fe5cc034285d0114

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-19 20:25:18 +0100

      Commit message:


	  
		
 Improvement in detecting rows with constant (nonzero) values
 

    

  
    

      Package: profileplyr

      Commit: 4e14aef249c9092674719ad246c5c4ae6a8295c7

      Author:  Douglas Barrows <dbarrows@rockefeller.edu> 

      Date: 2025-11-19 13:26:54 -0500

      Commit message:


	  
		
 version bump to 1.27.1
 

    

  
    

      Package: profileplyr

      Commit: 806148d31eeeffdd9ce3cbec5ba04cfdefbb72c7

      Author:  Douglas Barrows <dbarrows@rockefeller.edu> 

      Date: 2025-11-19 13:26:31 -0500

      Commit message:


	  
		
 fixed testthat functions that have been deprecated
 

    

  
    

      Package: RnBeads.hg38

      Commit: 654a4d82903d38d123082e888883988f744636e4

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

      Date: 2025-11-19 17:47:34 +0100

      Commit message:


	  
		
 Reduced RData sizes
 

    

  
    

      Package: nullranges

      Commit: 2713e72819b46abf85f8d377eb48998ebb67b7d3

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

      Date: 2025-11-19 08:45:47 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: nullranges

      Commit: 62bd3fc0274add620c27e05aa939166c3d95465a

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

      Date: 2025-11-19 08:45:24 -0500

      Commit message:


	  
		
 more fixes
 

    

  
    

      Package: BioNAR

      Commit: 13d35574396b2a271bb0a2acf5a3fa01c7916534

      Author:  Anatoly Sorokin <lptolik@gmail.com> 

      Date: 2025-11-19 13:16:59 +0000

      Commit message:


	  
		
 fix tests
 

    

  
    

      Package: LimROTS

      Commit: 9fc08d34550fe0f7f0e65490447feddb949931dc

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 14:59:03 +0200

      Commit message:


	  
		
 Correcting the countLargerThan function name.
 

    

  
    

      Package: vsclust

      Commit: c5bb185bf36837c1e6de930cdc6b0fe671871b9b

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2025-11-19 11:25:17 +0100

      Commit message:


	  
		
 Merge branch 'master' into devel
 

    

  
    

      Package: vsclust

      Commit: 855e719bd1bf6af89651d0d260fb239aa97131d1

      Author:  Veit Schwämmle <veitveit@gmail.com> 

      Date: 2025-11-18 14:31:45 +0100

      Commit message:


	  
		
 Merge pull request #10 from computproteomics/devel

Branched shiny validate to warning 

    

  
    

      Package: vsclust

      Commit: 22da173ad766cc053c534121716e507ba140af1d

      Author:  Veit Schwämmle <veitveit@gmail.com> 

      Date: 2025-11-18 14:29:36 +0100

      Commit message:


	  
		
 Update man/pcaWithVar.Rd

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

    

  
    

      Package: vsclust

      Commit: e125f881ce47ed1ab728cb98422131dab76c9f9a

      Author:  Veit Schwämmle <veitveit@gmail.com> 

      Date: 2025-11-18 14:29:25 +0100

      Commit message:


	  
		
 Update R/PrepareData.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

    

  
    

      Package: vsclust

      Commit: 486979055b3f3cb3e9cf847318426795122ca777

      Author:  Veit Schwämmle <veitveit@gmail.com> 

      Date: 2025-11-18 14:28:50 +0100

      Commit message:


	  
		
 Update R/PrepareData.R

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

    

  
    

      Package: vsclust

      Commit: 636c50459b5d1d1d5831d4df8888dd1cd8bb7239

      Author:  Veit Schwämmle <veitveit@gmail.com> 

      Date: 2025-09-04 14:25:24 +0200

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: LimROTS

      Commit: f6c6a7a4cbc290a6ff99c8ddcb6cf02c07000d5c

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:32:31 +0200

      Commit message:


	  
		
 DESCRIPTION 1.3.4
 

    

  
    

      Package: LimROTS

      Commit: a8548e4bf2680f86c249068db16f9bd7c79fbb3a

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:31:43 +0200

      Commit message:


	  
		
 Refactoring the calOverlaps funciton
 

    

  
    

      Package: LimROTS

      Commit: c2506d9d1466c4bf9ae21794ea06c41af2c004b2

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:25:26 +0200

      Commit message:


	  
		
 Refactoring the optimizing function.
 

    

  
    

      Package: vsclust

      Commit: f9c15198731336e94e49b3ce0eccbd3606c4cecb

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2025-11-19 10:25:25 +0100

      Commit message:


	  
		
 renames and commented C++ code
 

    

  
    

      Package: LimROTS

      Commit: 743cadf34b4b42ac3d320f2240a880521695ddc7

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:13:54 +0200

      Commit message:


	  
		
 DESCRIPTION v. correction
 

    

  
    

      Package: LimROTS

      Commit: 455868746c414a5ed2d3d6db1f2437de1554ca06

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:10:14 +0200

      Commit message:


	  
		
 Reimplementation of a faster calculateFalseDiscoveryRate function.
 

    

  
    

      Package: LimROTS

      Commit: 0698507e288811153c52ec1f3db41e0f8a684417

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 11:04:40 +0200

      Commit message:


	  
		
 Update the bootstrapS function to remove the nested loop structure.
 

    

  
    

      Package: dominatR

      Commit: 2c155d018d42d85c63fc2644d1b82d8a5ee45a7d

      Author:  slizarazo21 <simonl3@illinois.edu> 

      Date: 2025-11-18 21:16:55 -0600

      Commit message:


	  
		
 bump version to 0.99.5, fixed errors related to vignette present in bioconductor report
 

    

  
    

      Package: dominatR

      Commit: 63f0c6961203ac353f68e7f0d5a738df00573035

      Author:  slizarazo21 <simonl3@illinois.edu> 

      Date: 2025-11-18 21:15:17 -0600

      Commit message:


	  
		
 bump version to 1.0.0, fixed errors related to vignette present in bioconductor report
 

    

  
    

      Package: OSCA.advanced

      Commit: 55de68d2312c167e5f4746ad300b7fa65950152c

      Author:  Peter Hickey <peter.hickey@gmail.com> 

      Date: 2025-11-19 12:18:19 +1100

      Commit message:


	  
		
 Merge pull request #26 from OSCA-source/remove-pcatools

Remove PCAtools 

    

  
    

      Package: OSCA.advanced

      Commit: 1226e45c8aeb9a018fd66b2e6c9666bb9799c3f2

      Author:  Peter Hickey <peter.hickey@gmail.com> 

      Date: 2025-11-19 12:03:59 +1100

      Commit message:


	  
		
 Remove PCAtools

- PCAtools depends on ggalt which was removed from CRAN and PCAtools has been failing on Bioconductor for some time, according to Vince.
 

    

  
    

      Package: OSCA.advanced

      Commit: bd697691b2394d14fb3742f154d9dcb2f811370f

      Author:  Peter Hickey <peter.hickey@gmail.com> 

      Date: 2025-11-19 11:59:22 +1100

      Commit message:


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

    

  
    

      Package: OSCA.advanced

      Commit: 03d4cfcdd87edcb15c5510befc2fcebd52e13a4e

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-19 00:58:54 +0000

      Commit message:


	  
		
 Address lingering seed and variable use issues (#25)

* Address lingering seed and variable use issues

From #24

* Update more-reddim.Rmd

* Sum var not mean

* Dens lamba

* Use endothelial rather than astrocytes

* Only show tSNE and denSNE

* Text only t-SNE 

    

  
    

      Package: OSCA.advanced

      Commit: 75560efa9b00001a37df7f49403af0068d6e5af8

      Author:  Peter Hickey <peter.hickey@gmail.com> 

      Date: 2025-11-19 11:48:01 +1100

      Commit message:


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

    

  
    

      Package: OSCA.advanced

      Commit: 934d68e0bf2fefece332f71b3858da35071a9039

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:39:43 +0000

      Commit message:


	  
		
 Resolve biocpkg from #24
 

    

  
    

      Package: OSCA.advanced

      Commit: 7e5be624c15d642570499efd058f6aa9afa7da95

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:38:54 +0000

      Commit message:


	  
		
 Resolve #24
 

    

  
    

      Package: SparseArray

      Commit: 93f1afe9a78883042aeeebe9c295e3ce091295ef

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

      Date: 2025-11-18 16:53:51 -0800

      Commit message:


	  
		
 some work on SparseArray:::.subassign_SVT_with_SVT()
 

    

  
    

      Package: LimROTS

      Commit: 15137945dd58bfa297b62f0ee6f83c415092be23

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-19 00:27:07 +0200

      Commit message:


	  
		
 Adding Citation and Disclaimer Information
 

    

  
    

      Package: BiocPkgTools

      Commit: 121890f5d6f2096e249cbd38645d68165196d2e2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 13:56:40 -0500

      Commit message:


	  
		
 version bump 1.29.2
 

    

  
    

      Package: BiocPkgTools

      Commit: 1043d36bc5faef9fb4fc345b97d89be03b858b26

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 13:55:52 -0500

      Commit message:


	  
		
 update RELEASE_3_22 branches in GHA
 

    

  
    

      Package: BiocPkgTools

      Commit: 6c73001d7e0493d9c4c03df971b5e11e0ceaad81

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 13:01:07 -0500

      Commit message:


	  
		
 fix formatting for biocPkgRanges
 

    

  
    

      Package: BiocPkgTools

      Commit: 5d61f473fe386adb1215d72940688d6edaa8c1e3

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:57:06 -0500

      Commit message:


	  
		
 use updated names in biocPkgRanges
 

    

  
    

      Package: BiocPkgTools

      Commit: ae0ffc0b35815bcd5fcf59e2d515b75a18323594

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:51:42 -0500

      Commit message:


	  
		
 exclude .html from .gitignore
 

    

  
    

      Package: BiocPkgTools

      Commit: 1e0e0f027b0c6160e4356c6e2e63143c19f63d99

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:25:58 -0500

      Commit message:


	  
		
 bug fix: coerce to as.package_version
 

    

  
    

      Package: BiocPkgTools

      Commit: cec4cbe2d2d96c1a53ab0c5eed66584a697fb12c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:10:29 -0500

      Commit message:


	  
		
 minor fixes to examples
 

    

  
    

      Package: BiocPkgTools

      Commit: cfdeda91d4db3586621f630b5d83bb5d32082c41

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:10:11 -0500

      Commit message:


	  
		
 update authors email
 

    

  
    

      Package: BiocPkgTools

      Commit: cd626ad0541e211bf7cb571b077f698a39b9a1ec

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-18 12:09:45 -0500

      Commit message:


	  
		
 minor longtests formatting
 

    

  
    

      Package: BiocPkgTools

      Commit: 4f9b2c8f5523a2175bf9fea255e6af4c51663456

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 18:24:51 -0500

      Commit message:


	  
		
 add longtests for CRANstatus and biocDownloadStats
 

    

  
    

      Package: BiocPkgTools

      Commit: a0bcd79da97a3c838c0006086d67ed6d52d8f99b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 18:24:37 -0500

      Commit message:


	  
		
 add longtests directory
 

    

  
    

      Package: GSVA

      Commit: 0e2807badc6a82ff67341043049fcc58ff63441e

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-18 18:48:35 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: 660327924153f7a832286bd68179fb8aea72dfca

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2025-11-18 18:48:21 +0100

      Commit message:


	  
		
 Fix in detecting rows with constant (nonzero) values
 

    

  
    

      Package: nullranges

      Commit: d86b15548c1187a3d406ab6e328387507f2f6885

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

      Date: 2025-11-18 11:21:01 -0500

      Commit message:


	  
		
 and namespace...
 

    

  
    

      Package: nullranges

      Commit: 491b3b64218ef2ff174aa80bb634308d4cf0dc59

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

      Date: 2025-11-18 11:11:05 -0500

      Commit message:


	  
		
 more fix plyranges
 

    

  
    

      Package: nullranges

      Commit: b47dee62fbdf1a9486e748149c16d0da3e4b69c9

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

      Date: 2025-11-18 10:57:36 -0500

      Commit message:


	  
		
 more fix plyranges
 

    

  
    

      Package: nullranges

      Commit: ab94084f33c26282969c066b2755338e2a51dcab

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

      Date: 2025-11-18 10:47:27 -0500

      Commit message:


	  
		
 gha fix
 

    

  
    

      Package: nullranges

      Commit: 18dc73da847c199951211b5af4ab7f1ae135c76c

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

      Date: 2025-11-18 09:45:37 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: nullranges

      Commit: 780e9867735b2f8f7ac91c5df0f3a21263d0ba1c

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

      Date: 2025-11-18 09:44:13 -0500

      Commit message:


	  
		
 fix plyranges upstream issue in release/devel
 

    

  
    

      Package: EpiCompare

      Commit: eac0a103ba066364e83db1ed5234f943c0b6be79

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-11-18 14:23:36 +0000

      Commit message:


	  
		
 Merge pull request #161 from neurogenomics/peak-score

Add peak score distribution section 

    

  
    

      Package: EpiCompare

      Commit: 903114f8c5bdb9d7a13b79c5ae5106c8322caed9

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

      Date: 2025-11-18 14:19:15 +0000

      Commit message:


	  
		
 White-space cleanup
 

    

  
    

      Package: EpiCompare

      Commit: 590c71022612fd3004a8e7ad127da637d8f4382d

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2025-11-10 11:59:34 +0000

      Commit message:


	  
		
 Clean whitespaces

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

    

  
    

      Package: EpiCompare

      Commit: 47524c9c7e9570b7611a4ae4a1ffdaf4eed08d29

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

      Date: 2025-11-07 14:57:30 +0000

      Commit message:


	  
		
 git ignore jpeg files
 

    

  
    

      Package: EpiCompare

      Commit: 2516be0a48e14d413f2cf108f1e9d21565c31bdf

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

      Date: 2025-11-07 14:57:04 +0000

      Commit message:


	  
		
 Add peak score distribution
 

    

  
    

      Package: DESeq2

      Commit: 2ba09a95cc6aa38bb4f6c9296793890329150b74

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

      Date: 2025-11-18 08:52:29 -0500

      Commit message:


	  
		
 more cleanup
 

    

  
    

      Package: DESeq2

      Commit: 6670a2149a3c816ea15d4c50ff9e9dabe2d20973

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

      Date: 2025-11-18 08:51:50 -0500

      Commit message:


	  
		
 cleaning up outdated code and adding contributors
 

    

  
    

      Package: DESeq2

      Commit: 8c924bced1102a8dc6d6e9619433d2dc774f36a0

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

      Date: 2025-11-13 14:43:14 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: DESeq2

      Commit: 667c7b91215e5b58da939ffcd511adf36bb1f9b9

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

      Date: 2025-11-13 14:42:58 -0500

      Commit message:


	  
		
 fixing some stray bugs
 

    

  
    

      Package: vsclust

      Commit: c1328df5b47b6a01031e43bc62015c045586b550

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2025-11-18 14:19:49 +0100

      Commit message:


	  
		
 fix for visualization
 

    

  
    

      Package: vsclust

      Commit: 318a2e747cf3332c5596ec31b7876b2da575dd1e

      Author:  veitveit <veits@bmb.sdu.dk> 

      Date: 2025-11-18 14:06:16 +0100

      Commit message:


	  
		
 branched shiny validate to warning
 

    

  
    

      Package: extraChIPs

      Commit: 980cc7879595949382d218ec101fc076fcf1092d

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-18 21:49:20 +1030

      Commit message:


	  
		
 Version bump after bugfix
 

    

  
    

      Package: extraChIPs

      Commit: 784e7039a3f72a877e50c61c3e0e84fa16d2a77e

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-18 21:03:38 +1030

      Commit message:


	  
		
 Bugfix in name handling
 

    

  
    

      Package: rhdf5

      Commit: 65346c5b038e056ff5f11e443504556555161e56

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-18 11:45:52 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: 52b19a46ec086937171c7f315dd1a42ebecc6280

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-18 11:45:28 +0100

      Commit message:


	  
		
 Document change about skipped tests
 

    

  
    

      Package: rhdf5

      Commit: 0cab22cf254d2f59e7b7ed0dc3effa0ff189e41b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-18 10:55:25 +0100

      Commit message:


	  
		
 Close open H5 connections
 

    

  
    

      Package: rhdf5

      Commit: 7d34f18d2cfa31b852447bf874f914388496ab81

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-18 10:47:56 +0100

      Commit message:


	  
		
 Use skip() to skip tests

So that we get a report of how many tests were skipped
 

    

  
    

      Package: rhdf5

      Commit: 64cb21ad806ce1f5c667d50c62bf0fef02c35b72

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 22:56:44 +0100

      Commit message:


	  
		
 Remove lines manually deleting tempfiles
 

    

  
    

      Package: rhdf5

      Commit: 3b46297b2264f10fc6c6553ccc8398b1c9a2af9e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 22:47:28 +0100

      Commit message:


	  
		
 Use withr::local_tempfile() in tests
 

    

  
    

      Package: rhdf5

      Commit: 1a8bd63dbf00b1cf4eb2ed56e78c61f519175111

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-03 16:07:45 +0100

      Commit message:


	  
		
 Use testthat::set_state_inspector() to ensure all connections are closed
 

    

  
    

      Package: PhyloProfile

      Commit: 139f3a1c66a0967b8dd7b09d699e492582823497

      Author:  AnnamTran <trvinh@gmail.com> 

      Date: 2025-11-18 11:18:17 +0100

      Commit message:


	  
		
 fixed selectTaxonRank
 

    

  
    

      Package: gDRcore

      Commit: 0db6c774dcddcbcdf7f0600395a515c479cbfd4e

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-11-18 10:49:21 +0100

      Commit message:


	  
		
 Merge pull request #187 from gdrplatform/GDR-3179

Gdr 3179 

    

  
    

      Package: gDRcore

      Commit: 81a03f07b8c1b25480974a2a991ca99cec69ecf5

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-11-17 10:06:29 +0100

      Commit message:


	  
		
 refactor: resolve conflict
 

    

  
    

      Package: gDRcore

      Commit: ba235bd9e02bd748dabfcdb22d28c754861f750f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-11-12 11:53:42 +0100

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRcore

      Commit: 4cbe2acb385c3e13b98a989128c761dcbf1a5cb2

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-11-12 11:52:40 +0100

      Commit message:


	  
		
 refactor: remove empty clid in day0 data
 

    

  
    

      Package: MetaboCoreUtils

      Commit: 6ca986fc81978e06c2aa961df79dad5ec06c69ea

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-18 10:28:10 +0100

      Commit message:


	  
		
 fix: update deprecated unit tests
 

    

  
    

      Package: sangeranalyseR

      Commit: a8787bd3d888e6d8fb0162ec25a21a194463db60

      Author:  Kuan-Hao Chao <kuanhao.chao@gmail.com> 

      Date: 2025-11-17 22:44:07 -0800

      Commit message:


	  
		
 Port DECIPHER Treeline fix to devel; bump version to 1.21.1
 

    

  
    

      Package: sangeranalyseR

      Commit: cb3e43a4621ee1e3a13ce18406e10021f00831bd

      Author:  Kuan-Hao Chao <kuanhao.chao@gmail.com> 

      Date: 2025-11-17 22:31:12 -0800

      Commit message:


	  
		
 Fix DECIPHER Treeline import; update DECIPHER minimum version
 

    

  
    

      Package: igblastr

      Commit: bafd441f280dd2a31745c37ac9f72d1c35bc83d5

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

      Date: 2025-11-17 21:10:59 -0800

      Commit message:


	  
		
 igblastr 1.1.1: More built-in AIRR germline dbs for human

Add the following built-in germline dbs:
    _AIRR.human.IGH+IGK+IGL.202401
    _AIRR.human.IGH+IGK+IGL.202401.src

These were obtained from the following AIRR-community/OGRDB datasets:
  - IGH_VDJ:     version 8 (released on 2024-01-11)
  - IGKappa_VJ:  version 3 (released on 2024-01-11)
  - IGLambda_VJ: version 2 (released on 2024-01-11)
 

    

  
    

      Package: stPipe

      Commit: 69fee697d172f26dac99b2ebefc4cb6bc12c798f

      Author:  YangXuuu <xuyang1121wws@gmail.com> 

      Date: 2025-11-18 15:26:22 +1100

      Commit message:


	  
		
 Fix testthat updates.
 

    

  
    

      Package: knowYourCG

      Commit: 7d8cd8a3b9fb018b9d755b4726add37aea3dda96

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 23:24:32 -0500

      Commit message:


	  
		
 bump to 1.7.3
 

    

  
    

      Package: knowYourCG

      Commit: 4b9ea9eb7b6c89a0cf54ee3b846015ae4ddcb9eb

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 23:16:20 -0500

      Commit message:


	  
		
 added visualization vignette
 

    

  
    

      Package: knowYourCG

      Commit: e95ff6f63da07fe649b1b12e5738fbac6ba58164

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 23:11:52 -0500

      Commit message:


	  
		
 bump to 1.7.2
 

    

  
    

      Package: knowYourCG

      Commit: c4cc864cab7db1e8b483b264a2f105845b27330a

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 22:04:16 -0500

      Commit message:


	  
		
 eliminated aes_string
 

    

  
    

      Package: knowYourCG

      Commit: dad14f966efbb910a2a6a625cada27555aaf6df9

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 21:48:14 -0500

      Commit message:


	  
		
 reorged codebase
 

    

  
    

      Package: knowYourCG

      Commit: aa4fa922a325dc1640010977bed0a28517f29b86

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-03 08:26:59 -0500

      Commit message:


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

    

  
    

      Package: knowYourCG

      Commit: 2ed9fee2370d739ed2d2beff884e1e889ab554c1

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-03 08:23:08 -0500

      Commit message:


	  
		
 tweaked array vignette
 

    

  
    

      Package: GBScleanR

      Commit: d7db53b38e747397635d43296760ef88036e03bb

      Author:  tomoyukif <f.tomoyuki@okayama-u.ac.jp> 

      Date: 2025-11-18 10:27:49 +0900

      Commit message:


	  
		
 Fix a minor bug at code to use seqOptimize().
 

    

  
    

      Package: Pirat

      Commit: c962d20af3cdd69b2b2ebc59355b120c8aabedbf

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-18 00:44:55 +0100

      Commit message:


	  
		
 Change versions
 

    

  
    

      Package: lefser

      Commit: 333fd2411085100ddc70fdbffbf1cbebb735df8d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 17:51:54 -0500

      Commit message:


	  
		
 version bump 1.21.7
 

    

  
    

      Package: lefser

      Commit: 181f02f2c98e95cf620ff55ba7b4844fe89eb122

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 17:51:35 -0500

      Commit message:


	  
		
 add unit tests for ldaFunction
 

    

  
    

      Package: BiocPkgTools

      Commit: cf66eb9b19a8e1c8f25656b15fa4ec6f68082c0c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 17:21:05 -0500

      Commit message:


	  
		
 version bump 1.29.1
 

    

  
    

      Package: BiocPkgTools

      Commit: cb7fdc193db2d40765a9ae83f6b1423a5382e087

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 17:20:13 -0500

      Commit message:


	  
		
 bug fix: use helper .get_VIEWS
 

    

  
    

      Package: doppelgangR

      Commit: ba4ccbaec90de73f6da529fa11b2b75df0bc670d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 16:50:03 -0500

      Commit message:


	  
		
 version bump 1.39.1
 

    

  
    

      Package: doppelgangR

      Commit: 96e3cf91150b06faa9577086f1c6e66bcd31f947

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 16:49:53 -0500

      Commit message:


	  
		
 .gitignore *_cache and *_files folders anywhere
 

    

  
    

      Package: doppelgangR

      Commit: 4370557f202d1a271a08ab74e27abb638761d1d1

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 16:49:02 -0500

      Commit message:


	  
		
 update README.md from vignette
 

    

  
    

      Package: doppelgangR

      Commit: 10d2bd829a24ce1fdd35f8663ae18ae0dca8c745

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 16:48:09 -0500

      Commit message:


	  
		
 update formatting in vignette
 

    

  
    

      Package: doppelgangR

      Commit: 1a565b6e3291cc9192d98a307a5db13ec9f35a61

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:59:17 -0500

      Commit message:


	  
		
 update spelling
 

    

  
    

      Package: doppelgangR

      Commit: 8e44f29bdbe60f5438298fac96cf3959c706362b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:59:09 -0500

      Commit message:


	  
		
 add info from README.md
 

    

  
    

      Package: doppelgangR

      Commit: 363ce2331921fa29a0739cbed5f92e34f2c02ca9

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:58:20 -0500

      Commit message:


	  
		
 add .gitignore files
 

    

  
    

      Package: curatedTCGAData

      Commit: 4abac81011aafbab7180702613035a585f92f40f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:34:49 -0500

      Commit message:


	  
		
 version bump 1.33.1
 

    

  
    

      Package: curatedTCGAData

      Commit: e6e1e4fc1a16efed37ec223612027f6998fdbaf5

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:28:13 -0500

      Commit message:


	  
		
 minor formatting
 

    

  
    

      Package: curatedTCGAData

      Commit: f17882506857a4dde017850744e2655e28671f7e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:27:07 -0500

      Commit message:


	  
		
 use with_mocked_bindings for testthat 3.3.0
 

    

  
    

      Package: VisiumIO

      Commit: 751bb9692d2e9a30f7166d6f20df7b301ddf0458

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:10:25 -0500

      Commit message:


	  
		
 version bump 1.7.3
 

    

  
    

      Package: VisiumIO

      Commit: 04d5bc789d30a996dbf08a0a45ba8b0c3f09eaa6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 15:10:19 -0500

      Commit message:


	  
		
 fix unit tests to not error when outs dir is available as subfolder
 

    

  
    

      Package: rigvf

      Commit: e8b16a70a401e98083e10c92774d59abfd2f9874

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

      Date: 2025-11-17 14:47:26 -0500

      Commit message:


	  
		
 fixing some test errors
 

    

  
    

      Package: rigvf

      Commit: 1c2ff31e9dac0c6337ce185c101925687334de06

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

      Date: 2025-11-17 14:11:48 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: rigvf

      Commit: cdc90b4c9ec63ad57252aba595c2eff57395c5a6

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

      Date: 2025-11-17 14:11:32 -0500

      Commit message:


	  
		
 vignette: removing plyranges pkg prefix
 

    

  
    

      Package: rigvf

      Commit: 4dea47d8b96cc33be655116eb8cf1369ce099e36

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

      Date: 2025-11-14 12:44:31 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: rigvf

      Commit: 6ae81f29c7aec9cf4cd37b1f4ec830555e2d1507

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

      Date: 2025-11-13 11:54:26 -0500

      Commit message:


	  
		
 switch gha to watch devel
 

    

  
    

      Package: terraTCGAdata

      Commit: 5c6b43b7117e0549ef61cd13518a3add08d61e83

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 13:58:31 -0500

      Commit message:


	  
		
 version bump 1.15.2
 

    

  
    

      Package: terraTCGAdata

      Commit: f7949eb6563fbaee6d8cfee2e79e721d8e1d7f01

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 13:58:26 -0500

      Commit message:


	  
		
 use GCPtools::gcloud_exists() in vignette
 

    

  
    

      Package: terraTCGAdata

      Commit: 26be867d90b9a6c31bcf73a24aa864374c5bd64d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 13:58:00 -0500

      Commit message:


	  
		
 add GCPtools to Suggests in DESCRIPTION
 

    

  
    

      Package: sesameData

      Commit: 23556bdf48cc45cfcc0e29d7c20940606dcc0507

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 12:55:12 -0500

      Commit message:


	  
		
 bump to 1.29.5, updated metadata.csv
 

    

  
    

      Package: sesameData

      Commit: b87485e4efa54cf7898026cae71a80756d81c752

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-17 12:45:06 -0500

      Commit message:


	  
		
 bump to 1.29.4, added KYCG MSA knowledgebases, EHID assignment pending
 

    

  
    

      Package: OmnipathR

      Commit: 0f1c5d0e14d3600b477a01079b0f70bbebce56d8

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-17 18:47:44 +0100

      Commit message:


	  
		
 Bump version: 3.19.1 → 3.19.2
 

    

  
    

      Package: OmnipathR

      Commit: cae3032e27bf115a7bc7c9472ec004539b8dde88

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2025-11-17 18:47:36 +0100

      Commit message:


	  
		
 `ensembl_organisms`: on build servers access the rescued repo right away; required to address timeout on BioC build machines
 

    

  
    

      Package: KEGGREST

      Commit: 70af70eded05eed08414992f8eb22f67514cd322

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 12:31:42 -0500

      Commit message:


	  
		
 version bump 1.51.1
 

    

  
    

      Package: KEGGREST

      Commit: a4877231ed7516e287b83b6612958569452440ed

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 12:30:20 -0500

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: KEGGREST

      Commit: 07d99b360163e64ce5c1492936c25e20d8064971

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 12:31:10 -0500

      Commit message:


	  
		
 remove mark.pathway.by.objects from docs
 

    

  
    

      Package: KEGGREST

      Commit: 75354737b3c110f375582e9683ad906a3e940a1d

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-17 12:30:02 -0500

      Commit message:


	  
		
 remove defunct mark.pathway.by.objects
 

    

  
    

      Package: rhdf5filters

      Commit: 9fa8553d60c2cae72c091d308b2abfa30c47af8b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 15:15:54 +0100

      Commit message:


	  
		
 Save patches applied to vendored code
 

    

  
    

      Package: rhdf5filters

      Commit: e8941a8ebaaa6bd28f2764755fa201cc836b7c8d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 15:15:32 +0100

      Commit message:


	  
		
 Fix LICENSE stub
 

    

  
    

      Package: rhdf5

      Commit: 3d819f766db99d49d26fa34bbce9912772c85419

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 13:36:23 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: f06c23e2921cbb6ce880f2a53148bf1ad74b5dc6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-13 11:34:31 +0100

      Commit message:


	  
		
 Mention pointer arithmetic fix in NEWS
 

    

  
    

      Package: rhdf5

      Commit: 4413a68ffc4791494ef3da0df2242114a8eb1813

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-11 09:37:06 +0100

      Commit message:


	  
		
 Store buf as unassigned char * for pointer arithmetic
 

    

  
    

      Package: rhdf5

      Commit: ff2a28aa44ef27667677264f2a516345e4459d83

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-11 09:36:22 +0100

      Commit message:


	  
		
 Compute H5Tget_size() outside of loop
 

    

  
    

      Package: rhdf5filters

      Commit: 7ef03cc5365968581366d0b817b6107d36652e88

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 13:42:49 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5filters

      Commit: 35333d6ee99e3032c51a16fac6452057ac18e8bb

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 13:42:28 +0100

      Commit message:


	  
		
 Mention blosc compilation fix in NEWS
 

    

  
    

      Package: rhdf5filters

      Commit: 52b0eed07202f1371a6f4a98551493bbf6ac459e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 13:39:49 +0100

      Commit message:


	  
		
 Remove outdated type def

Fix #25
 

    

  
    

      Package: rhdf5

      Commit: a457d45f2cbf09614b25afb8ceb420f672f8c4ab

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 12:29:01 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: b95d900fddfc47340efca3c92849640da938bb53

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 12:28:53 +0100

      Commit message:


	  
		
 Document lintr CI change
 

    

  
    

      Package: rhdf5

      Commit: eec795f5fa75142c464b4ebab3ef339449df459d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:35:03 +0100

      Commit message:


	  
		
 Set up lintr CI
 

    

  
    

      Package: rhdf5

      Commit: 16cdeeddf69c24185642dc17cd627012e17eae9c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:33:28 +0100

      Commit message:


	  
		
 Silence some linters for now
 

    

  
    

      Package: rhdf5

      Commit: 9bc91325829465d61453c96c4c3e17d1c84eca2c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:33:15 +0100

      Commit message:


	  
		
 Remove unused variables
 

    

  
    

      Package: rhdf5

      Commit: e2af323cc153277411f4e9358cce271c8d0edac0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:31:17 +0100

      Commit message:


	  
		
 Silence false positive Sys.setenv() lint
 

    

  
    

      Package: rhdf5

      Commit: d4735e5bf4efdfc895d278322d23c098aa54fc5e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:30:59 +0100

      Commit message:


	  
		
 Merge some successive if statements
 

    

  
    

      Package: rhdf5

      Commit: 02e981cb1254d9059b50e1c7f04bffed227739b6

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:30:40 +0100

      Commit message:


	  
		
 Remove one unnecessary ifelse()
 

    

  
    

      Package: rhdf5

      Commit: b0e45fe9f2816c33417f67890a05632933aa86a7

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:30:19 +0100

      Commit message:


	  
		
 Remove one unnecessary paste()
 

    

  
    

      Package: rhdf5

      Commit: 00a490eb81ff268180dcd7220382b2ba7f3f5686

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:29:09 +0100

      Commit message:


	  
		
 Replace a else ... if by else if
 

    

  
    

      Package: rhdf5

      Commit: 93264f1f4eb56fe03f7d0f3d09dba1cb69293d65

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:22:41 +0100

      Commit message:


	  
		
 Fix undesirable_operator lints
 

    

  
    

      Package: rhdf5

      Commit: 13f47a66eeb22bd34f1ef17750de07f7e48704b2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:18:54 +0100

      Commit message:


	  
		
 Use fixed = TRUE on regexes where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 1feba8d55b1be498bcce3726b40b500bbd381c8b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:18:37 +0100

      Commit message:


	  
		
 Remove unnecessary c()
 

    

  
    

      Package: rhdf5

      Commit: f5e4248a6b63a497df4b2ea6441d4a312be059fe

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 11:15:17 +0100

      Commit message:


	  
		
 Simplify some if_not_else lints
 

    

  
    

      Package: rhdf5

      Commit: 0db7ed1462fc66b809b5d71b27e491f2e71a7d07

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 10:47:30 +0100

      Commit message:


	  
		
 Use double quotes
 

    

  
    

      Package: rhdf5

      Commit: 829f4567acc0c05a541b070e7d9bb3d9702b1de1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 10:33:44 +0100

      Commit message:


	  
		
 Use expect_identical() where possible
 

    

  
    

      Package: rhdf5

      Commit: 803ce142be32049b0606511ccc7f836d1b038f7c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-17 12:30:24 +0100

      Commit message:


	  
		
 Fix typo and run devtools::document()
 

    

  
    

      Package: mCSEA

      Commit: dadac722fac282153b2556f251fef1d99343a2b4

      Author:  jordimartorell <jmartorellm@gmail.com> 

      Date: 2025-11-17 12:13:26 +0100

      Commit message:


	  
		
 Minor fix
 

    

  
    

      Package: extraChIPs

      Commit: 24eade6729a787f625cf3d8e2be8700da8607007

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-17 21:23:01 +1030

      Commit message:


	  
		
 Version bummp after bugfix
 

    

  
    

      Package: extraChIPs

      Commit: ceb8c570d855d88e8d9250b66443cdf66829625c

      Author:  Stevie Ped <stephen.pederson.au@gmail.com> 

      Date: 2025-11-17 18:55:40 +1030

      Commit message:


	  
		
 Bugfix in PCA labels
 

    

  
    

      Package: plaid

      Commit: 5f1f173faa55e35979f7988a1dbe6440c7e35b9a

      Author:  ESCRI11 <xavier.escriba.montagut@gmail.com> 

      Date: 2025-11-17 10:26:05 +0100

      Commit message:


	  
		
 trigger build
 

    

  
    

      Package: plaid

      Commit: 13f7c1cee8405d198708e94a0b9f26e6a619918d

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-14 02:37:09 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: plaid

      Commit: 3ce8150af350cbf7e7102403f845b80c6bbb99b7

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-14 02:08:23 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: plaid

      Commit: 5b008dc23129ae11e9fd79c9e21e69212e2919dd

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-14 02:07:26 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: plaid

      Commit: dd525269538c8d0999d7156960f4f719a5ce9644

      Author:  Ivo Kwee <ivo.kwee@gmail.com> 

      Date: 2025-11-14 02:06:20 +0100

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: gDRutils

      Commit: 5ae03224e4cf54b80cb37fd63e3116d05b317625

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-11-17 10:03:12 +0100

      Commit message:


	  
		
 Merge pull request #176 from gdrplatform/GDRDS-73

Gdrds 73 

    

  
    

      Package: gDRutils

      Commit: 45277f70bbcc49d6a7a533afd13436c4fbf08cf4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-11-04 10:08:16 +0100

      Commit message:


	  
		
 refactor: update as per review
 

    

  
    

      Package: gDRutils

      Commit: 49b5a2c1be643d5cfbb94767e5870a73f7770da2

      Author:  Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com> 

      Date: 2025-11-03 14:45:23 +0000

      Commit message:


	  
		
 chore: bump version and update changelog
 

    

  
    

      Package: gDRutils

      Commit: f310ed6c96fe2fd926ba43fda36774d9b06f58d1

      Author:  Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com> 

      Date: 2025-11-03 14:44:57 +0000

      Commit message:


	  
		
 refactor: add support for merging SE with different batches
 

    

  
    

      Package: GloScope

      Commit: 458539a814210fafed1c5b0b800a06af9b3edcaf

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-17 01:02:55 -0800

      Commit message:


	  
		
 bump verson
 

    

  
    

      Package: GloScope

      Commit: fe1dcd32da2846789c9e2e13e431e16275a32b00

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 05:40:03 -0800

      Commit message:


	  
		
 update maintainer of package
 

    

  
    

      Package: GloScope

      Commit: 009759b89d937581ec3c3118b3fa9c2f3173776c

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 05:38:55 -0800

      Commit message:


	  
		
 update maintainer of package
 

    

  
    

      Package: GloScope

      Commit: 03c5be97273a3feedda31fa51373105e00dcc553

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 05:25:57 -0800

      Commit message:


	  
		
 small updates to tests
 

    

  
    

      Package: GloScope

      Commit: bc86140a34c2adff761253d16ea56cf699cb37a8

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 05:23:23 -0800

      Commit message:


	  
		
 correct error I introduced
 

    

  
    

      Package: GloScope

      Commit: 9df9abc53f98a1b8d7ff4681ddd9867b7f2bb9c0

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 04:25:15 -0800

      Commit message:


	  
		
 Merge branch 'devel'
 

    

  
    

      Package: GloScope

      Commit: 71895262267ad36bbf266b64e032f3af04e81154

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 04:13:09 -0800

      Commit message:


	  
		
 add test about data frame and update documentation
 

    

  
    

      Package: GloScope

      Commit: 6334e8409b65131fd027cc3dec40dd6779a4d620

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 04:09:14 -0800

      Commit message:


	  
		
 change how handle missing column names
 

    

  
    

      Package: GloScope

      Commit: d3763022106c474f3154912d6df5c49ca4ab252a

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 03:58:26 -0800

      Commit message:


	  
		
 Merge branch 'main' into TerrySu1016-add-prefitted-error-msg
 

    

  
    

      Package: GloScope

      Commit: 22f9246bffae93f282a219f9da60a149bc619149

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 03:56:43 -0800

      Commit message:


	  
		
 change tests so colnames issue only checked once
 

    

  
    

      Package: GloScope

      Commit: 6b52bd3d0c58641ddff3af197631e2cde049f7c9

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 03:47:59 -0800

      Commit message:


	  
		
 add check if user gives no column names
 

    

  
    

      Package: GloScope

      Commit: 89c0dce28d4c20520feeba4746dd9d16f5ad585b

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 03:41:56 -0800

      Commit message:


	  
		
 small formatting change
 

    

  
    

      Package: GloScope

      Commit: 2807a4eea7af9b7762f6145a4bca91d7d432b97b

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 02:42:28 -0800

      Commit message:


	  
		
 add expect_silent to some tests
 

    

  
    

      Package: GloScope

      Commit: bab1e097d75332510a7efe862e165665aac70a52

      Author:  Elizabeth Purdom <epurdom@stat.berkeley.edu> 

      Date: 2025-11-13 02:30:52 -0800

      Commit message:


	  
		
 edited error message
 

    

  
    

      Package: GloScope

      Commit: 4bdd19ece90a4556ed27a9fd785fca0f290357cd

      Author:  TerrySu1016 <suquanjin178@hotmail.com> 

      Date: 2025-11-12 21:27:16 -0800

      Commit message:


	  
		
 edit calc_dens.R for new version R 4.5.2
 

    

  
    

      Package: GloScope

      Commit: 1a9c2a2ed2f340956bc4a826ec61e4c7a967f6a5

      Author:  TerrySu1016 <suquanjin178@hotmail.com> 

      Date: 2025-11-12 19:02:54 -0800

      Commit message:


	  
		
 finished error message editing
 

    

  
    

      Package: SparseArray

      Commit: e4d33fe301dd0be5e112493de423055c671ec149

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

      Date: 2025-11-16 22:55:00 -0800

      Commit message:


	  
		
 more renaming at the C level
 

    

  
    

      Package: BiocSingular

      Commit: 9c87cf678596f0c7b47cd2e23a3ff0f18d362262

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

      Date: 2025-11-17 15:57:46 +1100

      Commit message:


	  
		
 Minor fixes to docs and tests, updated ignore file.
 

    

  
    

      Package: BiocSingular

      Commit: 0d67d7b7910687f1b7b640ef55c149e372c49134

      Author:  Nolan H. Hamilton <57746191+nolan-h-hamilton@users.noreply.github.com> 

      Date: 2025-11-16 23:47:18 -0500

      Commit message:


	  
		
 Fix compute_center_and_scale() when number of rows is 1. (#19)

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com> 

    

  
    

      Package: SparseArray

      Commit: 3d20f3cdc1691e6ee93357cd1f3fe33c4ca992c6

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

      Date: 2025-11-16 21:50:32 -0800

      Commit message:


	  
		
 try to use a more consistent naming scheme at the C level
 

    

  
    

      Package: SparseArray

      Commit: 242899c21acd5e47168cd1a582befefcdc584e1d

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

      Date: 2025-11-16 18:37:46 -0800

      Commit message:


	  
		
 SparseArray 1.11.2: Complete refactoring of .subassign_SVT_by_Mindex()

Internal function .subassign_SVT_by_Mindex() is the workhorse behind
subassignment of an SVT_SparseArray object by a matrix subscript
(a.k.a. M-index). This new implementation is based on C-level helper
subassign_leaf_by_OPBuf(). It's more than twice faster and uses
about 20% less memory compared to the original implementation.
 

    

  
    

      Package: iSEE

      Commit: 827fb90424da69c0ff977e7243941f478532fb69

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 21:54:33 +0100

      Commit message:


	  
		
 Minor bug fixes (#702)

* Use linewidth instead of size for lines (and require ggplot2 >= 3.4.0)

* Allow sampling resolution and guide sizes to be non-integer

* Strip Windows line endings when validating inputs in ace editor (to avoid errors e.g. when pasting a list of genes from Excel)

* Load ggplot2 in the tracked code

* Harmonize call to .create_box_observers with function definition

* Fix tests

* Fix bug in the communication of collapsible box status

* Update Bioc version in GHA

* Bump version, update NEWS

---------

Co-authored-by: Kevin Rue-Albrecht <kevinrue67@gmail.com> 

    

  
    

      Package: bettr

      Commit: 4877911aaebfcbe1d176e2a95a9180c26020eeb8

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 19:22:40 +0100

      Commit message:


	  
		
 Edits to vignette chunks (BiocCheck notes)
 

    

  
    

      Package: bettr

      Commit: 8e5d2f3c3d4bb5a15d038ccb3fb914a6afa634c8

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 19:21:49 +0100

      Commit message:


	  
		
 Add missing import
 

    

  
    

      Package: bettr

      Commit: f58a02b8349d31b54ecd05aaf812f2c8b4739c67

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 19:11:51 +0100

      Commit message:


	  
		
 Add unit tests
 

    

  
    

      Package: bettr

      Commit: 1681b8c8beecc9d8c3a59a40225bc30f03e2ad6d

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 16:22:47 +0100

      Commit message:


	  
		
 Add missing imports to bettr(), reoxygenize
 

    

  
    

      Package: bettr

      Commit: 60d14be0c208fd61f709a0709f40f003188c94dd

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 16:20:51 +0100

      Commit message:


	  
		
 Check validity of serverMode and cacheVersion in bettr()
 

    

  
    

      Package: bettr

      Commit: 09eb4af8b606f50ab6b0f3a4f9a6b4526e9905cb

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 16:18:29 +0100

      Commit message:


	  
		
 Simplify .assertScalar call
 

    

  
    

      Package: bettr

      Commit: b1f0eebcd4de62e040ecf77d9f6f2e657336626d

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 16:17:38 +0100

      Commit message:


	  
		
 Add Daniel as author to function documentation
 

    

  
    

      Package: bettr

      Commit: d1e6981a682a581205f427f946a4c613f4aae981

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 16:14:35 +0100

      Commit message:


	  
		
 Fix indentation
 

    

  
    

      Package: bettr

      Commit: ce6ce2d31db5e6baf59a1b7b45ea94e0a8b9c0f7

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 15:57:08 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: bettr

      Commit: db91bdc606914e94cdd5880e6e0a48dfceedadaa

      Author:  Charlotte Soneson <charlottesoneson@gmail.com> 

      Date: 2025-11-16 15:52:35 +0100

      Commit message:


	  
		
 Merge pull request #25 from DanInci/feature/render_results_on_the_fly

Hot-reloading datasets 

    

  
    

      Package: bettr

      Commit: c671399a7014f2ae30880fd922fae30d7c02c70a

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-16 13:10:34 +0100

      Commit message:


	  
		
 Restore missing code blocks
 

    

  
    

      Package: bettr

      Commit: 7dfae1ed030c58886756dbf019b246a5e132647b

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-06 12:57:59 +0100

      Commit message:


	  
		
 Some identation fixes
 

    

  
    

      Package: bettr

      Commit: 7deb89991b616463df95d5b2680dc1057f27f8ef

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-06 12:53:06 +0100

      Commit message:


	  
		
 Early return when checking for serverMode in UI components
 

    

  
    

      Package: bettr

      Commit: 92988b2533d400d97da44155c4270b7c09bf1d2c

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-06 12:05:35 +0100

      Commit message:


	  
		
 Reorder UI components, such that diff with dev is easier to observe
 

    

  
    

      Package: bettr

      Commit: 08d07142baed3bcc6c783393fb68e1bad5a73e74

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-06 11:57:53 +0100

      Commit message:


	  
		
 Refactor duplicated code
 

    

  
    

      Package: bettr

      Commit: 830153f2422307b647a5e3f37d0e4c551e257c2d

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-11-06 11:51:47 +0100

      Commit message:


	  
		
 Renable metric transformation UI. Remove .gitignore, modify example. Add myself to author list
 

    

  
    

      Package: bettr

      Commit: 63c02bd8391628689a7917074b6f4c727360afab

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-28 13:02:48 +0100

      Commit message:


	  
		
 Resolve PR comments
 

    

  
    

      Package: bettr

      Commit: 64b4b022ae3474687bb16ec7ee9139bc64bb6e2d

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-19 11:26:40 +0300

      Commit message:


	  
		
 Resolve PR comments
 

    

  
    

      Package: bettr

      Commit: 15a101d5a1617f8f39428ebd51097339e2baf738

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-18 21:01:33 +0300

      Commit message:


	  
		
 Remove Load Data accordion panel if better is not in server mode
 

    

  
    

      Package: bettr

      Commit: 7cf9103912c9044cbce4d21cb61b634bf2a66abb

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-18 20:42:03 +0300

      Commit message:


	  
		
 Cache and jsonFile and jsonUrl should only when when bettr is in server mode
 

    

  
    

      Package: bettr

      Commit: 9bc556cd04daeae385a6e9c1dc735bc9479f31d4

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-18 20:28:12 +0300

      Commit message:


	  
		
 Remove application state cache
 

    

  
    

      Package: bettr

      Commit: 09e0b72b0fbfa921aea44ee158332f4df212a317

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-16 23:46:59 +0300

      Commit message:


	  
		
 Fix issue with categorial metrics
 

    

  
    

      Package: bettr

      Commit: 422e286dce1f198cc1845eb39cd3ae068f331446

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-10 14:06:56 +0200

      Commit message:


	  
		
 Remove duplicated tests
 

    

  
    

      Package: bettr

      Commit: 0d5e0475272e7e336a0f37b429c8df0c69ff0e39

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-09 13:53:22 +0200

      Commit message:


	  
		
 add jsonlite to description
 

    

  
    

      Package: bettr

      Commit: da02ebb91d7a6b71a09997da4aab771905c49252

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 22:41:15 +0200

      Commit message:


	  
		
 Write a guide for newly proposed bettr server mode
 

    

  
    

      Package: bettr

      Commit: 51efd320f989157685f08c19d68e22f11ec881ca

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 22:28:05 +0200

      Commit message:


	  
		
 Add jsonFile and jsonUrl query params for programmatic loading
 

    

  
    

      Package: bettr

      Commit: c75bb4bdf7512cf36a6d8106dbe53cee76d339c6

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 22:01:14 +0200

      Commit message:


	  
		
 Rename uploadMode to serverMode
 

    

  
    

      Package: bettr

      Commit: cb147de9b129830c3a30cbecb87cdfc4bb9c7d20

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 21:55:27 +0200

      Commit message:


	  
		
 Add local caching for persisting both uploaded JSON data and session state
 

    

  
    

      Package: bettr

      Commit: 4da0521d0145a3fe92d0532f94c11c8bd9de1480

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 18:34:55 +0200

      Commit message:


	  
		
 Adapt bettr to accept bettr.json uploads for configuring the visualisations
 

    

  
    

      Package: bettr

      Commit: c99c4378606d6149752eeaedc06a1af33fe85c6e

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 16:37:30 +0200

      Commit message:


	  
		
 Add encoders & decoders for betterSE to json
 

    

  
    

      Package: bettr

      Commit: 3ea836ffa66a8b4bb4446d09f5dbd8e9cf059d40

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 16:04:42 +0200

      Commit message:


	  
		
 Fix initial rendering of the plots
 

    

  
    

      Package: bettr

      Commit: ba35c0f2db3a59840fe827168fa72d9d6448f555

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 14:30:08 +0200

      Commit message:


	  
		
 Merge branch 'devel' of github.com:federicomarini/bettr into feature/render_results_on_the_fly
 

    

  
    

      Package: bettr

      Commit: e761246c61d17308cd5bbdfefd457127719fefe2

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-10-07 13:35:03 +0200

      Commit message:


	  
		
 Move initialization of uploadMode after bettrSE initialization
 

    

  
    

      Package: bettr

      Commit: fd1e03af0d2b16743e97f04c3028736e89fb3144

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-08-12 16:49:52 +0200

      Commit message:


	  
		
 Some polishing touches
 

    

  
    

      Package: bettr

      Commit: 6a3ce8a0251a4f32b5d67a484ca3121ea716aaa9

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-08-12 16:30:13 +0200

      Commit message:


	  
		
 Integrate bettr-upload into bettr-main
 

    

  
    

      Package: bettr

      Commit: af5a9e300fc850aca1e0756e69ed555cd9551cb0

      Author:  Daniel Incicau <daniel.incicau@gmail.com> 

      Date: 2025-08-12 12:35:34 +0200

      Commit message:


	  
		
 Allow better to open in upload mode
 

    

  
    

      Package: sesameData

      Commit: e7e2f936fe0f64411935e64aaf769fb049b7b2bf

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-16 11:14:31 -0500

      Commit message:


	  
		
 bump to 1.29.3, updated MSA.address, added KYCG.MSA.Mask.20240513 KYCG.HM450.Mask.20240513 MSA.9.SigDF
 

    

  
    

      Package: sesameData

      Commit: 67ddfc50af546f4ef4ec210f1df2bde0002ec9ab

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-11 09:04:40 -0500

      Commit message:


	  
		
 minor, message omitted
 

    

  
    

      Package: LimROTS

      Commit: 5bf8d4ce62a8f8a81e82337ef8db5eb2c0260d68

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-16 14:35:50 +0200

      Commit message:


	  
		
 Add publication citation
 

    

  
    

      Package: LimROTS

      Commit: 2d096b736c6a3df9cefe8d5765ee90ad7514e041

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-16 13:31:27 +0200

      Commit message:


	  
		
 Merge branch 'devel' of https://github.com/AliYoussef96/LimROTS into bioc-devel

 Your branch is up to date with 'bioc/devel'.
 

    

  
    

      Package: LimROTS

      Commit: ebf750254af9971af0c3596ffc3ad8fde999248b

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-16 13:24:45 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: LimROTS

      Commit: 5431cbfeb71f194d32590523aa2a268ba52dceaa

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-16 11:53:26 +0200

      Commit message:


	  
		
 Add files via upload 

    

  
    

      Package: LimROTS

      Commit: fd7df7417feba0aced894953e5beae5de5075058

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-11-16 10:18:47 +0200

      Commit message:


	  
		
 Bump version from 1.1.4 to 1.3.0 

    

  
    

      Package: LimROTS

      Commit: e461c8572cd11abcbade3bafab490fe823cc7985

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2025-06-17 10:03:38 +0300

      Commit message:


	  
		
 Update README.md 

    

  
    

      Package: SparseArray

      Commit: b347c1b72766a694f064a36b8962799e1c7f23fa

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

      Date: 2025-11-15 23:41:02 -0800

      Commit message:


	  
		
 more refactoring of C-level helper subassign_leaf_by_OPBuf()
 

    

  
    

      Package: sfi

      Commit: 9019c191eca061f4e5fc4a9c731c04717657dfc1

      Author:  yufree <yufree@live.cn> 

      Date: 2025-11-16 11:04:17 +0800

      Commit message:


	  
		
 Change demo data with smaller size
 

    

  
    

      Package: CBN2Path

      Commit: 8ea4403a569f7f0de05b34d0aba71ec254cc49f7

      Author:  William Choi-Kim <will.choi.kim@gmail.com> 

      Date: 2025-11-15 16:04:20 -0600

      Commit message:


	  
		
 update maintainers
 

    

  
    

      Package: ImageArray

      Commit: 7466c0c25849b3c88c3ffc911900af74af1eddf7

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-15 12:35:38 +0100

      Commit message:


	  
		
 bump version for bioc review
 

    

  
    

      Package: ImageArray

      Commit: a769938a47e2bb39e325351ab72845bb8605133b

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-15 12:34:33 +0100

      Commit message:


	  
		
 remove some code commented out
 

    

  
    

      Package: ImageArray

      Commit: bc80de412ea0ecdde892e779c426e0ba462c7d8a

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-15 00:28:35 +0100

      Commit message:


	  
		
 update documentation
 

    

  
    

      Package: ImageArray

      Commit: 4116f97185bab667b98287fcc5970849ed24e04e

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-14 23:59:26 +0100

      Commit message:


	  
		
 update README
 

    

  
    

      Package: ImageArray

      Commit: 4b0ecd250f6d47270b8abb25a9efea0ae8fb69fa

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-13 01:10:06 +0100

      Commit message:


	  
		
 small changes to documentation
 

    

  
    

      Package: ImageArray

      Commit: 601d171d5d957c960c728864b50bd634ec32c4c9

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-13 01:00:51 +0100

      Commit message:


	  
		
 small updates to README
 

    

  
    

      Package: ImageArray

      Commit: 669d5c9a673f2ac6c75e22b06378a01163b0cfe4

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-13 00:52:03 +0100

      Commit message:


	  
		
 remove pdf
 

    

  
    

      Package: ImageArray

      Commit: a43d868128a04061c5fa5ce514305d44d8b06faa

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-13 00:51:27 +0100

      Commit message:


	  
		
 update vignette
 

    

  
    

      Package: ImageArray

      Commit: 5106c1ad4e9f4f0b44691c365facc7e03be7e538

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-11 09:10:59 +0100

      Commit message:


	  
		
 fix NAMESPACE
 

    

  
    

      Package: ImageArray

      Commit: 69764abaf90745c387b1c7cd9e29a8399409c24a

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-11 07:25:54 +0100

      Commit message:


	  
		
 send RBioFormats to Suggests
 

    

  
    

      Package: ImageArray

      Commit: 0402f55c2f4dd293c254a3004e0b6096e267a525

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-11 00:13:57 +0100

      Commit message:


	  
		
 remove plot
 

    

  
    

      Package: ImageArray

      Commit: 1a6aab7d43fc2d13a7739d7a15ada0daf6f563e6

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-11 00:13:33 +0100

      Commit message:


	  
		
 update vignette
 

    

  
    

      Package: ImageArray

      Commit: 1d970ccd3e304d5cad97b9480476b2774bdecc7e

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 20:21:11 +0100

      Commit message:


	  
		
 add remote installation to GHA
 

    

  
    

      Package: ImageArray

      Commit: 33aaab43c287442b1431e6f2d937d8f33b11ea26

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:42:42 +0100

      Commit message:


	  
		
 fix man and vignettes
 

    

  
    

      Package: ImageArray

      Commit: 0ef7f5cd0f2559123a79b23167cf2be59aa429cd

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:39:52 +0100

      Commit message:


	  
		
 update some wording
 

    

  
    

      Package: ImageArray

      Commit: a88d7e595ae8c00273c4233142093172b6b5d3e6

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:37:41 +0100

      Commit message:


	  
		
 final lining
 

    

  
    

      Package: ImageArray

      Commit: b91ff4fd1bb490cfc00b40b09013a8e054f45ead

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:36:15 +0100

      Commit message:


	  
		
 update lines
 

    

  
    

      Package: ImageArray

      Commit: 4fd7607696b999b58e3ce8a820d9283d0a95e75c

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:30:23 +0100

      Commit message:


	  
		
 add align to img
 

    

  
    

      Package: ImageArray

      Commit: 7a19c9871a5be4e1858c22415b1838a775d07aaf

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:25:58 +0100

      Commit message:


	  
		
 remove borders
 

    

  
    

      Package: ImageArray

      Commit: 76bab6b159f31e308bb6aabe6efa3a81d0db89a2

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:25:09 +0100

      Commit message:


	  
		
 remove borders
 

    

  
    

      Package: ImageArray

      Commit: f2d94a9c30e3e8bb284ee699cd2f350e982114bd

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:23:10 +0100

      Commit message:


	  
		
 remove lines in table
 

    

  
    

      Package: ImageArray

      Commit: 7f79eddac7abaef27403355893e511314c13ea52

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:15:42 +0100

      Commit message:


	  
		
 update README column
 

    

  
    

      Package: ImageArray

      Commit: 634329ae08c1ee6e5378d4acabb542dc29846312

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 15:13:40 +0100

      Commit message:


	  
		
 update README columns
 

    

  
    

      Package: ImageArray

      Commit: b024031f9542da1649cc7826260339c44876f588

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-09 14:58:19 +0100

      Commit message:


	  
		
 update README
 

    

  
    

      Package: ImageArray

      Commit: fbef151bcc092b8e6e17a90100132313efb15ae5

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-08 21:24:49 +0100

      Commit message:


	  
		
 update README
 

    

  
    

      Package: ImageArray

      Commit: 9b50166d65956b2b24221298dd45019d7696da6b

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-04 23:45:17 +0100

      Commit message:


	  
		
 change class name to ImageArray
 

    

  
    

      Package: ImageArray

      Commit: 39398e4a17687d1859258799772b8390c0e044a2

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-11-01 00:05:44 +0100

      Commit message:


	  
		
 fix as.raster bug
 

    

  
    

      Package: ImageArray

      Commit: 4ce4e8893a94a47b7ea92311eb6bc15271ee1071

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-29 23:56:11 +0100

      Commit message:


	  
		
 remove files
 

    

  
    

      Package: ImageArray

      Commit: 1614b5026ca99bb460888c1274e4ca5afcd8a8f6

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-29 14:34:37 +0100

      Commit message:


	  
		
 small update to show method
 

    

  
    

      Package: ImageArray

      Commit: bcc7fee75d0e24b848633c5935844cc804e3a76c

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-29 14:32:56 +0100

      Commit message:


	  
		
 replace series with levels, change show method
 

    

  
    

      Package: ImageArray

      Commit: 3ff670533eaeb7485e0e30cbb5cb9745914eb6fa

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-29 12:28:55 +0100

      Commit message:


	  
		
 remove suppress message
 

    

  
    

      Package: ImageArray

      Commit: b3ef68e01be6b8e91e0698e191ca6240415d3dce

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-29 02:01:03 +0100

      Commit message:


	  
		
 implement xyc metadata to ImgArray
 

    

  
    

      Package: ImageArray

      Commit: 0146a0b459b8f8d1c62136ee300d5ccaab0cb907

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-23 17:50:56 +0200

      Commit message:


	  
		
 add git(hub) to rbuildignore
 

    

  
    

      Package: ImageArray

      Commit: cb4b218f69c961f276a351ad5c620993307ece53

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-23 17:09:39 +0200

      Commit message:


	  
		
 add check GHA
 

    

  
    

      Package: ImageArray

      Commit: 7729f13ac540e2183e0d0e29270aac912ddfbfdf

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 16:49:32 +0200

      Commit message:


	  
		
 Merge branch 'aperm' into devel
 

    

  
    

      Package: ImageArray

      Commit: 4c344572d35a755e77cc5ab6f216707be72ada00

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 15:08:48 +0200

      Commit message:


	  
		
 remove commented out documentation
 

    

  
    

      Package: ImageArray

      Commit: 888d3b732c1d2d82c33ade843b97fbfe5eec0183

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 15:07:59 +0200

      Commit message:


	  
		
 Merge branch 'devel' into aperm
 

    

  
    

      Package: ImageArray

      Commit: 0622c9af842993c1921f0902d02ba30947f93df1

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 15:07:36 +0200

      Commit message:


	  
		
 remove BFArray(seed) documentation
 

    

  
    

      Package: ImageArray

      Commit: a755a9bd3727121869fe99c38b671c75f08a50cb

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 01:30:19 +0200

      Commit message:


	  
		
 allow max.pixel.threshold to be specified by writeImgArray
 

    

  
    

      Package: ImageArray

      Commit: 0cd857774d1fd98fd800a2f96c4d7d92702a51a4

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-19 00:53:32 +0200

      Commit message:


	  
		
 correct dimensionality of image arrays, remove aperm in tutorials and change examples
 

    

  
    

      Package: ImageArray

      Commit: 5df3f5ecc791fcba9dab2f65c9a88f98a07f0f3a

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 20:41:55 +0200

      Commit message:


	  
		
 remove pdf in tests
 

    

  
    

      Package: ImageArray

      Commit: 77ce655aacf88b7bf9b47c9b12c12075756c12d4

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 15:59:09 +0200

      Commit message:


	  
		
 remove documentation of BFArray(seed) class, remove BFMatrix ... drop export of BFArray
 

    

  
    

      Package: ImageArray

      Commit: 303811a11f6c54e5b7a758da4e4a1d12bbc6d984

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 15:47:40 +0200

      Commit message:


	  
		
 drop export on BFArray
 

    

  
    

      Package: ImageArray

      Commit: 091c006d9c9a4a6e80cd6489b17987515179b6b0

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 14:49:47 +0200

      Commit message:


	  
		
 suppress existing group message
 

    

  
    

      Package: ImageArray

      Commit: 2fdba96bb288a587144df72b1e2f508bc6b829e1

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 14:39:58 +0200

      Commit message:


	  
		
 remove knitr on top of vignette
 

    

  
    

      Package: ImageArray

      Commit: 4dd40c8df76024ee721e9508e5707c2c750e508f

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 14:36:14 +0200

      Commit message:


	  
		
 remove Array_OR_ArraySeed
 

    

  
    

      Package: ImageArray

      Commit: d7709d6ec92e22154db0a2c92d045ce87ecaf48e

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 14:06:34 +0200

      Commit message:


	  
		
 use BiocStyle in vignette and README
 

    

  
    

      Package: ImageArray

      Commit: 4e621d7f6d8a5a499f011a2cdeb5765bac5a0fb5

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 13:50:50 +0200

      Commit message:


	  
		
 remote `install_github` instructions
 

    

  
    

      Package: ImageArray

      Commit: 9a2d669fa728b5c6749e1bedff886f3adc225893

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 13:46:34 +0200

      Commit message:


	  
		
 update DESCRIPTION
 

    

  
    

      Package: ImageArray

      Commit: 1450de2576a669dbb778f59385fadcf08946cd9b

      Author:  Artur-man <artur-man@hotmail.com> 

      Date: 2025-10-18 13:18:43 +0200

      Commit message:


	  
		
 replace `mat` and `mat_list` with `arr` and `imgarray`
 

    

  
    

      Package: limpa

      Commit: 07af3cb7d6ecc780d049d9dc051ea1d25f792a84

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

      Date: 2025-11-15 09:22:42 +1100

      Commit message:


	  
		
 Add GitHub URL to DESCRIPTION.
 

    

  
    

      Package: limpa

      Commit: e4cda1feef336c8ecf7d04249a2c80e297d498ea

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

      Date: 2025-11-15 09:11:19 +1100

      Commit message:


	  
		
 limpa 1.3.1
- readDIANN() now detects format automatically from file extension.
- Default file name updated to "report.parquet" instead of "Report.tsv".
- Update default `q.columns` for readDIANN().
- Mention readFragPipe() and readMaxQuant() in vignette.
 

    

  
    

      Package: MultiAssayExperiment

      Commit: b9184840da9ae3697d19cc152aede68798841e30

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 17:23:31 -0500

      Commit message:


	  
		
 version bump 1.37.2
 

    

  
    

      Package: MultiAssayExperiment

      Commit: 125d1a185b96a2b83c294d7672a9a562d191f7d2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 17:06:33 -0500

      Commit message:


	  
		
 use with_mocked_bindings and mock internal thin wrapper
 

    

  
    

      Package: AnVILGCP

      Commit: a779c082280ed961d84c42c79205fa1a918fd9bb

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 16:24:10 -0500

      Commit message:


	  
		
 version bump 1.5.3
 

    

  
    

      Package: AnVILGCP

      Commit: 671ece45c1c28d56ff26ee176643908ca8526160

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 16:24:05 -0500

      Commit message:


	  
		
 use with_mocked_bindings
 

    

  
    

      Package: AnVIL

      Commit: 9e3c141066590d3d14c2b88b96297e065d34b872

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 15:52:51 -0500

      Commit message:


	  
		
 version bump 1.23.1
 

    

  
    

      Package: AnVIL

      Commit: 7fad8142980ce3d7267a06d3ff04eec315afd8e6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 15:52:48 -0500

      Commit message:


	  
		
 use GCPtools::gcloud_exists
 

    

  
    

      Package: lefser

      Commit: 7c5b8ae71d6c250e31da012e47ab546067beab9b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 14:13:09 -0500

      Commit message:


	  
		
 version bump 1.21.6
 

    

  
    

      Package: lefser

      Commit: 4834e58ef0eb856ec55d7a3cb89a2ff7ed135e1e

      Author:  Sehyun Oh <shbrief@hotmail.com> 

      Date: 2025-11-14 14:08:59 -0500

      Commit message:


	  
		
 Merge pull request #91 from waldronlab/bugfix/tax_strings_split

cut with | and get last position in taxonomy string 

    

  
    

      Package: lefser

      Commit: 62b1a46f6d5d6e9a69b43f79066a89900d033c9b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 12:05:59 -0500

      Commit message:


	  
		
 cut with | and get last position in taxonomy string
 

    

  
    

      Package: lefser

      Commit: f1bea8cd98805249bf0dd29c83cf903a40953558

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:49:00 -0500

      Commit message:


	  
		
 version bump 1.21.5
 

    

  
    

      Package: lefser

      Commit: 447161c640222da12697a44d4e843c5a9b7b1d45

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:46:02 -0500

      Commit message:


	  
		
 fix formatting lefser.R

- clean up spacing in example
 

    

  
    

      Package: lefser

      Commit: 4c77e9ad9f8982a0a9f17166048feca9050f0a8e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:39:31 -0500

      Commit message:


	  
		
 update NEWS.md
 

    

  
    

      Package: lefser

      Commit: 15bf801b8e12d7587f7fbadad0efc1970cd1f12e

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:27:33 -0500

      Commit message:


	  
		
 version bump 1.21.4
 

    

  
    

      Package: lefser

      Commit: b32f3b7cc73e8f841774fec971e4df7f59dcaf38

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:27:28 -0500

      Commit message:


	  
		
 update NEWS.md
 

    

  
    

      Package: lefser

      Commit: dcc410ad30a0c90087176a6bb5d45ad70dca9d28

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:25:10 -0500

      Commit message:


	  
		
 version bump 1.21.3
 

    

  
    

      Package: lefser

      Commit: 4e485d0bfd46c110ebf4a54a3f308aff7d4eb546

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-14 13:22:23 -0500

      Commit message:


	  
		
 compare data[, "class"] with actual value in classes
 

    

  
    

      Package: rhdf5

      Commit: 1da9c5800a02cbc48c8e3ee8ba9ae3f0b31548f7

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-14 18:09:01 +0100

      Commit message:


	  
		
 Fix more rchk issues
 

    

  
  


</div>

</div>