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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: PIUMA
Commit: 5ec02ede9ec802b040efad8082721d92877f8935
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2025-12-31 16:30:46 +0100
Commit message:

 updates for PIUMA 1.7.1
Package: CTCF
Commit: 193d94ec069089c199190250a5959f305e34fee3
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2025-12-31 12:41:46 +0000
Commit message:

 Comment out plyranges
Package: spatialHeatmap
Commit: 38d22d674e5f6347d3cfb26b65276add332b537e
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:52:38 +0800
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/spatialHeatmap into devel
Package: spatialHeatmap
Commit: 3ca3e109dffd3f3bb75f411363dcc4805e4064a2
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:11:52 +0800
Commit message:

 Version bump.
Package: spatialHeatmap
Commit: d15109a03a3012a38ef8687fd1a00ffffadb1c70
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:10:04 +0800
Commit message:

 Small update.
Package: spatialHeatmap
Commit: 72c815bdea92cfb199998d2013ea5fa63478a086
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:09:34 +0800
Commit message:

 Re-created srt_sc.rds to address the error related to "VisiumV1" object.
Package: annoLinker
Commit: f358cb55c3b16ab8744badc00890800b1ebadd0e
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 11:37:10 -0500
Commit message:

 update the code style.
Package: annoLinker
Commit: 63bb8f9a4400390c700b141dd1d328382a964748
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 08:22:43 -0500
Commit message:

 update code style.
Package: annoLinker
Commit: c94978291c84a195b2c43fcad1925bb90b502f0e
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 08:19:11 -0500
Commit message:

 update the installation instructions.
Package: singIST
Commit: 5c3ed38a2b102ce0d9bd0d9cf60c6c4c0f9fecba
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-30 13:19:43 +0100
Commit message:

 Solve error
Package: lcmsPlot
Commit: 3da402e8ec979d60fde680704a0989710d7fd4b5
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-29 21:34:44 +0000
Commit message:

 chore: Increase pre-release version
Package: lcmsPlot
Commit: 7c378f887c9f1f5dfbe7a68bd8bea79a439eb030
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-29 21:34:03 +0000
Commit message:

 feat: Enable Compound Discoverer support
Package: singIST
Commit: ecf12f0b87472cedca99be9f41616274ecc2961a
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 21:34:04 +0100
Commit message:

 Vignette aesthetics and version
git push upstream HEAD:devel
Package: singIST
Commit: 499c8d9b7f03e28fafe1cd1bc647694b87ef2879
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 21:32:13 +0100
Commit message:

 Vignette aesthetics
Package: gwascat
Commit: 47c8928af65175ec78bd8a9d31b81bf9a7a4d006
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-12-29 14:40:18 -0500
Commit message:

 introduce new URL for updated gwas catalog from EBI
Package: spammR
Commit: 7fcc35fc970f18fca7fb3dfa23a2507ff2cf7f9f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-29 11:26:22 -0800
Commit message:

 version bump
Package: spammR
Commit: e649626a30a49881ac45f7feb7aec98855223846
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 18:14:37 -0800
Commit message:

 Merge pull request #73 from PNNL-CompBio/reticulate_fix

Reticulate fix
Package: spammR
Commit: 284b4777574a1ce6d80316ff8e8cd35cf5edcdce
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2025-12-23 14:35:09 -0800
Commit message:

 added comment to explain name difference between `py_module_available()` & `py_install`
Package: spammR
Commit: 8be8dba489003ec7893b6bafe74add81d14cc0b9
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2025-12-23 14:33:03 -0800
Commit message:

 reverted change to python module availability check to reference correct module import name
Package: spammR
Commit: ab2e04bb4e9618f492a9e1687ee3f79938b63e84
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:33:56 -0800
Commit message:

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

thanks for the comments!
Package: spammR
Commit: 30ef682a0d41292808bbbbd9b97aed9d913618a4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:33:28 -0800
Commit message:

 Update retrieve_metaspace_data.R
Package: spammR
Commit: cd0b4f53d2d84ac212f9c7631152fc5dda55bcf8
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:32:28 -0800
Commit message:

 Update DESCRIPTION

i think depends is more stringent than imports
Package: spammR
Commit: 8e0b09e2eacb34f2c50630e282c4c935402abc4b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-19 13:37:42 -0800
Commit message:

 added more to confirm build
Package: spammR
Commit: a5491ec51f7d6d5a774bc96f462bf6ab81f4d852
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-19 10:28:59 -0800
Commit message:

 added manuscript figure script
Package: spammR
Commit: 555e6690bb8a33620fa32047c345c24c6fedece1
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-15 08:56:33 -0800
Commit message:

 refining package vignettes
Package: spammR
Commit: be852fb5d2c907478a0b2e937da45be2aecdbdb8
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-10 12:05:45 -0800
Commit message:

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

Metab prot integ
Package: spammR
Commit: dbef57c2c924efc01dd2b093ccf3afb19716a02d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-10 10:04:40 -0800
Commit message:

 update for package building
Package: spammR
Commit: 5f2e66d29176cbeafe8e105fa43b433e14d600d4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-07 18:36:33 -0800
Commit message:

 maybe we need vignette files?
Package: spammR
Commit: 9d1af329d6a2735b93ef6f18bfbae2d2a303b6be
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-05 22:00:02 -0800
Commit message:

 hopefully last updates
Package: spammR
Commit: 86557a3393da96b2f1f42fabdc6b26917e4fe6eb
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-05 15:39:36 -0800
Commit message:

 updated to make better sense of data
Package: spammR
Commit: 8bf97e1892fe3fb81abbe46393b0945b51985326
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-04 15:47:11 -0800
Commit message:

 updated with new bug find!
Package: spammR
Commit: 6e59073b19a043808cbb838f26738f4089107d19
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-04 15:29:02 -0800
Commit message:

 new changes
Package: spammR
Commit: a82c65fd1040a6fb0710e05363b6f65766fd2582
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 17:00:19 -0800
Commit message:

 Merge pull request #70 from PNNL-CompBio/metab-prot-integ

added dependency checking, small PR allowing vignette to run. as i forgot a file download.
Package: spammR
Commit: 612fcfd2332444d90a170b84fef0a988082f1de6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 17:00:02 -0800
Commit message:

 last updates
Package: spammR
Commit: 3d31b265e4cae086a6cdb697d0cd5cd948c2f37b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:46:24 -0800
Commit message:

 added dependency checking
Package: spammR
Commit: dfb517c3f38c854f7f1cbe86d0f60e091cede935
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:30:40 -0800
Commit message:

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

addition of a lipid/protein example
Package: spammR
Commit: 2eb3a7a4efde8598dec8831bee88429f46e40737
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:29:06 -0800
Commit message:

 passes build check
Package: spammR
Commit: 07010ef285f154071645a181717825a4274ad2e5
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 12:51:12 -0800
Commit message:

 more updates to the vignette
Package: spammR
Commit: 092a6427a4739a141e0097290d370a1525817e2c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 11:23:45 -0800
Commit message:

 working on updated vignettes and network
Package: spammR
Commit: 143c1525359b3d83260f9c9214e9c9613251cb4e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-13 15:01:53 -0800
Commit message:

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

Added outline of lipid/proteomic integration
Package: spammR
Commit: 774ae8e319649ddce9565b69ee552edd3c1c32e9
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-13 13:46:40 -0800
Commit message:

 reduced file size and made updates to pass build/check
Package: spammR
Commit: b511621aa2d00e8d1ca07aa25d2905d8929c09a7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-12 12:02:59 -0800
Commit message:

 working on  package building with vignette
Package: spammR
Commit: 0c9498073b7a404e0495ad20909ced12da144273
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 11:24:35 -0800
Commit message:

 added updates to markdown
Package: spammR
Commit: fe0c97f206a004c130275e158b9756e684e9b83e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 11:07:01 -0800
Commit message:

 added reduce function
Package: spammR
Commit: 1ee9ce042404bd84e24a3c68ed8793aec8b82f93
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 09:58:38 -0800
Commit message:

 updated with new plotting
Package: spammR
Commit: 06d6f917e0455aa20ce689da30c4fa5190f62204
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-09 15:16:39 -0800
Commit message:

 Added updated function to get metspace data
Package: spammR
Commit: 407055517fe3178f7b8f37d7ad232b8587535d6f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:52:25 -0800
Commit message:

 slight updates to ideas/thoughts
Package: spammR
Commit: 0008fc7fb08f3b92c8390fa84dd1eae11fa8e16a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:24:39 -0800
Commit message:

 updated spatial diffex fro counts

added support for voom.
Package: spammR
Commit: 78bbd1835801384ed2c3004cd24df9220997c870
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:06:23 -0800
Commit message:

 removed this for now
Package: spammR
Commit: 9b38ae8c1348fbea3ff646a72693102066630e7e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 08:37:34 -0800
Commit message:

 kept this in separate branch for now
Package: spammR
Commit: bff2877d0f101ed86f2e3da05b91392d00119bff
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 08:35:07 -0800
Commit message:

 added some draft files
Package: spammR
Commit: 6ca0ffc68f392f0e614eddd2c8bf4003788b6551
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-04 10:48:43 -0800
Commit message:

 testing out metabolomic/proteomic integration
Package: spammR
Commit: d95eb222194f6bdfe0d97c023f95ad9281fc6313
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-04 10:48:08 -0800
Commit message:

 trying out some code for SFE
Package: spammR
Commit: 8298328c34b7a50a24954748215460d878cb9cfc
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 20:16:57 -0700
Commit message:

 cleaned up line ending
Package: spammR
Commit: e466bf4acce32d4ddc35d0fa72c63165522c03ee
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 14:45:15 -0700
Commit message:

 updating spacing here
Package: spammR
Commit: 92ef380100d875a4faa3efc1b7e115fa0caf4601
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 08:43:04 -0700
Commit message:

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

Major bioconductor updates, trying to get ahead after seeing the leapR comments
Package: spammR
Commit: 3b8729dc9a00a88656086a662380c9eb06b9ed99
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-14 15:36:47 -0700
Commit message:

 more udpates
Package: spammR
Commit: 7a7ff005f9881440af15ae1bbed6929c1428b7bd
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-14 14:48:17 -0700
Commit message:

 updated ahead of new bioconductor version prep
Package: spammR
Commit: 91c317588bd70376d4ff140e94352f6f57bdb63e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-09-30 13:15:33 -0700
Commit message:

 Update README.md
Package: spammR
Commit: 78cc7d4e29ef9a7196435acb7510da8878d05266
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-09-30 10:40:07 -0700
Commit message:

 Update README.md
Package: spammR
Commit: 77e136f7fb6190a2cb75fcb6d1e9b1deb2c41b42
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-26 15:18:50 -0700
Commit message:

 Merge pull request #61 from PNNL-CompBio/edge-detection

updated vignette
Package: spammR
Commit: 1c5f016abb42282c6b5bb60d2243831bd625cc8d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-26 15:18:19 -0700
Commit message:

 updated vignette
Package: spammR
Commit: a65ee25fbf3c62de9b9862242b53612e6ae0f4c0
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-21 18:11:15 -0700
Commit message:

 Merge pull request #57 from PNNL-CompBio/edge-detection

Added non-square edge detection script
Package: spammR
Commit: 0e27ee2964079b3aa7f6d25c2c46697f05d640d2
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-15 10:15:07 -0700
Commit message:

 updated vignette
Package: spammR
Commit: f2d6e845f75eb30cf47c5cfbb58debfabe90eb9c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-14 16:03:25 -0700
Commit message:

 added python code for edge detection.

still need to integrate via reticulate and provide example
Package: spammR
Commit: 1fa9a71c53c53592e5e6ff5ecd8c8e285844dcea
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-08 10:18:40 -0700
Commit message:

 added python script to process edges of image automatically
Package: spammR
Commit: 8f6708960bb8ee3258bc32729bf06bc9d79004c0
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:59:24 -0700
Commit message:

 Merge pull request #54 from PNNL-CompBio/split-impute

added ability to calculate missingness
Package: spammR
Commit: bf52846989030f1e602146b9bf3b9396b75ffb0b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:58:44 -0700
Commit message:

 fixed issue
Package: spammR
Commit: fe10c50c7dd1e35c94efd2d1280bd1ebdff10313
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:51:04 -0700
Commit message:

 added ability to calculate misingness
Package: spammR
Commit: b02c8d1936d2cf764204ed2f83979845dfb8d282
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 13:02:54 -0700
Commit message:

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

Split impute
Package: spammR
Commit: 5ecf2bcec2a77f44f377ff6c192433c306ba46c7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 13:02:42 -0700
Commit message:

 more doc corrections
Package: spammR
Commit: 1c7b72471ca0697f12936a062d89a30f2fc48781
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:35:05 -0700
Commit message:

 cleaned up more issues
Package: spammR
Commit: 203125f8136cac3c7a4530fdd2a1e03a33b2af4b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:29:00 -0700
Commit message:

 cleaning up more functionality of the imputation function
Package: spammR
Commit: e80808e09b9c360da228f49c9992a408cb86afa7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:03:33 -0700
Commit message:

 updated documentation
Package: spammR
Commit: f6291dcce7a963e43e11e0df970e37c5cdf76caa
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:01:47 -0700
Commit message:

 bug present in group code
Package: spammR
Commit: a9693e4b2a83f05ddc878871ba8a7612ad9637a6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:21:12 -0700
Commit message:

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

updated split function
Package: spammR
Commit: db3892bcb71c2777a6c8a04eff7cb7607e928006
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:20:48 -0700
Commit message:

 updated split function
Package: spammR
Commit: e48ef81b23cdb0fabb76fe79ca1f3392885f408d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:01:42 -0700
Commit message:

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

Added split functionality and more methods to imputation
Package: spammR
Commit: e95ef73960a33a11c92f7a5a2e17218eac8edf89
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:54:40 -0700
Commit message:

 updated vignette
Package: spammR
Commit: 83f1db51fc32c556989fad8fafefd8ee9712345d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:48:14 -0700
Commit message:

 slight fix to vignette
Package: spammR
Commit: d741498147ef711184ffa4256a13da8cb5fbc186
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:46:23 -0700
Commit message:

 Delete spammR.Rproj
Package: spammR
Commit: 566eb0811cf8cd1a8d55604008df98d87bf5bf62
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:45:44 -0700
Commit message:

 updated ignore
Package: spammR
Commit: 84783a78509b6df6c95ba99173e0f64458a1b904
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:44:18 -0700
Commit message:

 updated files to pass test
Package: spammR
Commit: 603d51bd9a42ffd928bf0ca91073aecd2395548a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:25:05 -0700
Commit message:

 fixed imputation and aded ability to split

added split functionality to help with RA anlsysi, fixed imputation.
Package: spammR
Commit: d2e114fbaee203886b2e04ef4883a9c807d90f04
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-07-24 17:34:11 -0700
Commit message:

 updated to account for subtle leapR changes
Package: singIST
Commit: c0f1484000663001ba02e1e60c3e54faf6a713ce
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 20:14:48 +0100
Commit message:

 First reviewed version of Bioconductor submission
Package: BiocCheck
Commit: 927dc6465e8a83d3081b46dc648c70802db4772a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-29 13:47:04 -0500
Commit message:

 version bump 1.47.8
Package: BiocCheck
Commit: f78bb19a3edb02cd8c0c0989804cbc08b8c5ab56
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2025-12-28 13:45:38 +0100
Commit message:

 Add error message to output
Package: BiocCheck
Commit: 9817476c9a6c3561b47151c3c9a38c7f8a5a086a
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2025-12-27 15:12:40 +0100
Commit message:

 Add commonmark to DESCRIPTION dependencies

The `commonmark` and `xml2` packages are required for parsing the `NEWS.md` file, see `help('news', package = 'utils')`.

Fixes https://github.com/r-universe-org/help/issues/649
Package: BiocCheck
Commit: 0d5022b9139e4f46b31173ce65cc1f469d913278
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-10 17:25:28 -0500
Commit message:

 version bump 1.47.7
Package: BiocCheck
Commit: 6c6c3610c74ec25ed78f35ad1987ba6573a97df6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-10 17:25:24 -0500
Commit message:

 add exception to checkWatchedTag for maintainer@bioconductor.org
Package: BiocCheck
Commit: 4be4595e58ae1086bdc0f18b44ff930c59d6103d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-09 14:17:08 -0500
Commit message:

 version bump 1.47.6
Package: BiocCheck
Commit: 8e6bd2c922aa5e3b1f2b6d9bd59c4f6082958ff9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-09 14:17:01 -0500
Commit message:

 bug fix use stop instead of non-existent error()
Package: pathlinkR
Commit: 7f27e55c0689be90366bd4ad9edcf873eb9c2628
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-29 09:20:05 -0800
Commit message:

 Tweaked test to support release and development versions
Package: pathlinkR
Commit: abc980a4423434009c6a10f81c496a9ddb434b26
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-29 07:52:45 -0800
Commit message:

 Fixed test for development version.
Package: panoramic
Commit: 97f8c07ef6514e354f9752b584dd887d0b183e06
Author: Jacob Chang <jacobchang@Jacobs-MacBook-Pro-2.local>
Date: 2025-12-29 09:21:07 -0800
Commit message:

 Bump version to 0.99.1 for Bioconductor build
Package: panoramic
Commit: d0104d55f5fc4a41abfbac5cc853c6a73cd0a496
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:44:09 -0800
Commit message:

 Update README.md
Package: panoramic
Commit: 64002875a1ad5a6d40e5ebf6dcaec87923c9a4c7
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:43:47 -0800
Commit message:

 Add files via upload
Package: panoramic
Commit: af1533aa895c3fa2dc9041aff3aa4ebbddd9f3ac
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:42:45 -0800
Commit message:

 Add files via upload
Package: panoramic
Commit: 0d606e9a544177e6c9a538f623649983fc889776
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:42:25 -0800
Commit message:

 Delete panoramic_graphic.png
Package: panoramic
Commit: 41da1b59cd4512e8dac0f0875fc435b932f097ec
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:41:47 -0800
Commit message:

 Add files via upload
Package: panoramic
Commit: ad394c437f60b102414ad8f47a5ebc703be3ccc3
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:41:26 -0800
Commit message:

 Delete panoramic_graphic.png
Package: panoramic
Commit: 0798a1169aebdb0d9c5b41ffb4a81548f4568204
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:40:03 -0800
Commit message:

 Add files via upload
Package: bugsigdbr
Commit: 6348069535e9f3d5209d80acecfe3a4f3a13129c
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-12-29 08:57:03 -0500
Commit message:

 fixed cache issue
Package: HPiP
Commit: 68bd9a14f4c0c5b6e13a5d100e79734445cff800
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2025-12-28 17:34:02 -0600
Commit message:

 version bump
Package: HPiP
Commit: 4c07334225832ae84813b7fd0d1d1410ba92d5b6
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2025-12-28 17:31:13 -0600
Commit message:

 fix namespacee
Package: methodical
Commit: 68b0dfb95a39954fc617b65365ea03b63dde95dc
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-28 17:43:12 +0000
Commit message:

 Updated make_meth_rse_accessory_functions2.R
Package: zellkonverter
Commit: 0b30029f56ea445d66a013c591c465fc89aa8c9f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 13:46:54 +0100
Commit message:

 Bump version to 1.20.1
Package: zellkonverter
Commit: bb352916e44e623ece0559525a9d9f9d82a92a9b
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 13:45:39 +0100
Commit message:

 Fix documentation links
Package: zellkonverter
Commit: 5f76c3bd132a216f9e418cb6859f6f26ea378f40
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 10:51:25 +0100
Commit message:

 Fix expectation in validation tests
Package: zellkonverter
Commit: 0127f9b004fff00f73dc7c839a5109287a46e802
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-11-25 07:33:36 +0100
Commit message:

 Bump actions/checkout from 5 to 6 (#155)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Package: zellkonverter
Commit: 8a5a5a2a19cbbb84ed22f77d420e920de5ca10ee
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-11-11 07:24:25 +0100
Commit message:

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

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Package: fluentGenomics
Commit: c296633b332a65253b6c86148d1b30954bf160a8
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-12-17 12:37:24 +1100
Commit message:

 correct package name
Package: memes
Commit: bb7e7dc7d2f8775f91fb08a5b70113d51d8c89e4
Author: Spencer Nystrom <snystrom@users.noreply.github.com>
Date: 2025-06-14 02:48:04 -0400
Commit message:

 Merge pull request #124 from karawoo/gha

update cache action
Package: memes
Commit: 3aa940302f33de0a8b5956f6174d22c51d25b4f3
Author: Kara Woo <woo.kara@gmail.com>
Date: 2025-06-13 23:43:23 -0700
Commit message:

 update cache action
Package: CPSM
Commit: dc1acc4718df35de2591069c12414332f9c19674
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-12-26 17:29:30 -0500
Commit message:

 CPSM 1.3.1: Update in DESCRIPTION and NEWS.md, cross-validation updates, feature stability metrics, and documentation
Package: CPSM
Commit: 7d04cc634cbc988c55bde4e3d28856fe94ba89c5
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-12-26 16:46:42 -0500
Commit message:

 CPSM 1.1.4: cross-validation updates, feature stability metrics, and documentation
Package: Rigraphlib
Commit: 7cfc7f9f925ac74025a15308ded3554b1d42bbc5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-07 17:44:21 +1100
Commit message:

 Streamline configure script when the output directories already exist.
Package: scrapper
Commit: d28799af985eed1bef0910e5e74eeec468fe65cb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 00:13:54 +1100
Commit message:

 More realistic example for fitVarianceTrend.
Package: scrapper
Commit: 0c67ab2ba01430088a11c9da913dbecfc6364893
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 00:05:36 +1100
Commit message:

 Added seealso links to the SE wrappers for each non-SE function.
Package: scrapper
Commit: a30e01d814c93b968cedd71eb982a6865e377572
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 21:13:11 +1100
Commit message:

 Elaborated on the tests in scaleByNeighbors.se.

- Added some tests for deduplication of the reddims.
- Added tests for correct names of the scaling factors.
- Removed some extraneous scrapper:: namespace.
Package: scrapper
Commit: 90dcc7acd3d038e658ccf7a34dfd18e3fb3afae8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 16:42:29 +1100
Commit message:

 Removed some extraneous scrapple references.
Package: scrapper
Commit: a90702e9a39a0bfc3fdc731b0fb532b3b4860658
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 14:48:16 +1100
Commit message:

 Updated NEWS file and bumped version.
Package: scrapper
Commit: f0a22ee71278fef0ea1f0ba906d46c4de131f1de
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 14:00:02 +1100
Commit message:

 Collapse the neighbor search for greater speed by default.
Package: scrapper
Commit: 04b49036ff26af842867d631f9a45a5e97f7ebfb
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 13:51:17 +1100
Commit message:

 Integrate SE-compatible wrappers from scrapple back into scrapper. (#19)

As it turns out, there wasn't much point in keeping the packages separate
because it's become increasingly unlikely that I'll get any resources for
separate maintainership. So, we might as well merge everything into one package
and keep things simple for the end-user.

We deprecate the analyze() function in favor of analyze.se(). We also direct
readers of the vignette to the analyze.se() function.
Package: lcmsPlot
Commit: f5001e2c2ffc6700d142ca8f5bcdf999d34fbaf9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:51:06 +0000
Commit message:

 chore: Update lcmsPlotClass documentation
Package: lcmsPlot
Commit: 5ae024c773b9f35d8993dc89c39cd9717de341ae
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:41:16 +0000
Commit message:

 chore: Remove lcmsPlotClass example
Package: lcmsPlot
Commit: fc6a71420ac5c60e12660b436b6927a11a0c84a9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:22:30 +0000
Commit message:

 feat: Codebase improvements for Bioconductor standards
Package: ClustIRR
Commit: fedad9771dc85fa705375e4df060f6dea2a65cb5
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 20:56:29 +0100
Commit message:

 minor updates
Package: ClustIRR
Commit: 4e2c28612f22837d525c81438a317dab7be4e4dd
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 20:37:16 +0100
Commit message:

 bugfix namespace, simplify .stan models
Package: ClustIRR
Commit: f1c549b3d48ff88e107b0c98833dcdb6617d68ad
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 18:55:20 +0100
Commit message:

 merge
Package: ClustIRR
Commit: 5ea3a3db95927643e15f2e64d22a5eca5448c8ed
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 18:46:17 +0100
Commit message:

 merge
Package: ClustIRR
Commit: 3ca7164000fa8f8ee426de9305ab693dffdbc3da
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-12-25 16:49:14 +0100
Commit message:

 faster community summary
Package: ClustIRR
Commit: 60afd60f8e9652120ed6cc1a608b0881491e5a2a
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-12-05 16:26:50 +0100
Commit message:

 KNN implementation
Package: PLSDAbatch
Commit: 50c28a1d75729dd659588f18a573cc8a6e18dbd7
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-12-26 03:28:53 +1100
Commit message:

 improve usability
Package: PLSDAbatch
Commit: 77b91a664366ccf76213eb28eba2ab29ae8b3817
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-11-06 11:20:14 +1100
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: PLSDAbatch
Commit: e5d2954225d057e5c7a5bf72693193f36444b858
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-05-05 17:02:58 +1000
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: VisiumIO
Commit: f81ae8ecdd3fd0a31d6e8e1c0229fbb85bc06c07
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-24 11:10:25 -0500
Commit message:

 version bump 1.7.6
Package: VisiumIO
Commit: 7e55a9d5fddfb793651cfd60ff9368982a697692
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-24 11:10:19 -0500
Commit message:

 re-add spatialCoordsNames input to .import_binsize, closes #21
Package: Modstrings
Commit: f830d42b85d1dbbc9d408d471277b2b2d8476621
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2025-12-24 14:33:31 +0100
Commit message:

 Updated comparison to work with Biostrings 2.79.3

comparable_seqtypes was changed in Biostrings to allow for seqtypes "ModRNA" and "ModDNA" to be used efficiently. Performance improvements by avoiding the constructor calls as suggested by Herve Pages were implemented.
Package: StatescopeR
Commit: 65ab0011084c7152e8ac25e8050b18e1faa02c97
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:04:06 +0100
Commit message:

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel
Package: StatescopeR
Commit: 911ddba7ce55cd45322dd2f58807e0513076c14c
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:02:21 +0100
Commit message:

 Added function to fetch signatures from https://github.com/tgac-vumc/StatescopeData and did some code cleaning
Package: StatescopeR
Commit: 164ff5adba1b1e654643a4c8188ad0725df71206
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:02:21 +0100
Commit message:

 Added function to fetch signatures from https://github.com/tgac-vumc/StatescopeData and did some code cleaning
Package: StatescopeR
Commit: 1bebb97a17a59fac24c3d43bce44f51ae97c3c1b
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-23 16:36:13 +0100
Commit message:

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel
Package: StatescopeR
Commit: d44ee627e8babed4a901093f9b0ba81245540f42
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:35:28 +0100
Commit message:

 Remove all check bioc.yml differences again

didn't end up doing anyhing
Package: StatescopeR
Commit: 91a2681c9e6fa375e81fd7ab4aceeb0f5cc889e6
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:29:40 +0100
Commit message:

 Update check-bioc.yml
Package: StatescopeR
Commit: 814c27fc38346d6cc87922c9ca4d23a09012204c
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:26:48 +0100
Commit message:

 Update check-bioc.yml
Package: StatescopeR
Commit: 5570bd142ff686e9668604346b64dff9c3810f7f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:25:33 +0100
Commit message:

 Update check-bioc.yml
Package: StatescopeR
Commit: 10e5df580a4552690c49826fb54d5b577c98b975
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:10:37 +0100
Commit message:

 Update check-bioc.yml
Package: StatescopeR
Commit: ec2a7da87fdbe2ed06620737bb9d2a6641397501
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:51:08 +0100
Commit message:

 Update check-bioc.yml
Package: StatescopeR
Commit: 3820ef3a7c6493127cc5520747867147a86de04f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:42:43 +0100
Commit message:

 Update check-bioc.yml

Next try
Package: StatescopeR
Commit: ff094108284bbf6c08b1027cb15b809bbddc450f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:31:58 +0100
Commit message:

 Update check-bioc.yml

Switched to newer free disk space fork
Package: StatescopeR
Commit: 81f8028eca0d833ad5283e5903ea4d2073c1e0ad
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:12:47 +0100
Commit message:

 Update check-bioc.yml

New variation of freeing up space
Package: StatescopeR
Commit: 8837a7a12b33aa61e40adfd706597b977fc466f0
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:06:08 +0100
Commit message:

 Update check-bioc.yml

Now actually rm -rfing I hope
Package: StatescopeR
Commit: 5a97fb4cbb4540763e9e360105f8aeb8f2a85c30
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:01:25 +0100
Commit message:

 Update check-bioc.yml

Last try to free up space for ubuntu GHA
Package: StatescopeR
Commit: 56dd4b5633368ce2b614c9dd7a19e054a1d8a142
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 14:17:45 +0100
Commit message:

 Update check-bioc.yml

Forgot #
Package: StatescopeR
Commit: e9a24b58933a7fda7aa0d668d644cfa8748b6c3b
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 14:17:17 +0100
Commit message:

 Update check-bioc.yml

Other version of removing unnecessary files
Package: StatescopeR
Commit: eb2e3f7f721d34bd09bd1de854bb558a898c9a66
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-23 14:08:22 +0100
Commit message:

 Adjused autogenes environment to python 3.7 (most recent with pip <24.1
Package: StatescopeR
Commit: 5b2af1a915dfdcc624c1fb9f4b5ecfdcf5c2b71a
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 13:29:25 +0100
Commit message:

 Update check-bioc.yml

Fixed small bug
Package: StatescopeR
Commit: 211d8a5049da958857e75aced4ebb6afdd83ec96
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 13:27:04 +0100
Commit message:

 Update check-bioc.yml

Claim disk space by removing unused tools, see:
https://github.com/actions/runner-images/issues/2840#issuecomment-3641541098
Package: StatescopeR
Commit: c8611539ca8c1612ca3b87670c88474225b5666a
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 11:18:57 +0100
Commit message:

 Update check-bioc.yml

Clear cache to see if this fixes storage issue for ubuntu
Package: carnation
Commit: 2e6987bd429322847c07f4dd08e9e6a9f7ae4490
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-24 00:31:36 -0500
Commit message:

 Merge pull request #21 from NICHD-BSPC/bioc_timing

make bioc check more efficient
Package: carnation
Commit: 2c575b88a208716b4f8a0ec2ee1621074320acda
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-24 00:14:25 -0500
Commit message:

 version bump
Package: carnation
Commit: 4058a9286518071d1b27e1bee65a3ea14b5efaea
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 23:53:48 -0500
Commit message:

 use included data in ex
Package: carnation
Commit: c64ce03c12aed4ae42878802aab8b3e466dcf909
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 23:52:38 -0500
Commit message:

 fix radar ex
Package: carnation
Commit: 2bb9685b131c555945c2b245c6a343005798ed2c
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-23 19:34:18 -0500
Commit message:

 Merge pull request #20 from NICHD-BSPC/bioc_debug

troubleshoot bioc build issues

- removed clusterProfiler from Suggests
- tweaked vignette to use data obj
Package: carnation
Commit: 36c1d64b7e1872a0f4bd8668449795281121ebf9
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 19:17:12 -0500
Commit message:

 version bump
Package: carnation
Commit: 96b512af2b7dae36feee14f0f5d6eefe4e5bf454
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 17:25:31 -0500
Commit message:

 typo
Package: carnation
Commit: 641510f08d5ed81865d388760fa5cf158105cb13
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 17:22:35 -0500
Commit message:

 add DEGreport back to reqs
Package: carnation
Commit: 5f9dd73f6135e7a5cec64b02bf30c87ab51d73b3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 17:02:12 -0500
Commit message:

 fix vignette
Package: carnation
Commit: 7747fc33219503c4001ac577b00fe4ff88c44511
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 16:45:16 -0500
Commit message:

 turn on enrich chunk
Package: carnation
Commit: 685a1e0688bb5ac3a454570edf2bd75eae710d24
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 15:47:35 -0500
Commit message:

 updt data obj
Package: carnation
Commit: 31b39394c85fd9b917ce2f25f33612d8fb5a1bb2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 15:47:12 -0500
Commit message:

 rm clusterProfiler, DEGreport frm deps, vignette
Package: carnation
Commit: d9105e6107759b2390dbd5905068893b57253031
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 09:11:27 -0500
Commit message:

 bump R version in reqs
Package: carnation
Commit: e33c5ca024827295f8e254f65c1d26d479d3952f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-23 07:11:02 -0500
Commit message:

 revert to R 4.5.0
Package: carnation
Commit: 16219e1b581dfaadb8e90909ce4749a3bb64ced1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 20:53:12 -0500
Commit message:

 use env-unpinned fr R CMD check
Package: carnation
Commit: e67f1db8f94188f3b6ca5bbb0d7307ae4ac90ce5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 20:52:29 -0500
Commit message:

 bump R version in requirements.yaml
Package: carnation
Commit: 2a94fe4ec4d608593ef71e2cd70355ad8a589d3e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 20:49:06 -0500
Commit message:

 bump R version to 4.6.0
Package: RedisParam
Commit: 45027f99ec3291eddb70c789d90c1b198ce558b0
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-12-23 18:56:36 -0500
Commit message:

 version bump and NEWS update
Package: RedisParam
Commit: a4dd89e6ec636ed32329de3759a8c59849ce3df9
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-12-23 18:52:48 -0500
Commit message:

 use 'logger' rather than 'futile.logger'
Package: CrcBiomeScreen
Commit: 19b9c5626a5c9dbe7d1f9c0ef91fbce5c366cb33
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 18:12:44 +0000
Commit message:

 Update the TRUE example.
Package: CrcBiomeScreen
Commit: d434f2353bcf2cbe988194e72adf42472e152874
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 17:58:00 +0000
Commit message:

 Change the Examples.
Package: CrcBiomeScreen
Commit: 2c121e5b66197f6124c2188e38c77093f491b050
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 17:44:30 +0000
Commit message:

 Update the function.
Package: CrcBiomeScreen
Commit: e4537c62beccbde6d3d40265241596afdb59ffa4
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 17:16:55 +0000
Commit message:

 Update the Description for the biocheck.
Package: CrcBiomeScreen
Commit: 6368fa9c42c27abc9c6a9f47a919c925de55bea6
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 17:16:04 +0000
Commit message:

 Update the example to deal with the report issue.
Package: CrcBiomeScreen
Commit: 80bce54c5503ea78075f2166d5be21d7f021465c
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-23 16:53:26 +0000
Commit message:

 Fix examples/tests and reduce package size.
Package: CrcBiomeScreen
Commit: 7d453282f80a80c858ed90aeba06839c2aea6ceb
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-04 14:37:57 +0000
Commit message:

 Remove class_balance_plot.pdf from tracking
Package: isomiRs
Commit: a053d30b756e7ceaef3db67c974614026246fffb
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2025-12-23 10:12:56 -0500
Commit message:

 fix ggplot2 label error
Package: plaid
Commit: 9594884fb9ea00c9cba50c7b9d2994fb00a0da52
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-12-23 15:18:43 +0100
Commit message:

 bump version
Package: plaid
Commit: 6c3fdf7f92d55cb2832126b9606b53a464cdd4ed
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-12-23 15:18:29 +0100
Commit message:

 fix import and run document()
Package: plaid
Commit: 587ff4ae6c7e4c3e87046ac368c1dc84553ae78b
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-12-23 15:02:06 +0100
Commit message:

 bump version
Package: plaid
Commit: d0bf8dec001352b9fb663d880ca75d48e28089d0
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-12-23 15:00:11 +0100
Commit message:

 use MatrixGenerics
Package: plaid
Commit: e0e14d4a1abf5e6b8fc40bd0a25e510f18ae65d5
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-12-23 14:58:22 +0100
Commit message:

 rename vignette files to avoid warning
Package: plaid
Commit: 27d84c5aad8fa8afce414166ff06b798e9b50146
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-12-10 18:10:50 +0100
Commit message:

 Merge pull request #7 from bigomics/fix-normfactor

fix normfactor for low number of genesets (fix issue #6)
Package: plaid
Commit: 3ba778d166f824142a6b196ae5ede2915ef8bfc9
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-12-10 10:02:02 +0100
Commit message:

 fix normfactor for low number of genesets
Package: Spectra
Commit: bdd8afaac9d80a101119b8b37cf3d824dded59e2
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-12-23 14:00:43 +0100
Commit message:

 Merge pull request #376 from rformassspectrometry/jomain

fix: precursorPurity with missing precursor peak in MS1
Package: Spectra
Commit: 09453208743b5cac86bd20492f06268747200525
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-12-23 13:35:33 +0100
Commit message:

 fix: precursorPurity with missing precursor peak in MS1
Package: miRspongeR
Commit: d05055e1ae46847ab23c3cbce0dbac7c57776985
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2025-12-23 20:05:29 +0800
Commit message:

 Update
Package: miRspongeR
Commit: d044b9caf79f55222f022fc24c0d245de6d0cd36
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2025-12-23 20:04:15 +0800
Commit message:

 Update
Package: miRspongeR
Commit: 9d3376ca48f9009250d1b27f328b6ec1800a6f17
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2025-10-16 12:30:26 +0800
Commit message:

 UPDATE
Package: SwarnSeq
Commit: a1b7200d52628a4a598faf5f67f1e42353891656
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-12-23 13:26:28 +0530
Commit message:

 Update News.md
Package: SwarnSeq
Commit: 2de84050e2235b98c8a70e88bd6ddeb717a631d9
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-12-23 13:17:16 +0530
Commit message:

 Organize codes.
Package: SwarnSeq
Commit: 86829a277e5196dc14f928378af47ea4651c0f6d
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-12-23 12:18:50 +0530
Commit message:

 Organize the code.
Package: edgeR
Commit: 5cd905c768b96724cd4907bebfc1816001135db4
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-12-23 17:09:34 +1100
Commit message:

 edgeR 4.9.2
- glmQLFit() with legacy=FALSE now caps any preset dispersions to be <= 4. Previously, large preset dispersions could lead to a segmentation error.
- glmQLFit() with legacy=FALSE no longer automatically estimates the NB dispersion from trended values found in the DGEList object, if present. The results will now be the same whether the DGEList contains dispersion estimates or not.
- Adding DTE and DTU references to intro.Rmd.
- Revise example code for sampleWeights.Rd.
Package: carnation
Commit: 1c3e2da8409267b3862ca2632d5f6f32828642df
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-22 20:31:01 -0500
Commit message:

 Merge pull request #19 from NICHD-BSPC/minor_fix

version bump
Package: carnation
Commit: 56da3f52b6d4b4186ee03e91a2f688bd2a973ef8
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 20:28:42 -0500
Commit message:

 version bump
Package: carnation
Commit: d96f29efb8300d392ee9784f7284927b83a028fb
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-22 20:25:14 -0500
Commit message:

 Merge pull request #18 from NICHD-BSPC/minor_fix

revert to R version >= 4.3.0
Package: carnation
Commit: 1bc37f14659a0d14eac7ef5803862e9c837a536d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 20:22:22 -0500
Commit message:

 revert to R version >= 4.3.0
Package: ReactomePA
Commit: cbad461708c72c9042e77ded76ac936a11d7300a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 09:06:44 +0800
Commit message:

 bump version
Package: ReactomePA
Commit: 2a450810e54b3136730ec53a863a39781329350e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 09:03:03 +0800
Commit message:

 bump version
Package: ReactomePA
Commit: c5c77ae3ed9bce715daa802875316dc959d38849
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 11:28:41 +0800
Commit message:

 use enrichit
Package: ReactomePA
Commit: 8fd3f55866a2162a782d77d824e8f29ac67a0b58
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:28:07 +0800
Commit message:

 update bioc version
Package: ReactomePA
Commit: edb8edc614ae30d61b79c65ae9bcfddb37c9e217
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:50:27 +0800
Commit message:

 update bioc version
Package: ReactomePA
Commit: 2b3f690c9ff75f726dda20dedbfb735c98f6ad8b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:50:23 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: ReactomePA
Commit: c64ca1842650154816e29f17ed5892cb4c047b6d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-30 12:19:25 +0800
Commit message:

 new release
Package: MicrobiomeProfiler
Commit: dddb3482eb1c0ac5ad08a8512c569aa5ef9a3dd3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 08:58:37 +0800
Commit message:

 bump version
Package: MicrobiomeProfiler
Commit: 4a8e4ed2b2cdbec7d7e6724a9c878d46ab320af9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 11:41:23 +0800
Commit message:

 use enrichit
Package: MicrobiomeProfiler
Commit: 0a6c3c1b148a9f474fc8ad65134ef63d330fdcb1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:18:49 +0800
Commit message:

 update bioc version
Package: MicrobiomeProfiler
Commit: 4973b1742a1980da33ef38a76f988cebdfbd494b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:18:42 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: MicrobiomeProfiler
Commit: 313b9cd424eb0a2b7725a126651008f08816d398
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:49:04 +0800
Commit message:

 update bioc version
Package: MicrobiomeProfiler
Commit: d3bbce58f53f1dec17340b5153b2be5e6650421c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:48:37 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: MicrobiomeProfiler
Commit: add353e36ec2fe6b949ea1c63ceaea1b5b39adc8
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-30 12:23:35 +0800
Commit message:

 update bioc version
Package: meshes
Commit: 4dbc7cb6e17fce0aca7833d99188cb4995e304bc
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 08:54:28 +0800
Commit message:

 bump version
Package: meshes
Commit: 3ffa086d167d3db29c03e242ed4fbe782d5c4f78
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 09:59:41 +0800
Commit message:

 import enrichit
Package: meshes
Commit: 5462890837324b8d6fe17eaa76170f1e8527398f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:14:20 +0800
Commit message:

 update bioc version
Package: meshes
Commit: fe776ab4c90a9ae146cc4c4f67c9744cf18e9819
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 22:14:14 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: meshes
Commit: be56aeba7033368926c8418c2c75509baa08ed5d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 10:28:08 +0800
Commit message:

 update bioc version
Package: meshes
Commit: 20a6c450fff8445336868a553940b26834d99023
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 10:28:03 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: meshes
Commit: 6e7c8f5352f08e10fc783cd24422b989ceaafd25
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-30 16:48:12 +0800
Commit message:

 update bioc version
Package: clusterProfiler
Commit: 6f4243ece76f768aab2c63d16b898de0f116f038
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 08:52:36 +0800
Commit message:

 bump version
Package: clusterProfiler
Commit: cec66a1e0eb2221d75e277492c82020e90e39005
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 15:09:42 +0800
Commit message:

 update
Package: clusterProfiler
Commit: ac455dae247b296c40996a6be673c758913ac975
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 14:50:13 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 6313244ed64bab1fbda16457600361322c37041f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 14:41:31 +0800
Commit message:

 update
Package: clusterProfiler
Commit: fa3dbe2cc57168c40779cf674a179536b367c651
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 14:26:05 +0800
Commit message:

 update
Package: clusterProfiler
Commit: c9cc67cab404d111f411b830fce8902f0df1d971
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 14:23:27 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 20228c77d282f3618798d5df79d277cbea320274
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 14:02:42 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 32164c1f813585f8593aec1dca5220d8d92addd1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-15 13:56:28 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 1c57c863442b8ce991eed3570d3b52adbe2e9868
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-09 15:27:39 +0800
Commit message:

 update
Package: clusterProfiler
Commit: 3830302cca5de48aee2a4910264b11d7d6cdf5c1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-09 14:42:31 +0800
Commit message:

 to work with release version
Package: clusterProfiler
Commit: cedf84c53b0a25e2f0d83958f9b6bafddc75ab38
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-09 14:35:21 +0800
Commit message:

 update data action
Package: clusterProfiler
Commit: aca51c9a83cf4ffaba6bf77d573bbdd2615e02e4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 13:23:06 +0800
Commit message:

 use enrichit
Package: clusterProfiler
Commit: 2376860b1cfba39426770d80966304ad6d8a0ff6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-20 15:02:28 +0800
Commit message:

 update readme
Package: DOSE
Commit: 3414fdc46ce908e7aa0cfb997ec8ec00d0f46489
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-23 08:42:40 +0800
Commit message:

 bump version
Package: DOSE
Commit: 143d42cf33f4575e37083ed786235bcad1bdc951
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 12:46:59 +0800
Commit message:

 correct DO url
Package: DOSE
Commit: 41aa47ada3ffdf7c9a14169142983e0df4de8c02
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:32:52 +0800
Commit message:

 use github version
Package: DOSE
Commit: ffbae3c168f53c920fcaf3dc8461e3be14705afa
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:29:21 +0800
Commit message:

 no deps parsed
Package: DOSE
Commit: b3640ac5c621759e60937ef857ae38861c0cefe2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:26:55 +0800
Commit message:

 no deps parsed
Package: DOSE
Commit: d0de451b04efde5c9a0f3130bc3c5c0558a0b054
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:22:53 +0800
Commit message:

 update
Package: DOSE
Commit: f83a98675efd6d012684343714e59e48a3f2b84b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:19:19 +0800
Commit message:

 do not parse dependency from DESCRIPTION
Package: DOSE
Commit: b0dfecdf886c35cca3c927ebc002f7e4c1c0cef5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:10:02 +0800
Commit message:

 setup env
Package: DOSE
Commit: dfcb931cf0bdb5e62534cc5ced58e12431823104
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 09:06:49 +0800
Commit message:

 more formal way to install dependencies
Package: DOSE
Commit: f7704742ccc0ce1d0ceb08953aa547136b9471ee
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-11 00:11:34 +0800
Commit message:

 correct url
Package: DOSE
Commit: 70a502cd1970d5417e5c7a82738d861c8a67bf04
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 23:44:34 +0800
Commit message:

 use wget
Package: DOSE
Commit: a4d59e6c4bb5eb9233e60441eeadda9066fae0d8
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 19:26:30 +0800
Commit message:

 update
Package: DOSE
Commit: 88fdf57387d16e59accc3e37e5687e9994a9fd8e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 18:52:52 +0800
Commit message:

 try to fix the download issue, the file maybe redirected
Package: DOSE
Commit: 4c67f509038319ddbdeb1ded6b8ee731a355e534
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 18:17:02 +0800
Commit message:

 fixed installation issues
Package: DOSE
Commit: ea31db6f1870617a2ed0c1dea3f0364b0962cb15
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 17:52:47 +0800
Commit message:

 more dependencies
Package: DOSE
Commit: aba08326f1534e497680a945853e954bf1cd48be
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 17:26:08 +0800
Commit message:

 install bioc pkgs
Package: DOSE
Commit: 5cc6fec88bea74bfbbeaa788f6352c9dea8c66c4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 17:11:18 +0800
Commit message:

 fixed workflow
Package: DOSE
Commit: db3d0016634534d5a436e172a8fb335ece171599
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-10 17:07:58 +0800
Commit message:

 auto-update data with github action
Package: DOSE
Commit: ba058487472de8f60c78a0c6cbab891a3d98c3d5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 09:01:25 +0800
Commit message:

 move get_organism to gosemsim
Package: DOSE
Commit: 57465e2743c5bf24cfe0224a510c2c7e7a217407
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-07 00:56:29 +0800
Commit message:

 use enrichit
Package: DOSE
Commit: 4a1d02d20a4533f7b3e8b76424af9e7f08763d82
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-05 22:47:29 +0800
Commit message:

 use enrichit for gsea
Package: DOSE
Commit: 4e7269b3daed48eab272b5c1fb1bb4d4035ff704
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-12-05 09:18:50 +0800
Commit message:

 use enrichit for ORA; and move helper functions to enrichit
Package: DOSE
Commit: c8c818598c608dca08a9a1cfcd2668c56c005c94
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 16:09:23 +0800
Commit message:

 update bioc version
Package: DOSE
Commit: cbba1e87beae5f55e37fa3087b0c55f249ca20f9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-01 14:50:46 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOSE
Commit: cc64179bccee169a3e102d28036f56e83b490f09
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-28 00:44:25 +0800
Commit message:

 update
Package: DOSE
Commit: 34a63655d1c24c4e855a669e61880187a28a7a1a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:46:08 +0800
Commit message:

 update bioc version
Package: DOSE
Commit: a4aa3e77372d845574b5654286971496dd0e0026
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:42:54 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOSE
Commit: 1ce3c6f3c1ba6485922308594f565a55279198a4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-03-25 10:44:47 +0800
Commit message:

 update
Package: DOSE
Commit: 4bdf261db7e2d088ca588a564f1db5a85ba522b7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-30 12:13:50 +0800
Commit message:

 update bioc version
Package: CatsCradle
Commit: 0f9d76fedea1976458c1d81b366281868db19e4e
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-12-22 23:28:13 +0000
Commit message:

 version bump in devel
Package: CatsCradle
Commit: 2bb2355f8cd4ea553df9043605625f8cc302cdf6
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-12-22 23:27:15 +0000
Commit message:

 bug fix: smallXenium.rda updated
Package: carnation
Commit: ae86688a1555f346de9c21a470f8aaf1d826d1e1
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-22 17:29:37 -0500
Commit message:

 Merge pull request #17 from NICHD-BSPC/minor_fix

updt R version fr bioc
Package: carnation
Commit: e377a403cd895aeec9bc562910bf9f7a491f48d1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 17:07:42 -0500
Commit message:

 updt R version fr bioc
Package: carnation
Commit: 075f01f1fafd37f84519ab659dcd9823ca71cbe7
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2025-12-22 17:04:25 -0500
Commit message:

 Merge pull request #16 from NICHD-BSPC/bioc-submit2

update repo for bioconductor submission

- added examples to exported functions/objects
- added data to use in examples
Package: carnation
Commit: 816b8839c7d94ed82beb86aa5ed38eec81d9bd35
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 16:48:28 -0500
Commit message:

 version bump
Package: carnation
Commit: ee534cfb8b33a97145e87d17d364210f050e5bc6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 16:02:31 -0500
Commit message:

 add examples
Package: carnation
Commit: 3476004a26bfdb8c527c18088da5c931946cd585
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 15:07:06 -0500
Commit message:

 fix gs_radar docs
Package: carnation
Commit: fb895401473107b5b23467d8dd0b050c9d32d732
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 15:06:45 -0500
Commit message:

 add helper func to get upset tbl
Package: carnation
Commit: 2b82f5c13bcbcfe07900f4400844af3215218a16
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 14:26:25 -0500
Commit message:

 add upset ex
Package: carnation
Commit: df8d62be8331342dd430545affff452a09b41849
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 14:26:10 -0500
Commit message:

 add NEWS
Package: carnation
Commit: c61a5cc2683ddae09ae63795d6ce79a1edaee08f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 14:16:17 -0500
Commit message:

 fix typo
Package: carnation
Commit: 4a548f0e73d26d0573b2f44bccdbbb3f802d8bfa
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 14:16:03 -0500
Commit message:

 add more examples
Package: carnation
Commit: 99404c4e1c894182a7fab92129180e6ccbe91343
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 14:15:33 -0500
Commit message:

 fix gs_radar ex
Package: carnation
Commit: f5a431bff4a173392c793583173b2f95b25d7904
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 13:22:34 -0500
Commit message:

 fix examples
Package: carnation
Commit: c66a803de5e7b59de9ead68b5cc39c25476c9731
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 13:04:25 -0500
Commit message:

 rm geneSets slot frm enrichResult to reduce size
Package: carnation
Commit: caf04f3074a9ae1c59c4404747246456f5bf7df1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 13:03:51 -0500
Commit message:

 fix unloaded function calls with ::
Package: carnation
Commit: 30dd56388b3b61c9e6ad5b9815fde0cd4eff1426
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 12:48:02 -0500
Commit message:

 add missing lib call
Package: carnation
Commit: 0d383b5a1a976de0737ad2269f4313906591027d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 12:29:18 -0500
Commit message:

 rename data obj
Package: carnation
Commit: e4bdd31eac8cab6f50bc7be0ac240bcb753f66b3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 11:53:19 -0500
Commit message:

 add format tags to data obj
Package: carnation
Commit: 5d7ac0bd26a06bd6e95c201b4bd7ee804ee3e039
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 11:52:48 -0500
Commit message:

 use data obj in examples
Package: carnation
Commit: 34f79e0808cd643ec00c3603a273abfc03314e02
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 11:08:19 -0500
Commit message:

 use obj frm data in examples
Package: carnation
Commit: 001a0298fd330ba861bc54ecb16b9fe3ed0c8063
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-22 10:41:21 -0500
Commit message:

 add data, docs & script
Package: carnation
Commit: 97a2baab2a06df852fb6b2fc773b1d35cab29b1f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:49:35 -0500
Commit message:

 add docs for save obj module
Package: carnation
Commit: 22ff7fa35d888e38337872b3f16a949d7b632d36
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:40:55 -0500
Commit message:

 updt docs for settings module
Package: carnation
Commit: 088ea9bdbfe4ed65e329ee0d0fa809883170ed8e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:31:56 -0500
Commit message:

 add docs for load data module
Package: carnation
Commit: d967b8353d945a32b17b5a37326482fc8e78d8d3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:24:43 -0500
Commit message:

 add pattern plt docs
Package: carnation
Commit: e740c5db22eb9908e499c038d6761425ff28a39d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:09:26 -0500
Commit message:

 fix upset docs
Package: carnation
Commit: f558eec1983ce1d6e326b3383c92706cdefeb340
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 22:09:05 -0500
Commit message:

 updt func enrich docs
Package: carnation
Commit: 3a689b3f88ca6b69abefd5aed05163e222037e64
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 21:56:06 -0500
Commit message:

 updt heatmap, upset module docs
Package: carnation
Commit: 35d2ef39b14ed560b712254bf4dca10e94b1417e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 21:46:11 -0500
Commit message:

 add docs/ex fr fuzzy plt
Package: carnation
Commit: 2c2b8ea9057769d6d3b048fa9226687e78d8ea4e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 21:28:09 -0500
Commit message:

 mv donttest tags
Package: carnation
Commit: aba63620086719c14ecc0793c9e81dd7c9a889a3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-21 14:03:41 -0500
Commit message:

 fix biocCheck folder path
Package: carnation
Commit: 0fdedeb2e7b0d59de99e603fcc8ac37d8e7bea01
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 16:28:12 -0500
Commit message:

 updt @name tags to match @rdname
Package: carnation
Commit: 282bb7c78990a61c586b900e2fe0babe71c6837c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 16:27:16 -0500
Commit message:

 add donttest to get_degplot
Package: carnation
Commit: 24317a5868200af301d93d7dfa3a2c1955c0d209
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 16:02:21 -0500
Commit message:

 add distill plt ex
Package: carnation
Commit: a5311487aaaf6682641ef7cb4df101b83ed1c87b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 16:01:49 -0500
Commit message:

 add missing library(shiny) to ex
Package: carnation
Commit: 01a9c31ee775e188fc24db412cf140111d75eac0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:33:14 -0500
Commit message:

 repl dontrun w donttest
Package: carnation
Commit: 66e507c5df294164c8f4b21ee20da970d2413621
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:26:19 -0500
Commit message:

 add horizon plt ex
Package: carnation
Commit: 2034538900e1175dd7f1f12254f3f6ed63c7afe3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:24:55 -0500
Commit message:

 add dendrogram ex
Package: carnation
Commit: 140cbdd62396abd0c826b6bce18a608c76be60e0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:24:30 -0500
Commit message:

 add alluvial plt ex
Package: carnation
Commit: 3fdb2fd0db2c9db1b0d28fde0b02ddbb2916bbf5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:23:59 -0500
Commit message:

 add radar plt ex
Package: carnation
Commit: 5080a563df517013ade7d26bd3b15aa732fd7977
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:23:31 -0500
Commit message:

 add cnetplot ex
Package: carnation
Commit: 4fa262b9ad1381d7fb547dd9e1c5f70ffaa2eb0e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:23:01 -0500
Commit message:

 add emap plot ex
Package: carnation
Commit: d16fdd9502a52ca4172e07cd147da90a596d0b26
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-20 15:21:39 -0500
Commit message:

 fix sumov plot ex
Package: carnation
Commit: 33d3c2df560c29386d221e5aa1cfed8192b08190
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 16:59:17 -0500
Commit message:

 add \dontrun to long running ex
Package: carnation
Commit: aa7a163eb30844c70f60d4e76c2dd9441a8d7853
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 16:59:00 -0500
Commit message:

 add docs,ex fr sumov plt
Package: carnation
Commit: 0a7fe1ceb32b91554715affb1860a52c01350dc5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 16:36:34 -0500
Commit message:

 rm miniforge script after install
Package: carnation
Commit: d073f02566ecdc956557d6f945747f67e156d959
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 16:22:56 -0500
Commit message:

 add docs,ex fr ma plot
Package: carnation
Commit: 5ccea554e8db99376bb336a26494c3be06144b72
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 16:18:04 -0500
Commit message:

 add docs, ex fr help/dl buttons
Package: carnation
Commit: dd57e85e57696ee79a4e1b727eb87ef18e46d478
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 15:27:25 -0500
Commit message:

 add pca plot module docs
Package: carnation
Commit: 259c7a340c1308b42ecfc0fa5ae8c029be32289a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 15:27:02 -0500
Commit message:

 add metadata module help
Package: carnation
Commit: cc287508709b86b0850d78835efdcd5729749d7f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 15:26:41 -0500
Commit message:

 add func docs
Package: carnation
Commit: 89c59aacdd6e15c401a26d92ca34e23f675fb34a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-19 15:26:12 -0500
Commit message:

 fix geneplot ex
Package: carnation
Commit: 303d807b8f6f3936b60068282f4eeacd6f53932b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 16:52:35 -0500
Commit message:

 updt scatter plt ex
Package: carnation
Commit: 13c09b28b8fbfd5c0b88e8b55124d2a491185b77
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 16:52:17 -0500
Commit message:

 add metadata ex
Package: carnation
Commit: c8be683edea7288083cc2875e7ec7c2f2c50f081
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 16:51:52 -0500
Commit message:

 updt gene plt ex
Package: carnation
Commit: 6e401b0f331b3569603e5a5fcd16f5d3254e5c1f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 16:50:30 -0500
Commit message:

 updt NAMESPACE, add function fr examples
Package: carnation
Commit: 7ab13a678e4145417ad23d249cff94229e5cdcd2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 16:49:47 -0500
Commit message:

 updt biocViews
Package: carnation
Commit: b1e2541f188ede667deb1e02a6b36c644b841067
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 14:24:24 -0500
Commit message:

 add geneplot ex
Package: carnation
Commit: 5bd7aebc6924645ed1714186ae781bc5a63e1d8e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 14:22:11 -0500
Commit message:

 fix scatterplot ex
Package: carnation
Commit: 849aa5d2c18a69030d9e7ef9a76616d49ea3345f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 14:04:39 -0500
Commit message:

 updt bioccheck action
Package: carnation
Commit: f1d147a407364582ec6e053a493c4dc993b49671
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 13:41:47 -0500
Commit message:

 factor out bioccheck to new action
Package: carnation
Commit: 8b2ca78cf9d929bbdc1b3665f965b4d572b8001f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 13:38:10 -0500
Commit message:

 make new env fr bioccheck
Package: carnation
Commit: 394d0a5f32a1a5f0edf180c10b2eda403a15d500
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 13:33:22 -0500
Commit message:

 add scatterplot docs
Package: carnation
Commit: 5a3fe1e4470d91d1808208f011d58a1abffa9be1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 13:11:01 -0500
Commit message:

 add bioconda for bioccheck install
Package: carnation
Commit: 3117bd28b0ce9b377cac9b501fa09359dc58d38c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 10:53:46 -0500
Commit message:

 more example fixes
Package: carnation
Commit: 2f03c66d77b34a6937242fb3a806f0f12a425152
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 10:32:45 -0500
Commit message:

 actually update the docs
Package: carnation
Commit: 1ac21f87d4f62bc4da2051d6a14e70aec89315ad
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 10:06:15 -0500
Commit message:

 fix examples
Package: carnation
Commit: febc3940dfcb6419c8dd17d42e4365a40c0023a1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 09:12:50 -0500
Commit message:

 fix geom_abline arg
Package: carnation
Commit: e4d9c52a6e5d34224eb0acb5be6e829489f004b6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 09:12:39 -0500
Commit message:

 add scatterplot examples
Package: carnation
Commit: 5e87d4513bb8e1c46e1f10434ce2371988a0bad2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 09:09:30 -0500
Commit message:

 fix examples
Package: carnation
Commit: e07d5042fce714c92626ccbdd9b39e94aab1f7eb
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-18 09:07:03 -0500
Commit message:

 use get_gene_counts instead of reshape2::melt
Package: carnation
Commit: bebea27a8bba533a8732f707fc59d61f771a9c51
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 13:34:29 -0500
Commit message:

 fix examples
Package: carnation
Commit: 43d80508cc30355f94c3047caa64b1509b99eeaf
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 13:08:01 -0500
Commit message:

 fix add_metadata examples
Package: carnation
Commit: ff9d039ac539df2402175b0940d976a75d5c730e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 12:10:04 -0500
Commit message:

 updt docs
Package: carnation
Commit: c0a7744aa808723fa64f5e5aeb03fd6b2a8bb1aa
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:52:57 -0500
Commit message:

 add BiocCheck action
Package: carnation
Commit: ee8fcd4b2ecfdfc2a46b20e15f74e1f567677c43
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:50:50 -0500
Commit message:

 fix example
Package: carnation
Commit: 253d9e7e1a21b9cf6743ab53355831ada1edc195
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:50:42 -0500
Commit message:

 fix typos
Package: carnation
Commit: b960725821a9d443bdec87b3e152c080f16799ce
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:35:37 -0500
Commit message:

 rm unused func
Package: carnation
Commit: 21089ef18d6534117194ac2efe25f0238cb4009a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:35:10 -0500
Commit message:

 dont filter proj desc if no staged data
Package: carnation
Commit: 380bc2b46f8c941d1b5e0597e19c5983703faa0c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-17 11:34:51 -0500
Commit message:

 add return & examples to docs
Package: carnation
Commit: f9cdac80541fe3ae797a9e54c219e945d29eddc2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-04 14:23:21 -0500
Commit message:

 repl stop w modal
Package: carnation
Commit: 3599a7e079c25f0cf9495b68c1503126ac4bf7e2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-04 11:15:58 -0500
Commit message:

 rm paste frm inside stop/message
Package: carnation
Commit: 7a421a08052d540bb53f86bd7706b78f8ac0c79d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:16:06 -0500
Commit message:

 repl T w TRUE
Package: carnation
Commit: 39d289ee0a97dbdd5d435273dbd53f79f8f35799
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:15:30 -0500
Commit message:

 name vignette code chunks
Package: carnation
Commit: 5224fcb82e19b740f1a3eb348faad36a97b8f989
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:14:49 -0500
Commit message:

 repl 1:.. w seq_len
Package: carnation
Commit: b95901a08e89ab5fcc00b380a1162f4c71d09e3b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:12:29 -0500
Commit message:

 repl sapply w vapply/lapply
Package: carnation
Commit: 65807b3d006f3169f4837441ed2343fd98349e7d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:11:37 -0500
Commit message:

 rm paste inside message/warning
Package: carnation
Commit: 538b7f83acc5ce90305a518ad80707e57f69510f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2025-12-03 21:09:30 -0500
Commit message:

 add bugReports
Package: transcriptR
Commit: b0b2357b20cf0307f8ce7ad43c79c06e5e7cc3ee
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 21:05:17 +0100
Commit message:

 Version bump in devel
Package: transcriptR
Commit: 34653c8358875aba2e0e8f23607ac6dbcf3e3383
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 21:04:50 +0100
Commit message:

 Updated NEWS file.
Package: transcriptR
Commit: 18f65cb51f03996d2eab2afa12f59aeaca55e68d
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:54:19 +0100
Commit message:

 Version bump in devel
Package: transcriptR
Commit: 70d0f540c3310f438640062fa9df35f693574c58
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:53:55 +0100
Commit message:

 Add .Rbuildignore and .gitignore files
Package: transcriptR
Commit: b010e522490cc82b447cbecc53cc19d00bee7125
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:48:41 +0100
Commit message:

 Version bump in devel
Package: transcriptR
Commit: d201fdda2da97b6d7ab777301387ddd8a8891cec
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:46:13 +0100
Commit message:

 bug fix: move e1071 to Suggests and update documentation:
- Moved e1071 from Imports to Suggests.
- Updated the roxygen2 version and rebuilt all manual pages.
- Fixed incorrect roxygen documentation for internal datasets.
Package: transcriptR
Commit: e37599715e8ac55fc24f7d91ff2c76ac84aeced8
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:30:18 +0100
Commit message:

 Version bump in devel
Package: transcriptR
Commit: 2731e082f804cca875cc5729585bee87d45d152c
Author: Armen Karapetyan <5734706+karapetyanar@users.noreply.github.com>
Date: 2025-12-22 20:29:29 +0100
Commit message:

 bug fix: fixed a failing unit test caused by an update to the TxDb.Hsapiens.UCSC.hg19.knownGene library. Replaced the external dependency with the internal annot dataset to ensure stability.
Package: FlowSOM
Commit: 0eee0c750889a2ff59737bf3ca5be58a36e541a4
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2025-12-22 16:57:55 +0100
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM into devel
Package: FlowSOM
Commit: dbc238ff5cc2292bddba87013694231d71d42567
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2025-12-22 11:20:34 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: FlowSOM
Commit: e09dabd2fc29b9f54dc6df9e98bc58eb4d440fc4
Author: sarahbonte <sarah.bonte@irc.vib-ugent.be>
Date: 2025-12-16 13:58:52 +0100
Commit message:

 Update Plot1DScatters: character vector as input for metacluster parameter (compatibility with metacluster levels after running UpdateMetaclusters)
Package: FlowSOM
Commit: 5dedae5f59ed987a0b4fbdf5e87ddfeadb4f883c
Author: sarahbonte <sarah.bonte@irc.vib-ugent.be>
Date: 2025-12-16 11:53:51 +0100
Commit message:

 Update Plot2DScatters: possibility to change font size of axes and title labels + character vector as input for metacluster parameter (compatibility with metacluster levels after running UpdateMetaclusters)
Package: FlowSOM
Commit: a4b78a9dee625044e9c3f70cddbb6a1ac2b3449f
Author: KatrienQ <katrienq@cn2361.local>
Date: 2025-12-16 10:38:12 +0100
Commit message:

 Updated version number in NEWS
Package: FlowSOM
Commit: aebebf015a1273154d8c9b6111ea41829de61827
Author: KatrienQ <katrienq@cn2361.local>
Date: 2025-12-16 10:36:56 +0100
Commit message:

 Updated FlowSOM version number
Package: FlowSOM
Commit: 8171eb81795d18b3292b74f7a9abd08c42124d08
Author: KatrienQ <katrienq@cn2361.local>
Date: 2025-12-16 10:35:36 +0100
Commit message:

 Depricated PlotFileScatters and aligned the x-labels to the top.
Package: FlowSOM
Commit: e1e6697a10f90a1d2603da3f5eeca0f3546caaa1
Author: Robbe Fonteyn <fonteynrobbe@gmail.com>
Date: 2025-12-16 09:55:42 +0100
Commit message:

 Update TestOutliers function and adapted example
Package: FlowSOM
Commit: ba39ae896562a9ced83b58b9f59ede564653a5e0
Author: sarahbonte <sarah.bonte@irc.vib-ugent.be>
Date: 2025-11-18 16:06:55 +0100
Commit message:

 PlotMFIHeatmap function added and included in FlowSOMmary
Package: FlowSOM
Commit: b9974b2ea66bdda3c45f60a88dc08dfb7fbfa77c
Author: Katrien Quintelier <katrienq@cn2361.local>
Date: 2025-08-01 16:18:38 +0200
Commit message:

 Added NewData parameter options to GetFeatures and warnings to NewData
Package: FlowSOM
Commit: 5f4dbd385ce7b43e06791c5e75a28ff42635f7ec
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2025-03-17 14:49:04 +0100
Commit message:

 Merge commit

Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	DESCRIPTION
#	inst/NEWS
Package: FlowSOM
Commit: bd4d3d4e3ce1fa2dc1f29a1c15f7a0e9bb9f6420
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2025-03-17 14:44:54 +0100
Commit message:

 Moved table overviews in FlowSOMmary to the end
Package: FlowSOM
Commit: 85cefc2b9bd80285354061e53bd50d911a781c44
Author: sarahbonte <sarahm.bonte@ugent.be>
Date: 2024-07-03 11:42:25 +0200
Commit message:

 added Plot1DScatters
Package: FlowSOM
Commit: 4a065be1274c26d8c99bc0f195f63134d953fdfe
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 17:03:37 +0200
Commit message:

 Added ToScale to readInput function
Package: FlowSOM
Commit: bc1584d1999d75666bec80f3a1eb07136c5fc5b1
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2024-07-01 16:59:44 +0200
Commit message:

 Replaced geom_text with annotate in FlowSOMmary
Package: FlowSOM
Commit: 9d35bedcc3c8d3b37acab639c73ef10b34dc020c
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 16:38:50 +0200
Commit message:

 Added (...) parameter to readInput to give to read.FCS
Package: FlowSOM
Commit: c5511fdfe5242d169033d8231117577052208de3
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 16:00:07 +0200
Commit message:

 Added .data$ in MajorityLabels function
Package: FlowSOM
Commit: 43430b3cd856d49839c6a9e94c974e8d5b3d91c0
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 15:45:05 +0200
Commit message:

 Update authorlist
Package: FlowSOM
Commit: b9db8ee7ed4cbefde16640505baa3ecfc6f98ff1
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 15:41:31 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: 18a1d676788eb1bb1b8a57719dc8eb8bad0db14c
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 15:41:04 +0200
Commit message:

 Backgroundcolors are automatically updated with equalnodesize
Package: FlowSOM
Commit: 45332519b6d564f1b6d93e89c15817f448610861
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2024-07-01 15:39:01 +0200
Commit message:

 Added GetMajorityLabels function
Package: FlowSOM
Commit: 97ebb8cac5e85069bc76a749fc762e3e7e383124
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 14:49:59 +0200
Commit message:

 Updated version number and fixed documentation bug in plotdimred
Package: FlowSOM
Commit: 210aad8746b7150a0436a17d5722a716192382b3
Author: AnneliesEmmaneel <annelies.emmaneel@hotmail.com>
Date: 2024-07-01 14:17:26 +0200
Commit message:

 Added parameters for read.FCS in PlotFileScatters
Package: FlowSOM
Commit: 2def00a5ab2e95d5e6663c4c2817f3305a664f04
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2024-06-20 11:05:15 +0200
Commit message:

 Updated version number to meet Bioconductor version number
Package: FlowSOM
Commit: d1dac063f5f85403956f7c19bb97a485cd489a19
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2024-06-15 09:46:32 +0200
Commit message:

 Added alpha parameter to plotFlowSOM
Package: FlowSOM
Commit: 698f76dc5ea98199fd88ff0fdf12f4028006102f
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2024-06-14 16:42:04 +0200
Commit message:

 Added alpha parameter to addBackground
Package: FlowSOM
Commit: 35b43a9de120e0f42ae95eca1b8d006401a631b2
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2024-04-26 16:49:57 +0200
Commit message:

 Fix typos in FlowSOMmary
Package: FlowSOM
Commit: d53c501627ec58d51e51b207c03637fb9edb3836
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2024-04-15 22:28:23 +0200
Commit message:

 Fix typo
Package: FlowSOM
Commit: 0737126b2e43ae4b8b13a1307458c207016e6496
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2024-04-15 10:05:49 +0200
Commit message:

 - Update to the plot metacluster labels in FlowSOMmary
- No longer supress warnings in GetFeatures
- Add outlier count to matrices returned by GetFeatures
Package: FlowSOM
Commit: 56892b583a0dbae5535665e45290ffce355bd503
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2023-12-13 11:44:31 +0100
Commit message:

 Merge branch 'master' of github.com:saeyslab/FlowSOM
Package: FlowSOM
Commit: fbeed83825e3fcfd644941769a3bd2760424fec1
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2023-12-13 11:41:09 +0100
Commit message:

 made GetFlowJoLabels more efficient
Package: FlowSOM
Commit: ec21465eb612a1a74cbbb5bd2cb21953f540a8af
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-10-13 15:37:08 +0200
Commit message:

 Added the option to adapt background size in PlotFlowSOM
Package: FlowSOM
Commit: 71294ca705bf0b7dd8af01732fdf666e22ba17aa
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2023-08-31 10:27:11 +0200
Commit message:

 Small adaptations to make the GetFlowJoLabels function more robust
Package: FlowSOM
Commit: 9540c624612a5eeb43f4b797839b3ddb6799f9b8
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-04-21 15:21:14 +0200
Commit message:

 Solve merge issues

Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	DESCRIPTION
Package: FlowSOM
Commit: e8afbc91b667ee4e9a78833deefb36a45e9813c8
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-04-21 15:16:39 +0200
Commit message:

 Fixed colored metacluster centers when using Plot2DScatters
Package: FlowSOM
Commit: 20dd5a699791b83e69e08753d26d2f07eeee0bb1
Author: SofieVG <sofie.vangassen@ugent.be>
Date: 2023-03-28 16:22:56 +0200
Commit message:

 Merge branch 'master' of github.com:saeyslab/FlowSOM
Package: FlowSOM
Commit: 773069718c6a76bd7225004f3ebbc3ee2630d8a3
Author: SofieVG <sofie.vangassen@ugent.be>
Date: 2023-03-28 16:19:36 +0200
Commit message:

 updates to plotOutliers
Package: FlowSOM
Commit: ef84db86ccb42e9a0d55d5dbf79bdddb61b274f3
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-03-28 15:44:50 +0200
Commit message:

 Edited the descriptions of readInput and FlowSOM
Package: FlowSOM
Commit: 02e541ef66a1e9dcb27256a8f3138e6341365279
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-03-22 15:57:06 +0100
Commit message:

 Added PlotOutliers and documentation
Package: FlowSOM
Commit: 20e897d87baee9bb44b958f68be7505c08f36f95
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2023-02-09 16:12:17 +0100
Commit message:

 Update to TestOutliers
Package: FlowSOM
Commit: 7ccfd8083563df7db6ff80f487b0f7480724a5fe
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2023-02-08 09:35:03 +0100
Commit message:

 Merge branch 'master' of github.com:saeyslab/FlowSOM
Package: FlowSOM
Commit: 724c3f5d721a57e55527e5d8116215fd8466f6a9
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2023-02-08 09:31:10 +0100
Commit message:

 Further updates to the testOutliers function
Package: FlowSOM
Commit: dd60a843d2a2c0603b7fd981b7b522e780855a7f
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2023-01-31 23:00:14 +0100
Commit message:

 Updating the outlier detection - will still be further updated
Package: FlowSOM
Commit: 028f1296dcce65508d357d5eac36e1c813bc254c
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2023-01-11 16:23:56 +0100
Commit message:

 PlotManualBars shows percentages and PlotDimRed only uses scattermore if it is installed
Package: FlowSOM
Commit: 4cc11306c0feebbbba156552e02c70962663f3d4
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2023-01-05 13:10:57 +0100
Commit message:

 allow resampling in AggregateFlowFrames
Package: FlowSOM
Commit: d5fc07fd81ff1840a4f8791e0e7526d86864cf1a
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-12-16 13:24:21 +0100
Commit message:

 Adapt C code to use int instead of Sint
Package: FlowSOM
Commit: f4936861ced78fb11903f568ba60e27999893c02
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-11-22 11:01:32 +0100
Commit message:

 Solve merge conflict
Package: FlowSOM
Commit: 6b1fe7104097b582fd57832a932aa0040ca46b28
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-11-22 10:56:56 +0100
Commit message:

 Return 0 instead of NA in case of an empty cluster in GetCounts/GetPercentages
Package: FlowSOM
Commit: b8163792bfaea3888d97bcba26632ba5cab21a25
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-11-08 09:10:11 +0100
Commit message:

 Align version number with Bioconductor
Package: FlowSOM
Commit: fd67e6fd998e7d22e5cfe76f3ebab965ccaf36f6
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-10-06 11:14:04 +0200
Commit message:

 Bugfix in aggregateFlowFrames
Package: FlowSOM
Commit: c70beb09ca2242e0d6e75956d460a5120a749898
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-09-30 10:25:41 +0200
Commit message:

 Update to AggregateFlowFrames for nicer handling of iterative aggregation  (+ according visualisation in FlowSOMmary). AggregateFlowFrames will now introduce 0 values if a channel is not present in one of the fcs files. If channels is not provided as an argument, the channels of the first file are used.
Package: FlowSOM
Commit: d729fab382b11785c8e45e23c967592f0e27e09e
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-09-22 10:00:00 +0200
Commit message:

 Merge branch 'master' of github.com:saeyslab/FlowSOM
Package: FlowSOM
Commit: 3f9888d0fb4f9d36e499d1b614101d2515af94fd
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-09-22 09:53:16 +0200
Commit message:

 Merge branch 'master' of github.com:SofieVG/FlowSOM
Package: FlowSOM
Commit: 486b4f728ef9615315709ead005c9c95d3569ec9
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2022-09-22 09:52:42 +0200
Commit message:

 Merge pull request #51 from angelolab/default_map

Add `map` parameter to `SOM` computation with default argument `TRUE`
Package: FlowSOM
Commit: a3f1d7e9ac32918123374e6569b821d521d26003
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-08-01 09:17:15 +0200
Commit message:

 Added abbreviations to PlotDimRed "colorBy"
Package: FlowSOM
Commit: 188fc9223f71e3eb096b56f08da4c918cccb7847
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-08-01 09:03:45 +0200
Commit message:

 Added abbreviations to PlotDimRed "colorBy"
Package: FlowSOM
Commit: 2862b9d519e96ff5ecdf20800a756cf42e6b06ab
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-07-29 17:00:58 +0200
Commit message:

 Reversed PlotDimRed to scattermore and added support for custom colors and color scale limits to it
Package: FlowSOM
Commit: 7eedb581ec40f7b7fdc6447eb78bbd7d59c76666
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2022-07-13 11:59:04 +0200
Commit message:

 Merge pull request #52 from DillonHammill/master

Add support for flowSets in AggregateFlowFrames
Package: FlowSOM
Commit: f733e4bb7a98a8d8b4a62dc85a05ffc64425a136
Author: Dillon Hammill <Dillon.Hammill@anu.edu.au>
Date: 2022-07-08 15:31:59 +1000
Commit message:

 Add support for flowSets in AggregateFlowFrames.
Package: FlowSOM
Commit: 422308cd901ba3b84f834a00fd444188d3977d02
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-07-07 13:52:06 +0200
Commit message:

 AddAnnotation works after UpdateMetaclusters + fixed wrong coloring in PlotDimRed
Package: FlowSOM
Commit: 7c837ac5a58cc7662ae6ec2413fb19898964b4ff
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-06-29 15:58:30 +0200
Commit message:

 percentage_positives in GetFeatures now works with a FlowSOM with updated metacluster labels
Package: FlowSOM
Commit: 01e07f2b5f341b3f255c8d11ede925b36d36f16a
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-06-16 16:01:55 +0200
Commit message:

 Small bugfix in GetChannels
Package: FlowSOM
Commit: cc0e7c8822ba94cda21abd66b25b0765cc6616a4
Author: alex-l-kong <alkong@ucdavis.edu>
Date: 2022-05-27 16:33:35 -0700
Commit message:

 Change default value of map to TRUE in SOM so original functionality remains the same
Package: FlowSOM
Commit: 095840bdbc5c0763595f36254c9eaa0b7babf18a
Author: alex-l-kong <alkong@ucdavis.edu>
Date: 2022-05-27 15:40:47 -0700
Commit message:

 Add flexible mapping functionality to SOM function
Package: FlowSOM
Commit: b9cfbd744dd4d1546cd371c029f5dc62149d4712
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-05-13 14:30:28 +0200
Commit message:

 Bugfixes to pass BioConductor check and now normal ggplot colors are used in Plot2DScatters when ggpointdensity is not installed
Package: FlowSOM
Commit: 31bf74c131e0c1bee2584a060e99ceff8b74b5af
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-05-06 16:56:19 +0200
Commit message:

 Version bump + several changes to pass BioConducter check + exported ParseNodeSize + changed some examples + check NEWS for more updates
Package: FlowSOM
Commit: 1db0e3b5975e9329be05daae2fe26ed7364b2f82
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2022-03-25 11:12:40 +0100
Commit message:

 Update version number to be in sync with Bioconductor
Package: FlowSOM
Commit: 841c929b0a7819947f86040bbbb2f33d4900c192
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-02-24 10:59:39 +0100
Commit message:

 Added possibility to provide a seed when using metaClustering_hclust, metaClustering_kmeans or metaClustering_som
Package: FlowSOM
Commit: bd5a6e435178468785c0cc5ce0e84bbf55c233bb
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2022-02-22 13:49:25 +0100
Commit message:

 Added possibility to provide additional arguments to the read.FCS function in SaveClustersToFCS() function
PlotFileScatters now accepts other File ID columns, not anymore stricted to "File"
Package: FlowSOM
Commit: bfcdedad46509ff9d86e9a0121bf9db56f53b106
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-02-15 11:44:17 +0100
Commit message:

 Added a warning when using "backgroundColor" instead of "backgroundColors" in PlotStars +
clusters centers in Plot2DScatters is now colored the same as the cluster cells when using manual colors
Package: FlowSOM
Commit: 08b3ef2af8bbf4194e8f666d5dd5e7c3b740b125
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2022-01-13 09:53:34 +0100
Commit message:

 Added a warning in UpdateDerivedValue when using FlowSOM on an FCS with NA value
Package: FlowSOM
Commit: 3750126f93bada42840a75df79634276047655b3
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2021-12-14 09:10:09 +0100
Commit message:

 Edited documentation of Plot2DScatters +
Outlier counts are also returned as attributes when extracting percentages with GetFeatures
Package: FlowSOM
Commit: 81ed258486edde62f0356b6242ae10cb6b6aa452
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2021-10-27 10:04:51 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	FlowSOM_Cheatsheet.pdf
Package: FlowSOM
Commit: 7de6e76ffa911c1cc61a8da8095b210ee341253e
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2021-10-27 09:58:34 +0200
Commit message:

 Plot2DScatters: title is fixed, extra warning when wrong manual colors are used, add marker/channel names on plots
+ Updated cheatsheet
Package: FlowSOM
Commit: 4e6af55957c563ae51eec2785e095cc234b5636c
Author: Artuur Couckuyt <artuur_couckuyt@hotmail.com>
Date: 2021-10-27 09:58:34 +0200
Commit message:

 Plot2DScatters: title is fixed, extra warning when wrong manual colors are used, add marker/channel names on plots
+ Updated cheatsheet
Package: FlowSOM
Commit: dd6160291007767fbb23f3e5421a67e0d3d7b855
Author: aemmanee <annelies.emmaneel@hotmail.com>
Date: 2021-10-22 13:53:05 +0200
Commit message:

 Add marker outliers in TestOUtliers function
Package: FlowSOM
Commit: 314dad112eaee506a267e1e9cced0d95491d8931
Author: aemmanee <annelies.emmaneel@hotmail.com>
Date: 2021-10-22 10:42:00 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: 872d45e81ffd297ff6b0d4a37d3fdbe2d3dc3466
Author: aemmanee <annelies.emmaneel@hotmail.com>
Date: 2021-10-22 10:41:57 +0200
Commit message:

 Add mad values in fsom updatevalues
Package: FlowSOM
Commit: ab60006edc4b088b3dd9037a24acbed7308dfc8e
Author: davnovak <davidnovakcz@hotmail.com>
Date: 2021-10-05 16:14:37 +0200
Commit message:

 NewData clones prettyColnames from the original fsom object
Package: FlowSOM
Commit: 7548bda0ae6444401df95df161af697e60d9b901
Author: davnovak <davidnovakcz@hotmail.com>
Date: 2021-10-05 10:31:31 +0200
Commit message:

 Add % positive cells to GetFeatures
Package: FlowSOM
Commit: 2f90b4d7a8aeafe96457c86602e63f4b0c0a2747
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-08-11 16:43:09 +0200
Commit message:

 Test
Package: FlowSOM
Commit: 15a2e9005f48f062d014d2dde0524fb6ed400fb2
Author: aemmanee <annelies.emmaneel@hotmail.com>
Date: 2021-07-30 11:39:46 +0200
Commit message:

 Update documentation
Package: FlowSOM
Commit: bc941b6d29059008330dbcb3d0d1a3f01bea4934
Author: aemmanee <annelies.emmaneel@hotmail.com>
Date: 2021-07-30 11:34:29 +0200
Commit message:

 Added height and width parameter to PlotFileScatters
Fixed bug in PlotFileScatters
Package: FlowSOM
Commit: 4291af0273def4c442ede4f836cf23cee1a8b073
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-07-27 15:56:35 +0200
Commit message:

 Fixed typos and more consistent spelling
Package: FlowSOM
Commit: 8f8d0e62ead32b85532bb9b135eccc024efb56a5
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-07-13 09:27:40 +0200
Commit message:

 Added colsUsed and prettyColnames description in GetMetaclusterCVs
Package: FlowSOM
Commit: 04776298fa2c32cebec555fb1b5e89e68e290561
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-07-13 09:22:28 +0200
Commit message:

 Adapted GetMetaclusterCVs function so that it works after using UpdateMetaclusters + Fixed typos
Package: FlowSOM
Commit: 85202092beedd2a679459b26d44099a46666d024
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-07-09 10:08:51 +0200
Commit message:

 Increased version number
Package: FlowSOM
Commit: 4e9dc7b4c2ee2c9299b251b094ee9171bc333af6
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-07-09 10:06:17 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: c306c032e5aeed615e3e639c3a0f6048a8c9a081
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-07-09 10:06:03 +0200
Commit message:

 Adapted PlotManualBars function so that it works after using UpdateMetaclusters
Package: FlowSOM
Commit: 1e5650e0ed6a554f3dc96c5f8793202453e94daf
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-07-05 11:17:37 +0200
Commit message:

 Edited description of the FlowSOM function
Package: FlowSOM
Commit: 205743f0b86036f61690839c22390733dce77e02
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-07-02 15:18:00 +0200
Commit message:

 Updated CheatSheet and added code from UpdateDerivedValues for metaclustersMFIs to UpdateFlowSOM
Package: FlowSOM
Commit: e454b2ad212021faaa0ff0dfe9b2c7b3933c3793
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-07-02 12:53:25 +0200
Commit message:

 Forgot to update the documentation at the previous push.
Package: FlowSOM
Commit: 27a5b23e50ddda2cf71413bc8286d2708a1f19ce
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-07-02 12:40:31 +0200
Commit message:

 Combined the RelabelMetaclusters, ReassignMetaclusters and ReorderMetaclusters finctions into one UpdateMetaclusters function.
Package: FlowSOM
Commit: 0df33c8c427a85d5a4b892b4e487975a18bd5ed6
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-07-01 11:09:50 +0200
Commit message:

 Fixes to pass R check
Package: FlowSOM
Commit: 9deea76e2a7c139f639420457fef8a3fea519dac
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-06-30 17:33:47 +0200
Commit message:

 Added checkNames = FALSE in MetaclusterMFIs
Package: FlowSOM
Commit: 5ee55a4b93449ce3153e1d0c2135bd8760cb90dc
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-06-30 17:24:22 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: 15f6f2e04cfdeb29bd61eddc6b3f89a269f65826
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-06-30 17:23:52 +0200
Commit message:

 Update to avoid @ call in GetMarkers
Package: FlowSOM
Commit: 6596c1cecefb99b0add859a12d696638fd7ea2fe
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-06-30 16:44:03 +0200
Commit message:

 Reordered code in UpdateDerivedValues, RelabelMetaclusters, ReorderMetaclusters and ReassignMetaclusters
Package: FlowSOM
Commit: a562d2916b397edc06ce97a7f655ac53638f006b
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-06-16 15:51:45 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	DESCRIPTION
Package: FlowSOM
Commit: 73470e7daea78bde0e4b1abbfd788bf2aee31dbe
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-06-16 15:50:46 +0200
Commit message:

 Added reorder metacluster to correctly reorder the metacluster levels
Package: FlowSOM
Commit: 019abbbf2cb8ad0b15d89445a1aceb6d0321346e
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-06-16 15:39:44 +0200
Commit message:

 Version bump
Package: FlowSOM
Commit: 378dbc5e4c5f701a08b53ca9817c0e49f8b14fa7
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-06-16 15:38:56 +0200
Commit message:

 use flowcore::parameters(ff) instead of ff@parameters to be more robust (e.g. for cytoframe)
Package: FlowSOM
Commit: a84983f716dc9ea265adad1826a7e8538a8eb3e2
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-06-07 14:02:01 +0200
Commit message:

 Updated PlotManualBars, Plot2DScatters and FlowSOMmary so that it works with relabeled metaclusters.
Package: FlowSOM
Commit: 049bf175da76ed3105b4411ce957a3941bea7942
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-06-03 15:31:08 +0200
Commit message:

 Silent parameter in GetFeatures now surpresses messages from NewData. NewData got silent parameter to surpress ReadInput
Package: FlowSOM
Commit: 22db44c8571c7a283fd762c4159c80afd0c84d6e
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-06-01 17:05:48 +0200
Commit message:

 Fixed the cluster/metacluster issue in PlotManualBars, part 2
Package: FlowSOM
Commit: 4224fed42b709763bc88bbd248f9694175007f12
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-06-01 16:59:42 +0200
Commit message:

 Increased version
Package: FlowSOM
Commit: 2832e7be491dc3d2a2c3bd1245638176898dff1d
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-06-01 16:59:02 +0200
Commit message:

 Fixed the cluster-metacluster issue
Package: FlowSOM
Commit: afec9a895b559e1c6e4e52144784d74eb500363c
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-05-25 18:35:03 +0200
Commit message:

 AggregateFlowFrames: works with one channel, gives warnings with non-matching files, works with markers.
FlowSOM: included info parameter, with version, date and call arguments.
PlotFileScatters: works with one channel, wokrs with markers, added silent parameter.
Package: FlowSOM
Commit: 1969fa0b31ad49988c9c546961c8ed3744f1b6ab
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-05-18 14:47:21 +0200
Commit message:

 Added the FlowSOM R Cheatsheet
Package: FlowSOM
Commit: 6f77488c676b868a913079204af5d136b3b2a2fe
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-05-18 14:41:44 +0200
Commit message:

 add quantiles argument to PlotFileScatters
Package: FlowSOM
Commit: bda4bfc32d61bbe351dc550d5836a07f4efe123c
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-05-11 11:30:50 +0200
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: 64f643319abaec252207dc4804043c7480e9f3cf
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-05-11 11:30:19 +0200
Commit message:

 Show quantiles in PlotFileScatters
Package: FlowSOM
Commit: 3dc496c59c51fa85cc4388f80f9a3f90fcf88703
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-04-16 14:53:07 +0200
Commit message:

 PlotFileScatters: makes duplicated filenames unique and now works with output of AggregateFlowFrames
Package: FlowSOM
Commit: 0579535991f38a4a6e200b6c073adb50a4e3c85e
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-04-16 09:57:41 +0200
Commit message:

 Small fix to not include FlowSOM::: in the package code itself.
Package: FlowSOM
Commit: 6493bdb9b236945261b39accb54178289bc47384
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-04-14 17:07:13 +0200
Commit message:

 Added ReassignMetaclusters to NAMESPACE
Package: FlowSOM
Commit: f9662c93868ae16a69f35f876de3245de6232995
Author: KatrienQ <quintelierkatrien@gmail.com>
Date: 2021-04-14 16:51:49 +0200
Commit message:

 Added ReassignMetaclusters function
Package: FlowSOM
Commit: 909c172294941c8f230184bef0928a893f10e33a
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-04-14 11:42:21 +0200
Commit message:

 Fixed issue with FlowSOMmary
Package: FlowSOM
Commit: d25da50f633855b6f52f1d4d557ab4f59d94dbb4
Author: Annelies Emmaneel (Admin) <annelieseAdmin@cn1365.UGent.be>
Date: 2021-04-13 15:44:39 +0200
Commit message:

 Allow NewData object for PlotManualBars
Package: FlowSOM
Commit: 828f8be5df5939f7704204fcb76b6d88fc5f4c0a
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-04-13 13:24:48 +0200
Commit message:

 Fixed warnings with ggtexttable in FlowSOMmary
Package: FlowSOM
Commit: fe27e0250547070d768f9c3c1076643b95f55f70
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-04-07 16:50:04 +0200
Commit message:

 Added xlim and ylim to Plot2DScatters and solved bug with colors
Package: FlowSOM
Commit: b2bebb65e45c3414bc0cd4c908d1234e6113b78a
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-04-07 08:58:48 +0200
Commit message:

 Increase version number
Package: FlowSOM
Commit: f64f9e3962868cfe747b0406b1f8707e30d8fb0a
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-04-06 17:02:46 +0200
Commit message:

 Increased PlotFileScatters width so it also shows something for smaller file counts.
Package: FlowSOM
Commit: 988d4bd95a604b5c148b38581b91cb03c66c8967
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-04-06 12:53:48 +0200
Commit message:

 Merge

Merge branch 'master' of https://github.com/saeyslab/FlowSOM

# Conflicts:
#	R/4_metaClustering.R
Package: FlowSOM
Commit: 383608334350d8ee246f3ca92789f3004ea90dde
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-04-06 12:51:19 +0200
Commit message:

 Extra check in RelabelMetaclusters
Package: FlowSOM
Commit: 7c18aaa24f1a11f6dd009914e4feba074e12e390
Author: Artuur Couckuyt <artuur.couckuyt@hotmail.com>
Date: 2021-04-06 12:20:04 +0200
Commit message:

 Added the option to change yLabel in PlotFileScatters to markers and/or labels, added error message to RelabelMetaclusters when no metaclusters are available, edited NEWS and description
Package: FlowSOM
Commit: cd7a7a757039adb988b1b4ed5eb1ab56f38fb6c2
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-26 17:15:29 +0100
Commit message:

 Version bump
Package: FlowSOM
Commit: 50e20529e6cd210315052a93bbce839d725718d5
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-26 17:14:51 +0100
Commit message:

 Added function RelabelMetaclusters
Package: FlowSOM
Commit: c5195974713c1c8b906b1720c3089249d5770d45
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-11 10:04:49 +0100
Commit message:

 Fixed some documentation to work with the "level" parameter instead of "population".
Package: FlowSOM
Commit: bb1282f04dd5972be744dd3dfc81396984ed15f6
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-11 09:26:59 +0100
Commit message:

 Allow TRUE/FALSE vector as input for GetMarkers / GetChannels
Package: FlowSOM
Commit: 259dee4f610be8c68f5e1146d82dc5878b40a208
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-10 15:55:35 +0100
Commit message:

 Merge branch 'master' of https://github.com/saeyslab/FlowSOM
Package: FlowSOM
Commit: 218971f9002ef756e0a8eb1cf75fbcac2d478875
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-03-10 15:55:20 +0100
Commit message:

 Fix to make sure print also works on FlowSOM object created by ReadInput only.