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Package: omicsGMF
Commit: 14caf2e25488f9b02293354ddff735a87ea1d534
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 23:03:34 +0200
Commit message:
Commit: 14caf2e25488f9b02293354ddff735a87ea1d534
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 23:03:34 +0200
Commit message:
version bump
Package: omicsGMF
Commit: 7e32fffed52d90a616d37f4772d1bb1138bf5cf9
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 21:52:40 +0200
Commit message:
Commit: 7e32fffed52d90a616d37f4772d1bb1138bf5cf9
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-10-21 21:52:40 +0200
Commit message:
minor changes
Package: igblastr
Commit: ed3b6c1dccb16d7faf06e92e52e36044d613ee39
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 12:35:57 -0700
Commit message:
Commit: ed3b6c1dccb16d7faf06e92e52e36044d613ee39
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 12:35:57 -0700
Commit message:
print message when the user selects a built-in AIRR germline db with .src suffix
Package: scGraphVerse
Commit: ba54489471821d43da58a8184769f1d7728f2962
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-21 20:22:51 +0200
Commit message:
Commit: ba54489471821d43da58a8184769f1d7728f2962
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-21 20:22:51 +0200
Commit message:
fix DESC and NEWs
Package: igblastr
Commit: 4836243ca5a3ac82054e48a18ab2bcc4acd9534c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 11:16:45 -0700
Commit message:
Commit: 4836243ca5a3ac82054e48a18ab2bcc4acd9534c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 11:16:45 -0700
Commit message:
oops, should have been '?list_germline_dbs' instead of '?germline_dbs_home' in previous commit message
Package: igblastr
Commit: bf159cf6108aff05a8abcd0e5a0b5d04bca2de2d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 10:55:49 -0700
Commit message:
Commit: bf159cf6108aff05a8abcd0e5a0b5d04bca2de2d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-21 10:55:49 -0700
Commit message:
igblastr 0.99.23: New built-in AIRR germline dbs for human
Replace built-in germline db _AIRR.human.IGH+IGK+IGL.202501 with the
following dbs:
_AIRR.human.IGH+IGK+IGL.202309
_AIRR.human.IGH+IGK+IGL.202309.src
_AIRR.human.IGH+IGK+IGL.202410
_AIRR.human.IGH+IGK+IGL.202410.src
See https://github.com/HyrienLab/igblastr/tree/devel/inst/extdata/germline_sequ>
and https://github.com/HyrienLab/igblastr/tree/devel/inst/extdata/germline_sequ>
for how these dbs were made.
Note that _AIRR.human.IGH+IGK+IGL.202410.src is exactly the same
as _AIRR.human.IGH+IGK+IGL.202501, only the name is different. The
new name is the result of a revisited naming scheme for the built-in
AIRR germline dbs for human.
See the Value section in '?germline_dbs_home' for more information.
Package: scDblFinder
Commit: 227116a0fe7378a0679f3a5137de2fd6445c75c2
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:06:14 +0200
Commit message:
Commit: 227116a0fe7378a0679f3a5137de2fd6445c75c2
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:06:14 +0200
Commit message:
version bump
Package: scDblFinder
Commit: 2bbcbf43e1bd7dc5732152be5c2cd6c4b8e7514b
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:05:37 +0200
Commit message:
Commit: 2bbcbf43e1bd7dc5732152be5c2cd6c4b8e7514b
Author: plger <pl.germain@gmail.com>
Date: 2025-10-21 18:05:37 +0200
Commit message:
verbos arg name to match different xgboost versions
Package: rhinotypeR
Commit: cd2e13f84c2d847d882fb634831f8c9db99ffd00
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 17:08:48 +0100
Commit message:
Commit: cd2e13f84c2d847d882fb634831f8c9db99ffd00
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 17:08:48 +0100
Commit message:
Merge branch 'main' of https://github.com/omicscodeathon/rhinotypeR
Package: rhinotypeR
Commit: 38a78893d0e2757f4bfc10d1836138d436902011
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 16:55:09 +0100
Commit message:
Commit: 38a78893d0e2757f4bfc10d1836138d436902011
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-21 16:55:09 +0100
Commit message:
solved check errors
Package: rhinotypeR
Commit: 9a149ec6819cf901908b979b321534ba60297685
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-05 15:05:08 +0100
Commit message:
Commit: 9a149ec6819cf901908b979b321534ba60297685
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-05 15:05:08 +0100
Commit message:
Merge pull request #10 from omicscodeathon/git-devel ms revisions
Package: rhinotypeR
Commit: ba339370eea09c7954551ba84d4f74e92a33a4f9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-05 15:04:05 +0100
Commit message:
Commit: ba339370eea09c7954551ba84d4f74e92a33a4f9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-05 15:04:05 +0100
Commit message:
ms revisions
Package: rhinotypeR
Commit: 8b164451e15bda19a4bafc6829ebd59300f64b30
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-01 19:06:17 +0100
Commit message:
Commit: 8b164451e15bda19a4bafc6829ebd59300f64b30
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2025-10-01 19:06:17 +0100
Commit message:
Delete rhinotypeR.BiocCheck directory
Package: rhinotypeR
Commit: 41199a585753827e0be3be2068a1cff7ae0488a9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-01 19:04:39 +0100
Commit message:
Commit: 41199a585753827e0be3be2068a1cff7ae0488a9
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-01 19:04:39 +0100
Commit message:
manuscript revisions
Package: rhinotypeR
Commit: 562ab4c84a3687a4f7eb883fd11c8a4fd83e11b6
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:16:43 +0100
Commit message:
Commit: 562ab4c84a3687a4f7eb883fd11c8a4fd83e11b6
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:16:43 +0100
Commit message:
undoing changes to readme.md as this modified via rmd
Package: rhinotypeR
Commit: 91d20661882dfee5163391de3b384d94b59ec288
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:10:33 +0100
Commit message:
Commit: 91d20661882dfee5163391de3b384d94b59ec288
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-09-13 15:10:33 +0100
Commit message:
Revert to: undo unwanted commits </pre> </div> Package: rhinotypeR
Commit: 4dea2691019c06294f2252212c004601de929b8c
Author: Olaitan I. Awe <laitanawe@gmail.com>
Date: 2024-11-23 02:21:32 +0100
Commit message:
how to contribute to rhinotypeRPackage: rhinotypeR
Commit: f8e640d40a03f11bf155d9ec3fee3ffb59aba9ca
Author: Olaitan I. Awe <laitanawe@gmail.com>
Date: 2024-11-23 01:53:49 +0100
Commit message:
how to contribute to rhinotypeRPackage: rhinotypeR
Commit: 309812f074cb8d9b90c313632abd4e13e756791a
Author: Olaitan I. Awe <laitanawe@gmail.com>
Date: 2024-11-23 01:53:10 +0100
Commit message:
how to contribute to rhinotypeRPackage: rhinotypeR
Commit: bacd8c433420d7e80a2a9a6ca759b3817773dbad
Author: Olaitan I. Awe <laitanawe@gmail.com>
Date: 2024-11-23 01:50:19 +0100
Commit message:
how to contribute to rhinotypeRPackage: rhinotypeR
Commit: 38274db37608cc4720b1dacd6a8fcb18e08c5143
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-10-03 17:10:11 +0100
Commit message:
Merge branch 'main' of https://github.com/omicscodeathon/rhinotypeRPackage: rhinotypeR
Commit: 5a6bf06537bae9e12ebb42518ada49eacf29c569
Author: Martha Luka <39192976+marthaluka@users.noreply.github.com>
Date: 2024-09-14 13:40:22 +0100
Commit message:
Merge pull request #9 from omicscodeathon/devel Update .gitignorePackage: iscream
Commit: bfe73bbc3086d8d49bd794e4d7f3f95b97d5d790
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 11:10:12 -0400
Commit message:
chore(DESCRIPTION): bump versionPackage: iscream
Commit: e3d33cc30e46432fab36cea2fb7e9f1f5a58296e
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 11:16:56 -0400
Commit message:
test: load required bioc packages to run functions returning themPackage: iscream
Commit: 6595f1007d77eebc1dbd5e4f4be39449779880ca
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 10:44:24 -0400
Commit message:
!fix(make_mat_gr|tabix_gr): error if the bioc package is not loadedPackage: iscream
Commit: 38c1ee4b7f199c76207c37012a6c89d5fe027842
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 10:43:34 -0400
Commit message:
fix(make_mat_bsseq): run example iff bsseq is available; namespace the callPackage: iscream
Commit: 6f10307cdf951995cac2cfa57a8d70b1a1a36570
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 10:22:44 -0400
Commit message:
chore(configure): fix typo in tabix check messagePackage: iscream
Commit: b7822a56cd6ab39f9fa23ca99584b48578a408f2
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-21 10:18:49 -0400
Commit message:
docs(vignettes): add require guards to SuggestsPackage: proBatch
Commit: 2ad0a3808467708f3655e4633a1cf99d887a77f0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-21 17:54:19 +0200
Commit message:
version bumpPackage: proBatch
Commit: 221a2610e018f1f916573bd92d601b3966194999
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-21 17:49:04 +0200
Commit message:
refactor pca plots examplesPackage: proBatch
Commit: b7e535402152c7538e81c5753f55fe6f9eaa1a6c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-21 17:35:18 +0200
Commit message:
Refactor examples to use subsets of data for faster checksPackage: proBatch
Commit: 6674936ec70f3f6a410cd7c694ed36d85ac1b926
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-21 16:12:29 +0200
Commit message:
Update vignettesPackage: transmogR
Commit: 3b27ef9ba4331c1482fdfb182ad8ce4210a3e283
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-22 01:35:30 +1030
Commit message:
Version bump after tweakPackage: transmogR
Commit: 045877d7a88b1dfbc5015940c5eb3126a27960ef
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-22 01:30:54 +1030
Commit message:
Made overdispFromBoots a public functionPackage: transmogR
Commit: 8b1207fa949f5458e8fd1cc2ad2bf609694115bd
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-22 00:45:08 +1030
Commit message:
Handled missing .idsPackage: pRoloc
Commit: 2f6ab451c54a39a38d14aac25823b2efbce98006
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-10-21 16:19:03 +0100
Commit message:
Merge pull request #160 from lgatto/tagm-mcmc-v2 new optimised version of tagm mcmcPackage: pRoloc
Commit: e15a5ccc7ac9f3e7398cd4d772e50a1d480c97d0
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-10-21 16:00:37 +0100
Commit message:
fix conflictsPackage: pRoloc
Commit: 3f197d4f106c097f9a0463b693aeaacd825b2e76
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-10-06 15:15:46 +0100
Commit message:
update docsPackage: pRoloc
Commit: 913a4f6bad9ba492e5a7af724865884223650ceb
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-10-06 15:13:25 +0100
Commit message:
switch default to new versionPackage: pRoloc
Commit: 3521f8b2b3e1576b29a873e9ff89f78257be917d
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-09-24 13:44:28 +0100
Commit message:
clearn RcppExportsPackage: pRoloc
Commit: 3b89c006714b2ae1b04865e1f3452780c2e64790
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-09-24 13:07:55 +0100
Commit message:
remove pRoloc.so in srcPackage: pRoloc
Commit: dc5f49dc2483da88f155fd4b6fcef6e1ae1eed3f
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-09-24 13:07:10 +0100
Commit message:
remove .o files from srcPackage: pRoloc
Commit: 980963cc480d08b98e0e1daec5d24de7369e3b81
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-09-23 19:47:17 +0200
Commit message:
Merge branch 'devel' into tagm-mcmc-v2Package: pRoloc
Commit: b344b17bdd53456c2eaec31a44e107fd066a7cfc
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-09-17 15:08:13 +0100
Commit message:
new optimised version of tagm mcmc - reimplemented tagm mcmc to be more memory efficient and speed increases.Package: smoppix
Commit: db5e143ba7523d82e7987107c7f8e8aa752ebdaf
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 17:23:35 +0200
Commit message:
Scale bar adding worksPackage: smoppix
Commit: fda6006f0996fdbb792dfcdbd37b8476d260e564
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 15:57:29 +0200
Commit message:
revert bad ideaPackage: smoppix
Commit: f149da9fc1c9b103706d14224f2e87dc4e9e97bf
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 15:57:16 +0200
Commit message:
bad ideaPackage: smoppix
Commit: ad58a3ab33c3bb136296b81985075e9de55efcee
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 15:31:55 +0200
Commit message:
With testsPackage: smoppix
Commit: 10c3310c5e73b2c3c3d791b1ea715603de7ef768
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 15:29:08 +0200
Commit message:
Finetuning the scale barsPackage: smoppix
Commit: e651c059be0bd1ee9d3ac1adf2ff0fcab9323846
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 14:23:00 +0200
Commit message:
plotcellsscalebar can be mergedPackage: smoppix
Commit: 7e39df9547cd79efea4bd084d672e77e647650e6
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-21 13:42:03 +0200
Commit message:
scale bars appear correctlyPackage: MSstatsResponse
Commit: 8bcca9c525023fffcbae7ddb1dccc9674afb55bd
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-21 10:14:15 -0400
Commit message:
fixed bpparam() usagePackage: biomaRt
Commit: 1fcf101187eb7cccbb34795037934a933ec962e5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-21 15:32:03 +0200
Commit message:
Fix if_not_else lintsPackage: EWCE
Commit: 0de5a8e9ba506c440660a235ab4023788d39fc85
Author: Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com>
Date: 2025-10-21 13:48:05 +0100
Commit message:
Merge pull request #103 from NathanSkene/dep-fixes Fix ggplot v4 related issuesPackage: EWCE
Commit: 920379ddb7cacbe710a6c1f14a84b75dc84c25c2
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2025-10-21 13:17:54 +0100
Commit message:
Fix `ggplot v4` breaking changesPackage: EWCE
Commit: 678ef22518d632bd96cd112112992ad45a02a946
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2025-10-21 11:32:20 +0100
Commit message:
Fix test for ggplot outputPackage: EWCE
Commit: 083af093e8f1ff681702a58e3c4e83963feef2bd
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2025-10-21 10:54:22 +0100
Commit message:
Update maintainer and documentationPackage: QFeatures
Commit: 205ad412cc8667a3ce754b25b074f4a24d5882ee
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-10-21 12:23:33 +0200
Commit message:
udate newsPackage: QFeatures
Commit: 6fe240b55cf65b7ad221bd6c3d4052e132077b34
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-05-26 18:57:44 +0200
Commit message:
new devel versionPackage: UMI4Cats
Commit: 2dfa73c06e8b262d3971e694f90f4aaf2d4fe197
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2025-10-21 12:59:01 +0200
Commit message:
Add session infoPackage: proBatch
Commit: 05ba72ac3f68004970e0371f8f56f4322114a222
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-21 12:57:18 +0200
Commit message:
version bumpPackage: UMI4Cats
Commit: bdc9420a52d3df5b8eebc0188375459c9566c1a0
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2025-10-21 12:48:56 +0200
Commit message:
Add OrgDb argument for creating gene annotation (#19)Package: consICA
Commit: 3739f03b217c4ef144d37a37afdff4201558d4e6
Author: Maryna Chepeleva <maryna.chepeleva@gmail.com>
Date: 2025-10-21 10:56:54 +0200
Commit message:
[fix][man]getGO(): Example running time on nebbiolo2 + bump version 2.7.3Package: SpaceTrooper
Commit: 5c86b34dc2ac512315e8a9da84c0442b804c0bb0
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-21 09:43:10 +0100
Commit message:
bump version to 99.46Package: SpaceTrooper
Commit: 7c7258ca352f406dfe835b08bbf74083aafe4a13
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-21 09:41:41 +0100
Commit message:
fixing major documentation problemsPackage: SpaceTrooper
Commit: fabb9418b031899ab904d71811c9a6ff55fb7d74
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-21 09:29:09 +0100
Commit message:
fixing problematic documentationPackage: SpaceTrooper
Commit: 0f2bf098725a3517941056c86f35efd001c40513
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-20 10:57:13 +0100
Commit message:
adding more informative error in computeQCScorePackage: SpaceTrooper
Commit: ecb83432f8972a80eeb39c47e2d770c4102204dc
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-20 10:16:10 +0100
Commit message:
updating readmePackage: SpaceTrooper
Commit: 662b7b6b3933d7215ff1ca09c0d368346960c266
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 20:23:13 +0100
Commit message:
fixing cache problems with GHAPackage: SpaceTrooper
Commit: 7935ccfcd5ae9a0cc69ec0c6051df2026360ac6f
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 19:19:12 +0100
Commit message:
fixing spaces in descriptionPackage: notameStats
Commit: 8a99705e8e6e2bf24feed1fa9ae8b94c4687b66b
Author: Atte Lihtamo <98050742+attlih@users.noreply.github.com>
Date: 2025-10-21 10:19:29 +0300
Commit message:
Refactor parallel processing handling in univariate statistics (#1) Only internal changes to speed up parallel processing, which was painfully slow on Windows machines. * Refactor parallel processing handling in univariate statistics * Fix auc computation * Version bumpPackage: limma
Commit: 65741f777afec629be52265ed1aad5a8352436f7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-10-21 18:24:15 +1100
Commit message:
limma 3.65.7 - Add `upshot` option for treat()Package: VariantFiltering
Commit: cafa29d5ab2fd090e8ce8b349b280316e40bd098
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-10-20 22:31:25 -0700
Commit message:
Fixed unit test for filtering variants by locationPackage: plyxp
Commit: abc76c81f4f6956b60a3cc2a31d931d658f0457d
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-20 20:24:37 -0700
Commit message:
version bumpPackage: plyxp
Commit: b79c2fe0a02afeb319f328a915b2734ef4bea4f0
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-20 20:23:58 -0700
Commit message:
update summarize behavior * `summarize.PlySummarizedExperiment` now allows no assay context arguments * Improve error handling in across() for `.fns` argument * Remove requirement for assay context in summarize_se_implPackage: enrichplot
Commit: a772cb08a0456a888076308a6e268d8c8e5a0bbd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-21 09:28:56 +0800
Commit message:
bump versionPackage: enrichplot
Commit: b178c139d2e2444d5d8611da54f8889a2f4f23de
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-15 09:54:14 +0800
Commit message:
fixed for #329Package: enrichplot
Commit: f401fa54a4f61753242c75f851182d961fcfe24f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-13 18:00:55 +0800
Commit message:
bug fixed, #329Package: enrichplot
Commit: bf86dcdc74316c7ee8d9e7f5fcac7e88392204e6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-16 14:39:42 +0800
Commit message:
testPackage: enrichplot
Commit: 945f86af9c25e6abdf85e9a0bfe6a96f62f749ed
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-14 14:04:49 +0800
Commit message:
bug fixed, #328Package: geomeTriD
Commit: 35117310c2a6b5e8cc27ed83d06883c3a1131f35
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-20 20:49:24 -0400
Commit message:
update readme.Package: scrapper
Commit: 39ebc39e8bd488ba48b4358037ba7cffb72d62c8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-20 15:36:57 -0700
Commit message:
Support character and logical vectors in sets= for aggregateAcrossGenes.Package: scrapper
Commit: 381e727ef8e42a0807205c7116ed74b7238aa637
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-20 14:22:34 -0700
Commit message:
More informative names and error messages for internal utilities.Package: scrapper
Commit: 2912b8da91216e5c5e8f5eb420d1001abd355a1c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-20 14:10:39 -0700
Commit message:
Obtain sorted and unique gene set indices for scoreGeneSet. This is a bit more explicit than coercing everything to a logical vector.Package: BioCor
Commit: ea914ce797bb19e8bffc8aa3ba7f3fab326df44f
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-10-21 00:08:50 +0200
Commit message:
Update examplePackage: BioCor
Commit: 34699c438ce321f6cb538835b537da6854aa50fa
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-10-21 00:08:41 +0200
Commit message:
Fix urlPackage: BioCor
Commit: a99b8f9305034717fd8484912a1826ccbb2ed4b0
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-10-21 00:08:20 +0200
Commit message:
Update Roxygen2 versionPackage: BioCor
Commit: 0ee6dcfb92b65bd94eb196119a4e0a39a0731826
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-10-15 20:49:05 +0200
Commit message:
Warn if NAs are detected: could trigger BioconductorPackage: BioCor
Commit: 82d86da311a0cf1483c2885ea18690e0d53df34b
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-10-15 20:48:42 +0200
Commit message:
Fix CRAN detected issuesPackage: BioCor
Commit: a86f532d32ab121298153c7238a9aaa717a09eaa
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-09-23 23:45:13 +0200
Commit message:
Increase version numberPackage: BioCor
Commit: 5fdb48dc002a53523ca03a2bd9187b64430e70fc
Author: Lluís <lluis.revilla@gmail.com>
Date: 2025-09-23 23:44:51 +0200
Commit message:
Update minimum version requirementsPackage: MultiRNAflow
Commit: abe36dd12ccc1a8b09c0a9adf775a3264084ef50
Author: Rodolphe Loubaton <loubaton.rodolphe@gmail.com>
Date: 2025-10-20 23:54:39 +0200
Commit message:
New version: 20251020Package: enrichViewNet
Commit: 1baf4419ad6616ab762fd33013797a68a20e15e5
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-20 17:37:08 -0400
Commit message:
Merge branch 'devel' of https://github.com/adeschen/enrichViewNet into develPackage: enrichViewNet
Commit: 735ddc3ab08bf4f4f21e3a6405870d25b6c1e336
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-20 17:37:00 -0400
Commit message:
Manage overlapping labels in graphsPackage: enrichViewNet
Commit: 478fd491f1093ffc15a49705c0712e2e083d0d0a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-15 20:26:34 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: 5902d7d0bc4d6b74e5205c7bac92b53bef57e3ad
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-15 20:02:09 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: 5824934df15b974907a28b8bed434f21748fba34
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-15 19:35:49 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: a3fb0f3c6c4d600c9c0149cd33aa8303bfc1808e
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-15 19:16:02 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: 7b6d5f77b1474a6bfaf6c2fbac082109e6636793
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-15 18:44:59 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: a6bdd0774de22ecca9c5ca18c87bad019551f928
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-15 17:34:14 -0400
Commit message:
Update check-bioc actionPackage: enrichViewNet
Commit: ad3741c87aaf9e0772e58241a6eba7f6db8c0b5b
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-09 19:00:18 -0400
Commit message:
Merge pull request #23 from adeschen/adeschen-patch-1 Update check-bioc.ymlPackage: enrichViewNet
Commit: 166d288023b6683570e234ed0dbe05e75c67cb86
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-09 18:45:37 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: b0b362f6d3622d5a082f40c77c751ce639a54269
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 18:24:36 -0400
Commit message:
Bump version in develPackage: enrichViewNet
Commit: aa7f5c786865f37f500201e1cc090941a3263424
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-09 18:12:10 -0400
Commit message:
Merge pull request #21 from adeschen/graphUpdate Public functions that generate igraph objectsPackage: enrichViewNet
Commit: a4e644fea33bb23c169061893c892577d2ee81af
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 17:59:08 -0400
Commit message:
Remove empty strings in similarityJaccard() function before calculating similarity coefficientPackage: enrichViewNet
Commit: 56867148c3c9cff0436b2bf6e632f6570976a02e
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 17:37:38 -0400
Commit message:
Add unit test for createEnrichMapAsIgraph() functionPackage: enrichViewNet
Commit: a14961d46d5129413e9e875f8478f7f4aca9c3b2
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 17:26:18 -0400
Commit message:
Remove unused functionPackage: enrichViewNet
Commit: f7ffb8e8479ca7695ddaeeb0f317be22482b27e0
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 17:16:21 -0400
Commit message:
Change unit test for createEnrichMapMultiComplexAsIgraph() functionPackage: enrichViewNet
Commit: 87a59b78ab412ce6890de374fdae60cdd6072cc9
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-09 16:54:09 -0400
Commit message:
Add unit tests for createEnrichMapMultiBasicAsIgraph() functionPackage: enrichViewNet
Commit: 2b6d766c7065728cc5218a248299c4dda7e7733c
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-08 18:35:13 -0400
Commit message:
Merge branch 'graphUpdate' of https://github.com/adeschen/enrichViewNet into graphUpdatePackage: enrichViewNet
Commit: 23aaddd1447871c9dd21fb82b734e8e34b33e5dd
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-08 18:33:34 -0400
Commit message:
Update documentationPackage: enrichViewNet
Commit: a39b6765758f32da633e1f5f32adb6759fb2fd26
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-08 17:40:09 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: 23a090637225084e8973a6a83873fed99fa5b53c
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-10-08 17:38:45 -0400
Commit message:
Update check-bioc.ymlPackage: enrichViewNet
Commit: 464bc43723c2b87a9167fcba84c4a8dc4e3061b0
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-08 16:43:15 -0400
Commit message:
Update github action check-biocPackage: enrichViewNet
Commit: 36e19be353ec7cf76f4bc9e3e53e91deb55ac206
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-08 16:33:51 -0400
Commit message:
Update github action check-biocPackage: enrichViewNet
Commit: bee72c080b7882fc5cca2d480c36b55ff833827e
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-08 16:01:41 -0400
Commit message:
igraph functions returns weight information in the igraph outpoutPackage: enrichViewNet
Commit: c54b5616c6982364fa8f7852487a76f3262301d0
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-07 17:27:54 -0400
Commit message:
Add unit testsPackage: enrichViewNet
Commit: c587a3e9a14dfe501085180ee99194f53e24ee4a
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-07 16:45:19 -0400
Commit message:
Adding unit testsPackage: enrichViewNet
Commit: 3a8f3ee6502bd34c5d2ba25421d5c9749ba7f261
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-07 16:07:49 -0400
Commit message:
Missing new functionPackage: enrichViewNet
Commit: d3949c06f96a1617d20519412c54e6d29705a555
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-07 15:25:47 -0400
Commit message:
Adding public method createEnrichMapMultiBasicAsIgraph()Package: enrichViewNet
Commit: 80e07737c8dd7d60d75537a93b92d45301a8fb3e
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-03 16:14:25 -0400
Commit message:
Update vignettePackage: enrichViewNet
Commit: 58d4ded23f5bad1e8ba284ad46694ebdfe39b374
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-03 14:25:37 -0400
Commit message:
Add unit testsPackage: enrichViewNet
Commit: 1cc14df757db2c2cf91b1dafddc852d1fc7b4f94
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-03 14:18:46 -0400
Commit message:
Add unit testsPackage: enrichViewNet
Commit: 4288f63adfd825282c3c37c6535529398d49d4fb
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-02 18:56:06 -0400
Commit message:
Adding unit testsPackage: enrichViewNet
Commit: 7e7a00816bb041c60b4f03e047d9435b6f98ef73
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-02 18:46:35 -0400
Commit message:
Adding unit testsPackage: enrichViewNet
Commit: 41a7d49715576c5d25e3583f011f8f88d54e5d65
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-02 17:46:20 -0400
Commit message:
Update error message and associated unit testPackage: enrichViewNet
Commit: 411434693f52226eb618c0ffe47c10a9fcddf5d8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-02 17:36:41 -0400
Commit message:
Adding missing ggnetwork in DESCRIPTION and validating similarityCutOff parameterPackage: enrichViewNet
Commit: 995f552323464102f0951bd418240729e305c8ad
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-02 16:42:15 -0400
Commit message:
Add createBasicEmapAsIgraph() and createEnrichMapMultiComplexAsIgraph() functionsPackage: enrichViewNet
Commit: cd3d8cef770d7c1de2174526655e4bece755e0c6
Author: adeschen <adeschen@hotmail.com>
Date: 2025-10-01 20:38:42 -0400
Commit message:
Creating Jaccard method()Package: enrichViewNet
Commit: 465cd04d0e5575e17674082bc1803673d0041ef1
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-30 18:43:26 -0400
Commit message:
Update function to removed duplicated edgesPackage: enrichViewNet
Commit: 535d417d22062f2216533f664471c36caf745add
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-30 17:09:22 -0400
Commit message:
Adding new functions that generated enrichment maps as igraph outputPackage: SPOTlight
Commit: 984a7ed4e20f41da2904938c4a99e8138845ec30
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-20 14:58:26 -0400
Commit message:
remove out of bounds test interactionsPackage: MSstatsResponse
Commit: b133b6720b858b0148f2a9f9972b916c9f81c930
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-20 14:52:24 -0400
Commit message:
update to version 0.99.1Package: MSstatsResponse
Commit: d39343f117fa07cf521bb75bd48cc5ba9a889b61
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-20 14:45:43 -0400
Commit message:
Update DIA_MSstats_Normalized.rdaPackage: MSstatsResponse
Commit: 4c62c95660b351707ceea293e622945acda3ff0a
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-20 14:45:39 -0400
Commit message:
additional MSstats/MSstatsTMT processing detailsPackage: MSstatsResponse
Commit: 772418f4413330b6599a113c3895d8f08ee1092f
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-20 14:44:10 -0400
Commit message:
update BiocParallel to use bpparam()Package: MSstatsResponse
Commit: f115043fc4af917476e735b381154dce30239f64
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-20 14:43:34 -0400
Commit message:
update BiocParallel to use bpparam()Package: MSstatsResponse
Commit: 9b8ca4b6189250d4434b90f5dd886007131a13a8
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 11:19:52 -0400
Commit message:
Update MSstatsResponse.RmdPackage: MSstatsResponse
Commit: 66562ae000bc3715f1e900ed151de618e29ad65b
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:43:38 -0400
Commit message:
changed to use BiocParallel for parallel processingPackage: MSstatsResponse
Commit: 39b7793f4cfcc4bcb8c817798c35804b51328027
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:12:27 -0400
Commit message:
updated function names and data descriptionsPackage: MSstatsResponse
Commit: 2d07950b474685af1e07034960ea762a07a62141
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:11:56 -0400
Commit message:
vignette dataset generation infoPackage: MSstatsResponse
Commit: ee2bf68a6e07d9dcc3b82c0894baa0c77366f80b
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:11:27 -0400
Commit message:
changed function names to 'camelCase' formatPackage: MSstatsResponse
Commit: 01cc42b16f24fff4f0bfb6e656bc62b5b5deefac
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:10:58 -0400
Commit message:
changed data locationPackage: MSstatsResponse
Commit: 1b73d60f02523b0d38ac704adb5782e5d09cde2d
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:10:21 -0400
Commit message:
Update DESCRIPTIONPackage: MSstatsResponse
Commit: 515f84a09e5de2837353533b78a3044cfc66d6c9
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:05:34 -0400
Commit message:
update imports and authorsPackage: MSstatsResponse
Commit: 6511987d81c18cf405d78afd26dce1a722f65c26
Author: Sarah Szvetecz <szvetesa@gmail.com>
Date: 2025-10-15 10:04:49 -0400
Commit message:
changed all function names to 'camelCase' formatPackage: ExperimentHub
Commit: b422aea6869e3efbe23e311e1c4b408665cbaf50
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-20 14:26:47 -0400
Commit message:
Merge branch 'Bisaloo-requireNamespace' into develPackage: ExperimentHub
Commit: 8913fde6ac9c66b9f0cd788c7c83b7f7239182b2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-20 14:26:24 -0400
Commit message:
Update installed.packages to requiredNamespacePackage: ExperimentHub
Commit: dbb055d28afca718a955ffb99c1f3c6e60493e73
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 11:19:03 +0200
Commit message:
Use requireNamespace() to test for pkg availability As recommended in ?installed.packages(): "This needs to read several files per installed package, which will be slow on Windows and on some network-mounted file systems. It will be slow when thousands of packages are installed, so do not use it to find out if a named package is installed (use find.package or system.file) nor to find out if a package is usable (call requireNamespace or require and check the return value) nor to find details of a small number of packages (use packageDescription)."Package: PhyloProfile
Commit: 1bd932f457f15c76172071d355e989acefedf0bf
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-10-20 20:26:46 +0200
Commit message:
fixed add sel genes from GeneAge, GroupCompare; species as default for demo sets; improve domainPlotPackage: smoppix
Commit: 55306b1601411c976dd65ee84490d0eb103782e3
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 17:30:11 +0200
Commit message:
works!Package: smoppix
Commit: a4b195c58058ce43c867f9b12e136517d5760400
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 17:26:07 +0200
Commit message:
Finally got it rightPackage: smoppix
Commit: 0d61a5eac8e43cb11535d337662e3bb02cc9ab8f
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 17:22:33 +0200
Commit message:
Finetuning scalebarsPackage: smoppix
Commit: 3d8c7967be88f5ead15da119737232bdd9e62883
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 16:53:56 +0200
Commit message:
Move scale bar slightly upPackage: smoppix
Commit: 7a682a35f77efccb1951f40c5ed70745e20f0a81
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 16:31:56 +0200
Commit message:
With scale barsPackage: MSstatsShiny
Commit: 6b7f51fad83ebeb0088cc0006245d625051322ab
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-10-20 10:10:51 -0400
Commit message:
Bump version from 1.11.5 to 1.11.6Package: MSstatsShiny
Commit: 532fdeaebb9d90c00677729a914802ac25ce63f6
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-10-20 10:10:12 -0400
Commit message:
Update NEWS.rd for version 1.12.0 changesPackage: MSstatsShiny
Commit: 73d870c562720784f819be829e32dce8519e7794
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-10-02 14:20:54 -0400
Commit message:
chore(network-interpretation): Increase font size for legend (#116)Package: MSstatsShiny
Commit: 7bb75e12f6db24b12ca73455650395b4089cd605
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-09-15 11:42:00 -0400
Commit message:
Remove 'OmniPath' from network data sources Removed 'OmniPath' entry from the network UI module.Package: mitology
Commit: fc2c43132042c5eb42cd8f7ad21a58c5367a6fc0
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-20 15:49:52 +0200
Commit message:
adjust warningPackage: imcRtools
Commit: 6088bda88e32ea5b619773ba5763c47cb3f447b7
Author: Daniel Schulz (dschulz) <daniel.schulz@uzh.ch>
Date: 2025-10-20 12:16:05 +0200
Commit message:
news and version bumpPackage: imcRtools
Commit: 0844c6fe7edec085b6c36d3e896f0d8949dcde7f
Author: Daniel Schulz (dschulz) <daniel.schulz@uzh.ch>
Date: 2025-10-20 12:00:00 +0200
Commit message:
fixed error in test_plotSpatialContextPackage: imcRtools
Commit: 9b7b96ad239886410d49f3db4a7393a0800c4091
Author: Daniel Schulz (dschulz) <daniel.schulz@uzh.ch>
Date: 2025-10-20 10:48:33 +0200
Commit message:
fixed machine preicision issuesPackage: mitology
Commit: 627346aaa098e5b9010dec5521880e8fd9b0a1dd
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-20 15:36:29 +0200
Commit message:
update versionPackage: mitology
Commit: 9b7193aeb87f6b07e129b1a942ae5b75551c901e
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-20 15:36:10 +0200
Commit message:
reinsert mitotreeheatmapPackage: mitology
Commit: ba31df8133d90534add5bbd853eb6dbe5b878ba5
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-20 11:49:42 +0200
Commit message:
update vignettePackage: mitology
Commit: de88f59a50193d8484581dd46b36e3d766004d16
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-07 15:28:41 +0200
Commit message:
Merge branch 'devel' of git.bioconductor.org:packages/mitologyPackage: mitology
Commit: c5efc4d30abb47edb44888c86c06b4d7316e2eb4
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-07 15:27:20 +0200
Commit message:
add new functionsPackage: mitology
Commit: 7426d7279e78546d3f85e3a24bf0836d3836ef49
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-10-07 15:25:48 +0200
Commit message:
update descriptionPackage: proBatch
Commit: 467f9bb2147516b4aedbd17bc81e82c86bb0b5f5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 15:30:47 +0200
Commit message:
version bumpPackage: proBatch
Commit: 3845172654c47811455d2394a8a6aca08c83bac2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 15:24:43 +0200
Commit message:
Do not run examples for subset_keep_colsPackage: proBatch
Commit: d521629037cdd2d3dd36fd25c6e312a7d061dd86
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 15:04:58 +0200
Commit message:
Export handle_missing_values functionPackage: proBatch
Commit: 880d702a3a99449f900b7f801fc29ccd42972cde
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 14:54:12 +0200
Commit message:
Add export for generate_colors_for_numeric and update documentation for data_matrix usage in plotting functions; reduced the size of example dataPackage: proBatch
Commit: ab2a3506f9b9c284b09118fe989a4345740722c9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 14:14:47 +0200
Commit message:
Refactor function signatures and documentation to use `data_matrix` and `sample_annotation` consistently; update examples and dependencies in vignettes.Package: proBatch
Commit: e3c08c55ea80f5ff09b0e13c4c64f08335ab3e2c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 13:25:21 +0200
Commit message:
Refactor plotting functions to replace deprecated parameters with updated names.Package: proBatch
Commit: c78d2e5dac066a18cccaa158eda1351c5875fa57
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 13:05:47 +0200
Commit message:
Refactor documentation and examples in ProBatchFeaturesPackage: proBatch
Commit: ae85114b22022ba1c1617f6e3069abfe572be39a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 12:37:35 +0200
Commit message:
Deprecate `sample_annotation` and `data_matrix` parameters in function signatures; update examples to use `Run` as the sample ID column in PBF examples.Package: proBatch
Commit: 93f946d5b385f7a83743d6d5532ef16142de687b
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 01:32:50 +0200
Commit message:
Refactor function signatures and documentation across multiple filesPackage: proBatch
Commit: 0bae2ab8b5ffafe7f850cf2bb2b37452a908cb6a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 01:31:01 +0200
Commit message:
Add parameters to functions for handling ProBatchFeatures objects and update DESCRIPTION to suggest cowplotPackage: proBatch
Commit: 666ff2690c78e8baebb947e2a6f0ee7d7a69f7fa
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-20 01:25:57 +0200
Commit message:
Fix comments and improve filtering syntax in CV calculation and ProBatchFeaturesPackage: proBatch
Commit: 79fff376b96d95a24342dd93271a88ccb71fe4e5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-19 23:23:34 +0200
Commit message:
Remove unused import of ggplotify from proBatch.R and fix dependenciesPackage: proBatch
Commit: a8e19fd640ed6ba901c18d5c99dababe691ccc5b
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-19 23:17:32 +0200
Commit message:
added doiPackage: proBatch
Commit: ef38d67cdbefd2afc5f880e3da8d6aa74c4fe4cc
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-19 23:14:31 +0200
Commit message:
Fix .gitignore to ensure /prep_code is ignoredPackage: RCM
Commit: 0ec81589e55fbae559f4f06c13c7cf4d88bb0249
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 15:11:05 +0200
Commit message:
Merging with remote Merge branch 'devel' of git.bioconductor.org:packages/RCM # Conflicts: # DESCRIPTIONPackage: RCM
Commit: 1b729e5866b998037573e0154ae778994b227e9d
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 14:27:57 +0200
Commit message:
Modernize data loadingPackage: RCM
Commit: e1f3114da4b3063a56222f7676e9d8d85806d22c
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-20 13:33:21 +0200
Commit message:
With references file and proper citationsPackage: RCM
Commit: b1f32241b8582f5dd896239fae68c86f60b56449
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 17:19:30 +0200
Commit message:
With lazydata true againPackage: RCM
Commit: 97fbf9819ead1a26eb36ab2825fb7aceef1af578
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 16:46:30 +0200
Commit message:
remove lazydata stuffPackage: RCM
Commit: 7ff14d285576eeb9492d65fa16456f7e756083a8
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 16:06:49 +0200
Commit message:
Solved title issuesPackage: RCM
Commit: 9d0a5d597ae2f2cb847e6310fa48e1572c1afa02
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 15:55:20 +0200
Commit message:
Fully documented now, also vignettesPackage: RCM
Commit: c28de3631c8b8a3f5f57a4cdfebeaba56afdec13
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 15:18:53 +0200
Commit message:
typo in tablePackage: RCM
Commit: cad7388181128e2021d00410f9a9b9a1fcfc2a2f
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 14:39:23 +0200
Commit message:
With full roxygen docuPackage: RCM
Commit: fe91c50079d5b5d2b05cf8d4a22873842a8d7c84
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 14:31:21 +0200
Commit message:
Testing and announcing permanovaPackage: RCM
Commit: d68fd48678eddd59a4e187846282fe043ed7df81
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 14:13:06 +0200
Commit message:
Some nam changes of function fikesPackage: RCM
Commit: a84066d8b9b7db0110ffba11da2369dd52ab31a1
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 14:12:13 +0200
Commit message:
Working on the permanova functionPackage: RCM
Commit: b2aeec2dada0ed1982aac9d3c2975027db2f4e2f
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 14:11:37 +0200
Commit message:
Create distance coordinatesPackage: RCM
Commit: 2ef40dbaa712f55a7191cb6e871d7654a2116a6f
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2023-03-29 13:14:30 +0200
Commit message:
Added pseudo F functionPackage: BgeeCall
Commit: 55ca0a4f7d19d4a60ea5198afc5e52ea801cbc19
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-20 14:58:32 +0200
Commit message:
added Alessandro's email adressPackage: BgeeCall
Commit: 2949f9f00ba2899ac45a9bcce4ae955d1a2c17f5
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-20 14:46:44 +0200
Commit message:
bumped versionPackage: BgeeCall
Commit: afefe074a50bd095946f31470c85edc104828370
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-20 14:46:20 +0200
Commit message:
update authors listPackage: BgeeCall
Commit: 694e818614d30b71a27cf71a4174370a67c49e6c
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-20 14:41:20 +0200
Commit message:
Merge branch 'galaxy' into developPackage: BgeeCall
Commit: 3618360357e26d1e6e149e8c55c733f71da70095
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-09 11:39:49 +0200
Commit message:
implemented wrapper for galaxyPackage: BgeeCall
Commit: 7dec98b456d8733b49e884a97d8f0179340fd622
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-09 11:39:11 +0200
Commit message:
minor typo correctionPackage: plyxp
Commit: 949c8327742e9f08265f5711572cd437963b2f3d
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-20 05:19:07 -0700
Commit message:
version bumpPackage: plyxp
Commit: 0448793db71ef96d00a4f26dc6cb8a69dc5b7265
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-10 15:43:43 -0400
Commit message:
Trying to address BiocChecksPackage: plyxp
Commit: 3731190ef52759cd78e1bb17b47b1b23cd501cdb
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-10 15:30:00 -0400
Commit message:
forgot to call devtools::documentPackage: plyxp
Commit: 5374a3f7418a3bc2963e53cec27e4ee76a323507
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-10 15:18:32 -0400
Commit message:
Passing AsIs must use S4Vectors implPackage: plyxp
Commit: ee4aa5ca4a026b3fe774cedcc40e16bf1de7c64a
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-10 14:54:37 -0400
Commit message:
Needed to document these functions. these will likely be removed in the 3.23 thoughPackage: plyxp
Commit: f91f9d0a0db2d95e253842b2a11f67891cd7c3e7
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-09 16:08:31 -0400
Commit message:
random stuffPackage: plyxp
Commit: 0dd8a7b76aa986727b714343da53286355574577
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-05 22:38:01 -0400
Commit message:
adding creating group id supportPackage: plyxp
Commit: 2e83344fba06f1dc44d5a4aac8cb2ab3a2c8b7a2
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-10-05 22:37:31 -0400
Commit message:
fix input?Package: plyxp
Commit: 2f1e26d1abd3d8e8c6fbac9ae93254b2ff801524
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-30 19:22:38 -0400
Commit message:
Adding a bunch of support for other vctrs functions for S4Vectors. Specifically unchop, and some version of vec_c ...Package: plyxp
Commit: cb94073b522fc5af9d39d13489b894b48320c997
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-27 13:37:12 -0400
Commit message:
exported the method properlyPackage: plyxp
Commit: c8d83c8c4cc6771055499f17977c5209007f4207
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-27 13:23:49 -0400
Commit message:
additional stuffPackage: plyxp
Commit: 78cf9bb72c124e37ffd1908c308c3305f75f1953
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-26 11:16:44 -0400
Commit message:
added dispatch for `se()` on SummarizedExperiment, basically just being identity.Package: plyxp
Commit: 739bf0f25379895da45aca6178cbd27c6694b8f0
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-26 10:56:18 -0400
Commit message:
a bit of refactoring - admitibly cheeky for my own grouping shenanigansPackage: plyxp
Commit: 7c481b994cf69b92ad1a0c8f963bf9c7deca5bac
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-25 16:26:09 -0400
Commit message:
cannot find a method with a class unionPackage: plyxp
Commit: f991306276c669a0731d83f93d16996621e8989e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-09-25 16:15:28 -0400
Commit message:
allow scalar values in arrange and ungrouped instancesPackage: CatsCradle
Commit: 8ba3770748e2f6a1b2cc9e9b1a7a6a75280ce722
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-10-20 12:08:29 +0100
Commit message:
version bump in develPackage: CatsCradle
Commit: b64c226448ec8eed229f0baf6ac692065c1d624f
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-10-20 11:28:33 +0100
Commit message:
version bump in develPackage: CatsCradle
Commit: ef90e47d8812636b50cb349943ab1f501c6e9e77
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2025-10-20 11:24:41 +0100
Commit message:
bug fix: example data compatibility with Seurat updatesPackage: MsBackendSql
Commit: d3bb3956a6389646631c5a4bfce3f5da21e7c5f1
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-20 08:19:09 +0200
Commit message:
Merge pull request #32 from rformassspectrometry/jomain tests: add additional unit tests evaluating longFormPackage: MsBackendSql
Commit: 5d33bb7c74ee3d6ec0cc31671e0920d6c49e807f
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-20 07:21:20 +0200
Commit message:
tests: add additional unit tests evaluating longFormPackage: Spectra
Commit: dcc0e56296c3317c09dfc341b57ae82850806bf9
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-20 08:17:44 +0200
Commit message:
Merge pull request #372 from rformassspectrometry/jomain fix: longForm for MsBackendMemoryPackage: Spectra
Commit: cc58cb0c5b71ea8c0dfe7fc00dc4c3e96b219059
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-20 06:51:25 +0200
Commit message:
fix: longForm for MsBackendMemory - Fix `longForm()` for `MsBackendMemory` when only peaks variables are extracted.Package: epiregulon
Commit: a04443510372fb80bc2b675fce39f759c338542c
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-20 05:51:19 +0000
Commit message:
version 1.99.3Package: epiregulon
Commit: d369481322e6adc550413eb75c7c703f2ebeea35
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-20 05:25:06 +0000
Commit message:
correct missing function imports and formatting errorsPackage: epiregulon
Commit: 9de922d30bd0717970e8b8e195e39ff10a4c3977
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-20 05:23:25 +0000
Commit message:
bug fix: pvalue and FDR transformed from natural log instead of log10Package: epiregulon
Commit: 682674469db4a6f86aad7e69b14de5f02529132a
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2025-10-20 05:20:01 +0000
Commit message:
add tests for addLogFC and aggregateCellsPackage: CaMutQC
Commit: ba161b5ffd4a03103ab25b861a6249239384c1a4
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 13:33:40 +0800
Commit message:
Merge branch 'master' into develPackage: CaMutQC
Commit: 25dac03802757e20490b896797b94022353d72c0
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 13:32:34 +0800
Commit message:
Merge branch 'WX'Package: CaMutQC
Commit: 0f090cb35fe8f14ad43210a49e03b3953ad81ddc
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 13:30:58 +0800
Commit message:
Roxygen version updatePackage: CaMutQC
Commit: 190f7e123b1d233f9a7638dfd3b9e84acd92435d
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 11:08:03 +0800
Commit message:
Bump up package versionPackage: CaMutQC
Commit: c7aee6786de6fe862e59e3199372ddb986da8c75
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 11:07:18 +0800
Commit message:
Add updatesPackage: CaMutQC
Commit: 034b204af983e17624d292029f9c694f10475821
Author: Xin Wang <sylviawang555@gmail.com>
Date: 2025-10-20 11:06:57 +0800
Commit message:
Update citation in manualPackage: singscore
Commit: 94d576b7b24352289a2afb1fa1c0a8576890b284
Author: Malviakh <malvika.kharbanda@adelaide.edu.au>
Date: 2025-10-20 14:49:22 +1000
Commit message:
Fix DESCRIPTION; devel at 1.29.1Package: ggtree
Commit: 75aa3fc5ed95125a5d5693bb23e333911ff86138
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-20 11:13:30 +0800
Commit message:
bump versionPackage: ggtree
Commit: 8d3ef3bccc3c0ed98d39045a35934f4733ac99f6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-20 11:10:21 +0800
Commit message:
Merge pull request #674 from jlingford/devel update msaplot to be compatible with ggplot2-4.0.0Package: ggtree
Commit: c7afc394becf7ef5274d75c17a2572090b259157
Author: jlingford <james.lingford@gmail.com>
Date: 2025-10-19 21:39:52 +1100
Commit message:
update msaplot to be compatible with ggplot2-4.0.0 rename "mapping" to "data_axis" to avoid name collisions with new version of ggplot2. Similar issue to #666, #667, and PR #668. Using "data_axis" term to be consistent with commit b6dffa9.Package: Rhtslib
Commit: fd16f2efaf5ac4fad2a32b8055124edb0bf4b82d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-19 17:39:32 -0700
Commit message:
Rhtslib 3.5.1 Tomas Kalibera's patch for compatibility with latest Rtools45.Package: SpaceTrooper
Commit: 6721e12fccd7d9246b9f61b53cdc38ddda446498
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 19:18:33 +0100
Commit message:
version bumpPackage: SpaceTrooper
Commit: 6f3ac0ca5ef0559b0952bc497f6f31c661a7228c
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 19:17:58 +0100
Commit message:
adding loading data vignettePackage: SpaceTrooper
Commit: ca3afcb9a150a92bf7d7a563f66c0b15e38beb3e
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 18:56:50 +0100
Commit message:
splitting xenium loader to work with speio loaded spePackage: SpaceTrooper
Commit: 9a81011f8ee8749ba45622cab899bd4bf86e9d87
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 18:20:19 +0100
Commit message:
splitting reading cosmx into multiple functions for SPEIO supportPackage: geomeTriD
Commit: 045522750538bbf65702708d6e6a47bbe200669d
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-19 13:30:28 -0400
Commit message:
update the description.Package: SpaceTrooper
Commit: 55808f0df9615d6900b7ea0b388ccd1af89936ae
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 17:05:33 +0100
Commit message:
version bumpPackage: SpaceTrooper
Commit: 622aa18907990cf34132bb531f1854e253db9b52
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-19 17:04:15 +0100
Commit message:
fixing all the errors for check/biocheckPackage: SingleR
Commit: b8dd9416ac88624d5eea9b4a1e42e588c9d57cf5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-19 01:25:09 -0700
Commit message:
Use the latest scrapper::scoreMarkers to find top pairwise markers. This is more memory efficient as it avoids creating a large 3D array.Package: geomeTriD
Commit: fd5a405ad906e9a8d46fb086eb6c1671882affe0
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-18 23:41:10 -0400
Commit message:
update documentations.Package: mitoClone2
Commit: b0e29b8b5b621adb95b9c9c2e4d6f8c994774ce6
Author: Story Benjamin <be9800@HOS62646.intranet.chuv>
Date: 2025-10-18 22:51:06 +0200
Commit message:
Add vireoPackage: geomeTriD
Commit: 8b0c634382b238d94fb21b912468d367a05edb54
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-18 11:20:55 -0400
Commit message:
change stop to warning.Package: trackViewer
Commit: 88a5f2f0a6663f7cfb4e8510023f19aca96458cb
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-18 10:39:55 -0400
Commit message:
Merge remote-tracking branch 'upstream/devel' into develPackage: trackViewer
Commit: 29150314f906f586c95ba8ac3c301c497c5a2128
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-18 10:38:26 -0400
Commit message:
return NULL before getting error message.Package: scrapper
Commit: 511f4df7e217d12ef3009dfec46aece2fa2ba763
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-18 03:38:30 -0700
Commit message:
Minor formatting fix to the NEWS.Package: scrapper
Commit: 5823b649b61a6bec04ffcf010c91900849146d64
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-18 03:05:04 -0700
Commit message:
Report row indices from scoreGeneSet to match up the weights. Otherwise callers could run into subtle errors if the input set was not ordered or contained genes that were not in the row names.Package: scGraphVerse
Commit: f754f4ba65137c155399f3cd41c30103379274cc
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-18 12:19:24 +0200
Commit message:
fix descPackage: scGraphVerse
Commit: 33c37bdc978f687c698fb1d6139cbc52d55360bd
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-18 12:18:46 +0200
Commit message:
fix BiocStylePackage: CBN2Path
Commit: a48e22da610fd21fb4a964d61d3c60799aa5d419
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2025-10-18 00:58:51 -0500
Commit message:
fixing up final thingsPackage: CBN2Path
Commit: 8148052667e7bfe2cec53fce71f68a2df7fe1f86
Author: rockwillck <william@williamck.com>
Date: 2025-10-17 07:29:53 -0500
Commit message:
bumpPackage: CBN2Path
Commit: 452fe1c10687bc7d9a5e20b4fd315b4a3d2963e5
Author: rockwillck <william@williamck.com>
Date: 2025-10-17 07:28:44 -0500
Commit message:
snowparamPackage: CBN2Path
Commit: 95e09038a75c9f1a3d63ac4aed3eb3cee8fbd50b
Author: rockwillck <william@williamck.com>
Date: 2025-10-17 07:26:31 -0500
Commit message:
remove traces of old parallelPackage: CBN2Path
Commit: e0c5de2c440ee084a05badc33c1bfc17a0e66ed2
Author: rockwillck <william@williamck.com>
Date: 2025-10-15 23:13:17 -0500
Commit message:
Add DOI badge to READMEPackage: CBN2Path
Commit: ed56a35c92fdcd61e4eb5b54adc54af5b353e79f
Author: rockwillck <william@williamck.com>
Date: 2025-10-15 23:11:24 -0500
Commit message:
Update version, DOI, and release date in CITATION.cffPackage: limma
Commit: f2592e4b8a1a58e1d0208ee4098d21381044e6a6
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-10-18 12:32:11 +1100
Commit message:
limma 3.65.6 - makeContrasts() now uses the contrast names if `contrasts` is a named vector. - Fix typo (pointed out by Marcel Schilling) in error message from makeContrasts() when the variable names are not syntactically valid. - Update NEWS.Rd ready for Bioconductor 3.22 release.Package: wompwomp
Commit: a59395ce07729b7c2a994d71277d78249fb863b9
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-17 14:26:13 -0700
Commit message:
removed python from readmePackage: wompwomp
Commit: f5912217abc86f15bf538df66c96eac3e39a0cf6
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-17 01:07:10 -0700
Commit message:
removed pythonPackage: wompwomp
Commit: 4de05a03a27c7200d4ab4d12eb49194ae20ad8c6
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 18:34:56 -0700
Commit message:
still working on removing pythonPackage: wompwomp
Commit: df1cf7ca57d24dd7dd34453444951f06f4491592
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 18:02:31 -0700
Commit message:
in the process of removing pythonPackage: wompwomp
Commit: 4130b85db66bf393fc14f606136d7d6c84c6ed4b
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:49:49 -0700
Commit message:
small readme changePackage: wompwomp
Commit: f67e31395f5c69bac1fe693d8c5e85091c193564
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:46:22 -0700
Commit message:
small docker changePackage: wompwomp
Commit: 6201ba5adbc7efc888a955ee9b5b5ea4b5e9b102
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:45:21 -0700
Commit message:
small docker changePackage: wompwomp
Commit: 012431eb79d80cc3922c0ddf211464032578e179
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-16 15:43:11 -0700
Commit message:
adding dockerPackage: CRISPRseek
Commit: cc307eae485b0e5c51bff27a50a881c68628aab1
Author: hukai916 <hukai916@gmail.com>
Date: 2025-10-17 16:40:04 -0400
Commit message:
update testthat scripts and dataset to accomodate bioc 3.22 releasePackage: MAST
Commit: 5c6e47f5279e14f6bea6e436da9ce588c2579bac
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2025-10-17 10:03:48 -0700
Commit message:
remove an undeclared call to gdata in obsolete codePackage: ACE
Commit: 8427b046ee3d424fed3955ab20e15ae99dc96993
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:38:49 +0200
Commit message:
Updated version in DESCRIPTIONPackage: ACE
Commit: aa18de8541787c6e47cf1e38616e2ed48dc48f61
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:28:41 +0200
Commit message:
Update accessory_functions.R same updates to standard and linewidth as described for ACE.RPackage: ACE
Commit: f6f5e4a1d9a9a94955976f27a2a2485fe114f837
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:16:51 +0200
Commit message:
also getadjustedsegments there was also a calculation for the standard in getadjustedsegmentsPackage: ACE
Commit: 607579c40cf24ac647077a46e2f8091359700a30
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 17:05:15 +0200
Commit message:
minor fixes ACE.R changed size to linewidth in ggplot line functions and now the X and Y chromosomes are excluded when calculating the standard for singleplot (as they already were for the fitting functions)Package: ACE
Commit: bc8e1608ac3b6f4138cc6314bacf9b4e23230896
Author: jpoell <j.poell@amsterdamumc.nl>
Date: 2025-10-17 16:41:18 +0200
Commit message:
Merge pull request #15 from petanska/master Add n=1 to tail() in ploidyplotloop to prevent multiple minima crashPackage: ACE
Commit: 164e1d3c725569986a01885e31c914f8a1aeb4a3
Author: petanska <50733801+petanska@users.noreply.github.com>
Date: 2025-10-03 10:45:58 +0200
Commit message:
Add n=1 to tail() in ploidyplotloop to prevent multiple minima crash Fix: prevent crash when multiple minima in rerror Specify `n = 1` in `tail(which(rerror==min(rerror)))` to ensure a single index is returned. This prevents `ploidyplotloop()` from crashing in rare cases where multiple minima exist, as reported in issues #10 and #11.Package: SPOTlight
Commit: cd2d48ba4617a764112644eec90b4f91490b5046
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-17 11:56:58 -0400
Commit message:
ggplot test updatePackage: SPOTlight
Commit: 88812e318a211f1c64cd6269792fc30e46372590
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:10:48 -0400
Commit message:
bump versionPackage: SPOTlight
Commit: f83b6aaf53154c7f43b03753ebdb97ff237a68e1
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:10:06 -0400
Commit message:
test ggplot 4.0.0Package: SPOTlight
Commit: 47ccd8e678d0a230e83a17a4b7e56c176ff371a6
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 10:55:24 -0400
Commit message:
dot-filterPackage: SPOTlight
Commit: 59ea875568bda278693ef57f2495c1a68cabd18a
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 10:54:57 -0400
Commit message:
roxygen versionPackage: SPOTlight
Commit: 9699ab5e35dba42162bd1a8089d03996a70afe2b
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-09-30 11:35:10 -0400
Commit message:
bump version 1.13.2Package: DESeq2
Commit: 2877f70a65cedc89c201947e6b971c1806614ca5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:56:28 -0400
Commit message:
version bumpPackage: DESeq2
Commit: 3af71a756963cdf63bb7bc692100b8d61e84ae3c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:41:55 -0400
Commit message:
fix for useT + greaterAbs from @rrrossPackage: DESeq2
Commit: 885ac787daf370cd3d7cf72547eb25b937d2b96e
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-10-17 11:34:41 -0400
Commit message:
Merge pull request #118 from rrross/patch-1 bug fix for greaterAbs when useT=TRUEPackage: DESeq2
Commit: 01c54bb1320563e288bde681bb1c67c0e7f7247e
Author: rrross <57932933+rrross@users.noreply.github.com>
Date: 2025-10-16 14:53:34 -0500
Commit message:
greaterAbs useT=TRUE bug fix greaterAbs would return an error when useT=TRUE, due to the df environmental variable being a vector and not a scalar.Package: TabulaMurisSenisData
Commit: f35b2cbe938409aef01b05673457d6d3307c890c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:32:21 +0200
Commit message:
Bump versionPackage: TabulaMurisSenisData
Commit: 588a1d6bf42d235f0edaa2406ea2bd5499db6fcd
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:41 +0200
Commit message:
Update roxygen versionPackage: TabulaMurisSenisData
Commit: 238f7871cf1428540351d0105200210c00974d5d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:28 +0200
Commit message:
Document "_PACKAGE" instead of deprecated package documentationPackage: TabulaMurisSenisData
Commit: 47d6a2c194d6ac85dd97210d09a774848a6093e3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:31:00 +0200
Commit message:
Fix links in documentationPackage: TabulaMurisSenisData
Commit: 6e935046b32b9f878a4547aa3722b8dc3db1377b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-17 16:25:31 +0200
Commit message:
Add README.Rmd to .RbuildignorePackage: scRepertoire
Commit: 74605e178570a711ca8e1fc9b3f669eea45df320
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-17 10:17:01 -0500
Commit message:
Update DESCRIPTIONPackage: scRepertoire
Commit: 77b772b58627dd663d1d163860c58eaf52818dab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 10:49:05 -0400
Commit message:
Merge pull request #542 from BorchLab/vizGenes-BCR Viz genes bcrPackage: scRepertoire
Commit: 48ef37283d53a61dbb2f7960bc7fdd5d4abf63ab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 09:12:31 -0500
Commit message:
Update Ibex.RmdPackage: scRepertoire
Commit: 6ebdd1997fa00411becbb18d9e4d971965d08bd2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-13 08:30:51 -0500
Commit message:
ensure chains Heavy and Light passed to getIR #541Package: RGMQLlib
Commit: 64be27b6eff0cb90c2980811be5f1aa88bef04f2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:58:19 -0400
Commit message:
Deprecated - Software deprecated in 3.21 for unresponsivePackage: chromstaRData
Commit: 3ccaf6be325a825a58d59fa988fcb0ed9b04244b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:56:38 -0400
Commit message:
Deprecated - Softare package deprecated in 3.21 for unresponsivePackage: AneuFinderData
Commit: 5fc87a5e2dd551b4c8c106e2988f4c2734173cfa
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:55:42 -0400
Commit message:
Deprecate - Software package deprecated in 3.21 for unresponsivePackage: netZooR
Commit: d918f07e19e221ea967fe5d7c31d21f9572fa4ba
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-17 09:54:25 -0400
Commit message:
Deprecated Failing for over a yearPackage: DMRcaller
Commit: 066119e0ae83e553b368a5bc95e7a5524bec0b82
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-17 14:51:50 +0100
Commit message:
improved multicores computing with BPPARAMPackage: metabom8
Commit: d99e264d5d0bb25eb5faef879ed68bd698086016
Author: tk <tkimhofer@gmail.com>
Date: 2025-10-17 15:36:04 +0200
Commit message:
add git.biocPackage: metabom8
Commit: 0a752ae7d5534fe501099f166ff874fb3e24b02d
Author: tk <tkimhofer@gmail.com>
Date: 2025-10-17 15:26:16 +0200
Commit message:
ignoring rstudio filesPackage: proBatch
Commit: 01335d493207db3e4692f77b305bab72be1787af
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 14:07:41 +0200
Commit message:
Remove deprecated .onAttach function from zzz.RPackage: proBatch
Commit: 439a6988fa8c113e21b4fadaaecbb8712e3e4bfd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 14:05:41 +0200
Commit message:
Align with Bioconductor devel (preserve both histories)Package: proBatch
Commit: 4e78ce58a242e05522ff7f29afb07f956471ba1a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 13:38:47 +0200
Commit message:
add back figure (cherry picked from commit 5addb09fe3c978361cb0ef117c94a61e3011e798)Package: proBatch
Commit: 5addb09fe3c978361cb0ef117c94a61e3011e798
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-10-15 13:38:47 +0200
Commit message:
add back figurePackage: proBatch
Commit: a2cf996ef34d788b8709bd7c99d97798118e2649
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-30 17:19:04 +0200
Commit message:
Change project URLs to new GitHub repository Updated repository URLs to reflect new ownership.Package: proBatch
Commit: 18691e944af5e19107d255b23e4a2918559633d6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-29 15:32:03 +0200
Commit message:
Add 'limma' to Imports in DESCRIPTIONPackage: proBatch
Commit: b0b20e130fc6be3699e73abd79e6127bb1aa0f66
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:25:23 +0200
Commit message:
Refactor documentation and examples]; remove unused example dataset and update installation instructions in vignettes.Package: proBatch
Commit: 087be75fdd8bda759e41f338cc8e052235c7b00d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:05:29 +0200
Commit message:
Update version to 1.99.1 in DESCRIPTION; remove example_multicenter_data.rda and update example_ecoli_data.rdaPackage: proBatch
Commit: 8ed1932e7ff51be20a40aec2bb5209d025821297
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:36:02 +0200
Commit message:
Bump version to 1.99.0 in DESCRIPTION and NEWS; update installation instructions in README and vignettesPackage: proBatch
Commit: 8d92cb842e6552d179e71b30ffd102c06599c0a2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:02:44 +0200
Commit message:
Add return value descriptions to functions in ProBatchFeaturesPackage: proBatch
Commit: 4d7660f225c922ff3d963e9fd962fef367b12dab
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:16:08 +0200
Commit message:
remove donottest from examplesPackage: proBatch
Commit: 7f9418bad0d7cd94527f49966fa19521f297a7d6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:14:56 +0200
Commit message:
Added examples fot ProBatchFeatures functionsPackage: proBatch
Commit: 44cf4ef3d20a6ddc88b0d81f22aec5f1f6717ea7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:13:23 +0200
Commit message:
Update version number to odd number; rename chunks in vignettesPackage: proBatch
Commit: 5d994f09e4181ae8f85a6eb50231fde562570f64
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:26:50 +0200
Commit message:
Enhance documentation and examples; add new exports and improve warnings in functions.Package: proBatch
Commit: 6c5f67a25c46794575bf168f4f82dffef522f480
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:07:18 +0200
Commit message:
Update documentation and examples; remove .travis.yml file and adjust .gitignore.Package: proBatch
Commit: 3787edae4153079f18ad9b6aa761857acb00f0cf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:23:07 +0200
Commit message:
Chenges sapply to vapply, removed set.seed.Package: proBatch
Commit: 52367cdee912515e8fc78ab41cb730120e5fa00d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:17:30 +0200
Commit message:
Rename code chunks in vignettePackage: proBatch
Commit: 72b2f2530dfb230e99dad252187c7436ee5dd4f1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:37 +0200
Commit message:
Update NEWS to include changes for version 2.0.1:Package: proBatch
Commit: 6e982dcccfc06db8b8ad0dafb49d9bdb0bd2a936
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:23 +0200
Commit message:
Update DESCRIPTION file for version 2.0.1; add missing author and improve biocViewsPackage: proBatch
Commit: fed18e2aa875a8048a8ce4fb068ef98275e9eb94
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:06 +0200
Commit message:
export `plot_boxplot` and `plot_sample_mean` functions in NAMESPACE.Package: proBatch
Commit: f6c145673fd9478c579bac185315593a42c75533
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 12:13:44 +0200
Commit message:
R version changePackage: proBatch
Commit: 52c4a9c4acf184f695e7a8596fb8dfca37f246c5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 19:54:05 +0200
Commit message:
Update code to change imports using :: to importFromPackage: proBatch
Commit: 3425f3e52f838d650d9a10cdfa90ad1de4ea2980
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:48:59 +0200
Commit message:
Refactor plotting functions to improve axis labeling and fixed message formatting in missing value handlingPackage: proBatch
Commit: d74988bc50af2101b266b2812ad138fd7d0e6e7e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:22:18 +0200
Commit message:
Update DESCRIPTION and code to include gridExtra; adjust base sizes in plotting functions and improve message formatting in handle_missing_values functionPackage: proBatch
Commit: 7a27fabd38515724aa4e787d27beb900d9ab2dcf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 16:39:22 +0200
Commit message:
Update ProBatchFeatures vignette and documentationPackage: proBatch
Commit: d7ed30914215de5d4b5111c031025de788fc0424
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:25:14 +0200
Commit message:
renamed ProBatchFeatures vignettPackage: proBatch
Commit: 6334567ca0a3f0b9d2b37f624d8bda1defb56ea7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:23:46 +0200
Commit message:
Refactor missing value handling and add batch effect correction methods. (limma and combat for pbf)Package: proBatch
Commit: 7d1ad4f5a36d52ce9956ae826b2bb79c8f67f8f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 18:56:54 +0200
Commit message:
Refactor batch correction functions; update tests to suppress unnecessary warnings.Package: proBatch
Commit: 6dd1fabd083364cc3264a9a901b4de382f556d4f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 10:28:52 +0200
Commit message:
Add return_gridExtra parameter to plotting functions and update tests accordinglyPackage: proBatch
Commit: d63381fabcb37504550e09b16c003c1d141e41c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-23 15:46:27 +0200
Commit message:
updated plotting to support multiple assays; add new helper functions for better plot management.Package: proBatch
Commit: 83059e29a7e006a5bf3a8ea713b417faeb4c831c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-22 10:22:27 +0200
Commit message:
Update pb_filterNA function to handle NULL pbf_name; update docs the vignette for clarity on missing data handling and normalization steps.Package: proBatch
Commit: 491b972053cded22a7cdb9f664985bb76663c2a8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 16:38:03 +0200
Commit message:
fixed plots missing and testsPackage: proBatch
Commit: d7d1da5710c9b4598ec2636ebd9e9637d1982aee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:52:35 +0200
Commit message:
fixed missing helpers df testsPackage: proBatch
Commit: 65506c8e420934cd4fdceec9162ce795ac21a0e4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:49:32 +0200
Commit message:
Review added missing values plotsPackage: proBatch
Commit: ed8ca79a98a1f86ac2ff71cf3f49cf1afa84dd5d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 23:43:36 +0200
Commit message:
missing values tables from QFPackage: proBatch
Commit: f6012b70bce6c57ddbad4e03727247b4ce56d873
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 17:06:50 +0200
Commit message:
added missing values info operationsPackage: proBatch
Commit: 1a96beef14c18e1a4669a544822bf9b648bb066d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:21:54 +0200
Commit message:
updated wide_diagnostics for pbf objectsPackage: proBatch
Commit: 3458b9116efb1436b14e028403a9cb2223252142
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:13:37 +0200
Commit message:
updated pca plotting for pbfPackage: proBatch
Commit: c08dee78b68d74af319dd25ece0bd7d077a366cf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 13:55:18 +0200
Commit message:
added plots from "fast" logs from operationsPackage: proBatch
Commit: 7af1e8f9f4496afda1b66162805e7729bdfcdd40
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 11:19:47 +0200
Commit message:
minor fixes in PBF logsPackage: proBatch
Commit: a33e2f92926705a117db0450430db2aedfd4a471
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 16:35:40 +0200
Commit message:
update show in pbf classPackage: proBatch
Commit: 1007d7fd36f2f382a9dc30db2e21280df9e9a84c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 14:35:50 +0200
Commit message:
updated log and chain structurePackage: proBatch
Commit: 7afc8752344dbb615e79d33ea194b667979bb232
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 13:10:55 +0200
Commit message:
added pbf support into initial_assesment funcsPackage: proBatch
Commit: 69a506368f8da6ec3f4e906b695f3eb01cc24edb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 11:43:48 +0200
Commit message:
fix a bug in metadata df creatid in pbfPackage: proBatch
Commit: e23e64c45aac51582d4550297464c9e33f191d9a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-10 16:34:52 +0200
Commit message:
added levels links into PBF classPackage: proBatch
Commit: ca697d992bb82b333b04a0f9afbe00fbddc1ecf7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 15:38:43 +0200
Commit message:
added E.coli test dataPackage: proBatch
Commit: bdaefb0047aef068497c9e9b3359c61ce8530f25
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 13:53:06 +0200
Commit message:
probatch class addedPackage: proBatch
Commit: 31d82df4691ea1c9e308d4a2fc2b55f9eca57ab7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 21:16:16 +0200
Commit message:
updated ProBatchFeatures classPackage: proBatch
Commit: 172c8b1e73f6ab6a8bf76b552a9f815be26d4b84
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 16:49:36 +0200
Commit message:
probatch classPackage: proBatch
Commit: ec6810bdc2d653532b54aa07cde8f117c6b38c51
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-25 23:47:35 +0200
Commit message:
added new TMT datasetPackage: proBatch
Commit: 5d718c23e88851eefd77b479cc7a2d599ccdb907
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-07-02 21:00:44 +0200
Commit message:
vignett updated (citation autoformatting added)Package: proBatch
Commit: 11b4705d2d5f7d059ec7a2b03c9fa00bc3aad173
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:16:26 +0200
Commit message:
typer checks, added tmp files ignoresPackage: proBatch
Commit: 00dd1a95510f49c5cbd5ec24b4fd912c3635c003
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:10:58 +0200
Commit message:
Refactor feature level diagnostics tests to include warnings for missing values; update vline_color handling in plots.Package: proBatch
Commit: 02c7b171209527f13bc5439d38e8a89418746d13
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:57:13 +0200
Commit message:
Fixed warnings in proteome_wide_diagnosticsPackage: proBatch
Commit: 30c03fb05aca02886ae0e34f51c568f8441f8f32
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:18:37 +0200
Commit message:
Add tests for normalize_data_dm to verify offset handling; include example_sample_annotation in hierarchical clustering testPackage: proBatch
Commit: b6c148d6fb57f8f5d08889a8ed89510e4452d2cc
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:58:34 +0200
Commit message:
Refactor plot_boxplot function (remove default NULL for sample_annotation); Added in log_transform_dm call in normalize_data_dm offset parameter. Adjust save_ggplot call position in plot_PVCA.df function. Added tests for adjust_units.Package: proBatch
Commit: 1e0678dec696b10bcdaf030d591d3f0c91f8b6cb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:50:28 +0200
Commit message:
Fix typos in documentation in feature_level_diagnostics.RPackage: proBatch
Commit: d47998ce64ee2d3c68e654e80acf919c65a8830a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:47:20 +0200
Commit message:
Improve fit_nonlinear function warnings and handling of insufficient data; added rle_func testsPackage: proBatch
Commit: 499b939d04a339cb4a6027d0238dc77cb6fcfe4f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:35:13 +0200
Commit message:
Refactor documentation in date conversion functions for clarity, improve error messages in fit_non_linear, and enhance tests for rle_func and fit_nonlinear behavior.Package: proBatch
Commit: 3509d8d2a7bf65ff57b84396fe12c80448a172de
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:37:30 +0200
Commit message:
Update adjust_batch_trend_dm to return corrected data directly and added fit column handling in error messagesPackage: proBatch
Commit: 4f008121a05fd588145c22fdcabe6e42d760943a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:25:46 +0200
Commit message:
Enhance adjust_batch_trend functions with additional parameters and improve error handling in date conversion testsPackage: proBatch
Commit: 76179a5a9250ab51c26b81174f9680e87ba7f1f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:15:38 +0200
Commit message:
Update return documentation in convert_annotation_classes for clarityPackage: proBatch
Commit: 5a9d0f2ca07d3679d63dfe5c0dddb53868962de7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 21:11:21 +0200
Commit message:
Refactor ggsave usage in plot_CV_distr.df, fix typo in auxiliary.R, and enhance date conversion testsPackage: proBatch
Commit: ebd8e19003297430c68602e5ecb7620321c0befa
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:44:13 +0200
Commit message:
Fix typo in warning message for asymmetrical heatmap and update horizontal line intercept in split violin plotPackage: proBatch
Commit: 815c6b27bbd06067942fe5d889f10db679f47e48
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 20:21:44 +0200
Commit message:
added and fixed for handle_missing_valuesPackage: proBatch
Commit: c606a0179ac50c02dcbf7d740e9039f0769e6ae5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 16:02:46 +0200
Commit message:
Improve error messages for missing columns in create_peptide_annotation and fix typo in normalize_sample_medians_dfPackage: proBatch
Commit: 8e30cc4916eca41c682f52bc2436e07f31315e12
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:54:57 +0200
Commit message:
refactored handle_missing_values function and added tests (fail now)Package: proBatch
Commit: 22f0b7ac704d107900d23c8368a7226e79942afd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:39:59 +0200
Commit message:
fixed typos in call plot_heatmap_genericPackage: proBatch
Commit: 1fd7ae4ff703dec682047c3596b828b918e0f26f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:38:47 +0200
Commit message:
refactored handle missing values functionPackage: proBatch
Commit: e72f019951a18a69cd6578a445ceaa16eb49398a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 15:18:46 +0200
Commit message:
color scheme fixes in initial assesmentPackage: proBatch
Commit: 9c32c06099d5ec0755d630c4d3c20033414b8e69
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:36:02 +0200
Commit message:
refactored plot_boxplot, added tests for initial assesmentPackage: proBatch
Commit: 7674326ab3118add8534bad741a51e747a2a9356
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 13:19:51 +0200
Commit message:
updated and refactored plot_sample_meanPackage: proBatch
Commit: 47960078785c2bc2b55ed325f05cfd35e49a31fd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 12:56:11 +0200
Commit message:
minor refactoring of plots in initial_assesmentPackage: proBatch
Commit: 810f58f3924dce3e62c820d8ec5c9be7b329a295
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:30:55 +0200
Commit message:
fixed warnings CV testsPackage: proBatch
Commit: e25187831dcab4022bb510269cd02023b06eddee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:25:49 +0200
Commit message:
fixed failed CV testsPackage: proBatch
Commit: aca754fe250f3839c1474288ca80a0774adb018f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 22:15:53 +0200
Commit message:
fixed majority of CV testsPackage: proBatch
Commit: a61e214f1cfd2addcbcf1b79dbcdd7529f0aeca7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:52:17 +0200
Commit message:
removed qual_value from columns codePackage: proBatch
Commit: fee264a00a85d42c91c51ad57b549ac1b4c07fe5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:40:52 +0200
Commit message:
added tests (not final) fo CV calculationPackage: proBatch
Commit: 56df5b68b0a81883de7d35b1efb9e7930f6e5893
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:39:05 +0200
Commit message:
refactored calculate_feature_CVPackage: proBatch
Commit: 86591def32c521950fc77969b774862e28171c5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 21:14:12 +0200
Commit message:
fixed bugs in CV calculationPackage: proBatch
Commit: 9b6c44b213149ff3228a9b830f364fbc147c17ed
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:57:01 +0200
Commit message:
fixed filtering in CV calculations]Package: proBatch
Commit: 8ae738a6482cfc027d41c5545d24db09897006ec
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:39:24 +0200
Commit message:
added warning catch to utility fuuncsPackage: proBatch
Commit: ae1c70bc7c2ac52112e85e5eb2e5d02060041a31
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:34:24 +0200
Commit message:
fixed correct_batch_effects_dm and added check to subset_keep_colsPackage: proBatch
Commit: 0e75d71cd781c1901f002357f21348c7c6bf032d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:02:31 +0200
Commit message:
fixed switch in subset_keep_colsPackage: proBatch
Commit: 32b36adbd85e3a1043c2f16f0652a3f495d08b5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 20:00:44 +0200
Commit message:
fixed unwanted warningsPackage: proBatch
Commit: 0b7951f2e4cb9450d85771a34a5d7171a244bf02
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 19:16:20 +0200
Commit message:
refactor define_sample_order in utility_funcsPackage: proBatch
Commit: 03d3c1a95b9fc904ed922033523a3b83b32bb777
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:24:45 +0200
Commit message:
fixed plotting, added check to check_sample_consistencyPackage: proBatch
Commit: 4fcac1fdd2d666cdb07e666908a27b67bf857878
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 17:01:44 +0200
Commit message:
fixed merge_df_with_annotation, correct_batch_effects_dmPackage: proBatch
Commit: 8f4760646afee3c17f5f4c4377b8768a9fab313f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 15:43:40 +0200
Commit message:
fixed all_of in subset_keep_colsPackage: proBatch
Commit: af70b5579db034f753673a7cb2de3e7565872f60
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 14:35:44 +0200
Commit message:
fixed unwanted warnings in tests - correlation based diagnosticPackage: proBatch
Commit: 24557db453083d372963f710a21c43aad02cdb64
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 13:52:38 +0200
Commit message:
fixed all_of selection, fixed tests warnings, added transform_raw testsPackage: proBatch
Commit: 7f231190c4a74ed4a24e9bbb576cdabc885513eb
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:54:16 +0200
Commit message:
4 spaces (BioCheck), added test for transform log funcs, fixed seed in colors to hex sortingPackage: proBatch
Commit: dd8fdfb454b17f567c01fa146b5a17a2718062ea
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 12:08:20 +0200
Commit message:
fixed unwanted warnings in color mapping testsPackage: proBatch
Commit: ee60a184606da98d4d0f2d3b9d05fe23830e4869
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:32:54 +0200
Commit message:
yepo in annnotationPackage: proBatch
Commit: c197a3f582738e85e522b6f08ad18cbe3ba87f52
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-21 11:27:16 +0200
Commit message:
minor fixes in colors - n_base and palletsPackage: proBatch
Commit: 9b6a7be529ea57804f05a83161d692e9c627f5d3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 23:08:02 +0200
Commit message:
fixed one_of/all_of,Package: proBatch
Commit: 199a6be16af652510e76d93ffc1583dcef9afaaf
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 22:14:18 +0200
Commit message:
color typo fixes, added palette_typePackage: proBatch
Commit: 82541eee308080daf33ef44f419b253335da6fb9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:22:09 +0200
Commit message:
fixed no_fit_imputed tests (set to False)Package: proBatch
Commit: 231943f65c30793865da38852014a871bd686e36
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 18:04:42 +0200
Commit message:
fixed missing columns in center_feature_batch_medians_dfPackage: proBatch
Commit: 8efe9d6df10fd7b58ad400ff22dd4e59709f9ae4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 17:50:48 +0200
Commit message:
expect_equivalent() was deprecated -> expect_equal(ignore_attr = TRUE), same expect_isPackage: proBatch
Commit: 08deba034bfef9b6cce4206632fc973a6548b534
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 16:14:59 +0200
Commit message:
context() was deprecated - removedPackage: proBatch
Commit: d9b34aa64b5dd5c3aff94364735c5ba9731a0201
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:20:57 +0200
Commit message:
fixed typo in loess fit?Package: proBatch
Commit: 5c2f543de7d035851e680a4ce1659b011b7b0239
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:17:17 +0200
Commit message:
styler run - formattingPackage: proBatch
Commit: 8f10560e0c40ad7bd4be653d688640138dbc8b0e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:08:01 +0200
Commit message:
subset_keep_colsPackage: proBatch
Commit: 4767850f3141aa1fe196a4c61b2527b22a522dcd
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-20 15:07:54 +0200
Commit message:
removed repetitions and added subset_keep_cols helperPackage: proBatch
Commit: b8b2d4876e802af00a346a9e88127583d3e37657
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-13 14:39:55 +0200
Commit message:
typo in docs fixesPackage: proBatch
Commit: e8ac7026353f3e94e75902480f8695ad67a156c8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:08:17 +0100
Commit message:
added mainteinerPackage: proBatch
Commit: 38cbca9ad04674cf0377eba0a9e56c9f08bf6ad6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 22:04:46 +0100
Commit message:
updated RMD and descriptionPackage: proBatch
Commit: 6c660e49432324b549885182f5958947f7c59606
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:26 +0100
Commit message:
updated .Rd filesPackage: proBatch
Commit: e9b0c7ab0813fd62efb67aca0137f93bcd62cff6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 21:41:07 +0100
Commit message:
refactor funcs to reduce cyclomatic complexityPackage: proBatch
Commit: 554048e9168a7c7de7c602201c2df2d4820a1def
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 20:54:14 +0100
Commit message:
fixed style issuesPackage: proBatch
Commit: 4bb37c7e658ba725f8a1f674828c94e4de82d8c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:53 +0100
Commit message:
fixed style issuesPackage: proBatch
Commit: 6325af083de0cd179305aba64fc61529cc77080b
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 19:27:39 +0100
Commit message:
updated descriptionPackage: proBatch
Commit: 05ed1df53ecd632a5064bb01b77fc3dcbd9f9fba
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 17:15:33 +0100
Commit message:
fixed code style with stylerPackage: proBatch
Commit: c9ca8e772ecde8e69050cf1afeac45fb85227342
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:49:21 +0100
Commit message:
fixed data loading for examplesPackage: proBatch
Commit: f4960b38188782e8ade0547a1f71aa8d634501cc
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:15:47 +0100
Commit message:
fixed loading data for examples docs after LazyData: falsePackage: proBatch
Commit: b766ad50efe2e3405a771f140aceed3843cbe4c0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:03:09 +0100
Commit message:
set LazyData: falsePackage: proBatch
Commit: 7fdc4fb3ffa33d9a819cc47de1146b0f2c6090f2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 16:02:49 +0100
Commit message:
added loading teest data in examplesPackage: proBatch
Commit: ae78c4bd21d9b5a191d91048f9178d13a9be7ef0
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:42:01 +0100
Commit message:
added "_PACKAGE" to main funcPackage: proBatch
Commit: 50e4fcd6db5f4a058d901a9015335aebe4091c14
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:40:47 +0100
Commit message:
fixed plot_sample_mean aes yPackage: proBatch
Commit: 7d57e675ff7ec94cc2fd3062dc11f46cf0a419f8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:38:30 +0100
Commit message:
fixed plot_protein_corrplot title for >1 proteinsPackage: proBatch
Commit: 5f702a27f861bcff3ee59b06fceaa08eb0d50e55
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-01-01 15:37:26 +0100
Commit message:
added merge_rare_levels examplePackage: proBatch
Commit: 57bba4e371420e9478dc071d9813fa223fdbfc6c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:36:02 +0100
Commit message:
fixed deprecated aes paramsPackage: proBatch
Commit: bb9aff84e6e872b4224c4f03a88108536fca4522
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2024-12-30 23:11:41 +0100
Commit message:
fixed select (deprecated->all_of) and base_size param(added)Package: proBatch
Commit: 97ea0bcbdf1779ad33b45481f88f6360d80d851c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 22:47:57 +0200
Commit message:
add default locale for dates_to_posixPackage: proBatch
Commit: d5cb21f595f3b768e9876917cc867207514ce3f4
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2023-10-07 20:45:56 +0200
Commit message:
Update CITATION, DESCRIPTIONPackage: proBatch
Commit: 1886a09cc73a88fd2650348b50815fa9feea49b7
Author: Jelena Čuklina <chuklina.jelena@gmail.com>
Date: 2023-04-01 09:58:32 +0200
Commit message:
new maintainersPackage: proBatch
Commit: dd82f814477aaabad012311a37a8a59058c81b23
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:17:20 +0000
Commit message:
Update README.mdPackage: proBatch
Commit: 6cff0e5ae08f5929f07d570bcad4db3733cfa853
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:16:37 +0000
Commit message:
Update README.mdPackage: proBatch
Commit: ecc00183934a12f84b6a949b331b815b845064cc
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-11-26 14:12:05 +0000
Commit message:
Update CITATIONPackage: proBatch
Commit: 30e4481b8a745978974a323d7dbe7582f71c655b
Author: Chloe H. Lee <43470195+ChloeHJ@users.noreply.github.com>
Date: 2021-08-31 17:24:40 +0100
Commit message:
Update README.mdPackage: proBatch
Commit: 17e1ff207126ae0e31046444dc451eda51fc4476
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-09-13 18:02:35 +0200
Commit message:
updated mansPackage: proBatch
Commit: e021d00d6d312a7a12eb748a6fbf014a86117e51
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-08-30 15:17:59 +0200
Commit message:
base_size = 20 for larger fonts in plotsPackage: proBatch
Commit: 4ef10a7d0f47fe0bd9b4f01791efb764cfb2afa6
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 14:08:30 +0200
Commit message:
corrected bug in multi-peptide facettingPackage: proBatch
Commit: 26880f96507ed2252023ff5e62393fe1f80119cd
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:55:11 +0200
Commit message:
corrected bug, preventing multiple peptide plottingPackage: proBatch
Commit: 86c1cbba784100ae0511f8b4fa6e24ca4456a5e1
Author: Symbiotic Me <chuklina.jelena@gmail.com>
Date: 2020-04-13 13:44:22 +0200
Commit message:
updated documentation for requant plottingPackage: proBatch
Commit: 422bd039b2cc0d88556456ff0ab9ad0a2d2d2f2d
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-30 17:19:04 +0200
Commit message:
Change project URLs to new GitHub repository Updated repository URLs to reflect new ownership.Package: proBatch
Commit: 609a5fddeecbdeb50edc0dc2c7d0e587fbeaeb62
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-29 15:32:03 +0200
Commit message:
Add 'limma' to Imports in DESCRIPTIONPackage: proBatch
Commit: 690aa7fee7077264f5353acf548837483ab04670
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:25:23 +0200
Commit message:
Refactor documentation and examples]; remove unused example dataset and update installation instructions in vignettes.Package: proBatch
Commit: 0a6e06193077040fdc08015432a290ee39bde755
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 20:05:29 +0200
Commit message:
Update version to 1.99.1 in DESCRIPTION; remove example_multicenter_data.rda and update example_ecoli_data.rdaPackage: proBatch
Commit: 92b302c0ca583e9df89c542c135d565482957c89
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:36:02 +0200
Commit message:
Bump version to 1.99.0 in DESCRIPTION and NEWS; update installation instructions in README and vignettesPackage: proBatch
Commit: 7f5f487c73fe842a4d57d7087d3b639f09806da8
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-28 19:38:25 +0200
Commit message:
Merge pull request #3 from Freddsle/new_class Documentation fixesPackage: proBatch
Commit: cc140d11c03cfdfb62a9cc3bfbf3859693fb36ca
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-09-28 19:16:39 +0200
Commit message:
Merge pull request #2 from Freddsle/new_class New proBatchFeatures class and limmaRBEPackage: proBatch
Commit: 25539ec83106d93912da53a55c6861292daeaae2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 19:02:44 +0200
Commit message:
Add return value descriptions to functions in ProBatchFeaturesPackage: proBatch
Commit: 71d03627e07990873870aec44911f8743f733bc9
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:16:08 +0200
Commit message:
remove donottest from examplesPackage: proBatch
Commit: cf14d631c391bce22310c67d5641e6200c7fe274
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:14:56 +0200
Commit message:
Added examples fot ProBatchFeatures functionsPackage: proBatch
Commit: 55dd343e0f889de3617c7fa29c3249329bf632f1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 14:13:23 +0200
Commit message:
Update version number to odd number; rename chunks in vignettesPackage: proBatch
Commit: 76ae8decb9837e1085e6b03fa16e517431793a53
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:26:50 +0200
Commit message:
Enhance documentation and examples; add new exports and improve warnings in functions.Package: proBatch
Commit: 49e93c860f4e9f551a659b7f4a9de42507171966
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-28 00:07:18 +0200
Commit message:
Update documentation and examples; remove .travis.yml file and adjust .gitignore.Package: proBatch
Commit: 8acbd1d5244445aa95717bf281066a95574d3ac7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:23:07 +0200
Commit message:
Chenges sapply to vapply, removed set.seed.Package: proBatch
Commit: 95e3a5d28e2080211e4ba7f56e042b8d1a118103
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:17:30 +0200
Commit message:
Rename code chunks in vignettePackage: proBatch
Commit: 05539988aa8cde10da59ce1f8ed1bdba16c96542
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:37 +0200
Commit message:
Update NEWS to include changes for version 2.0.1:Package: proBatch
Commit: 89478f2278bc9461162f5624b973fa4c05bfe070
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:23 +0200
Commit message:
Update DESCRIPTION file for version 2.0.1; add missing author and improve biocViewsPackage: proBatch
Commit: 539fb058df844697d426cd0c15d70ee007d1a84f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 23:14:06 +0200
Commit message:
export `plot_boxplot` and `plot_sample_mean` functions in NAMESPACE.Package: proBatch
Commit: 69e1215744d68bf8bf5bdd678677a01170962954
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-27 12:13:44 +0200
Commit message:
R version changePackage: proBatch
Commit: cf86cd21fcdd243ba4dde535eefc39f6930186de
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 19:54:05 +0200
Commit message:
Update code to change imports using :: to importFromPackage: proBatch
Commit: 5134ce898451b2eeff7f1e58a13bd1e70e715ce1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:48:59 +0200
Commit message:
Refactor plotting functions to improve axis labeling and fixed message formatting in missing value handlingPackage: proBatch
Commit: e9ec6ddc260bb029892161664bb9b48fbf2f16ec
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-26 18:22:18 +0200
Commit message:
Update DESCRIPTION and code to include gridExtra; adjust base sizes in plotting functions and improve message formatting in handle_missing_values functionPackage: proBatch
Commit: c80e38785aa666ca3e80b77d5248b069b4cdc806
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 16:39:22 +0200
Commit message:
Update ProBatchFeatures vignette and documentationPackage: proBatch
Commit: 7e0fae8e7d9506ba7aaf384eb1c6e8f9eb987f43
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:25:14 +0200
Commit message:
renamed ProBatchFeatures vignettPackage: proBatch
Commit: bbc19cb6afc929fb32126af642e460de9613efb3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-25 02:23:46 +0200
Commit message:
Refactor missing value handling and add batch effect correction methods. (limma and combat for pbf)Package: proBatch
Commit: ad92f66feb96c002561bc343daee033b5a000677
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 18:56:54 +0200
Commit message:
Refactor batch correction functions; update tests to suppress unnecessary warnings.Package: proBatch
Commit: bfd062afb77ebb925a559f68e901b97db3e176e7
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-24 10:28:52 +0200
Commit message:
Add return_gridExtra parameter to plotting functions and update tests accordinglyPackage: proBatch
Commit: b03cfc76f4e39b115ecfbbec7110a021b4d7b039
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-23 15:46:27 +0200
Commit message:
updated plotting to support multiple assays; add new helper functions for better plot management.Package: proBatch
Commit: 3f6d4148523055f7ea411946eec8c0a4cda4f73e
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-22 10:22:27 +0200
Commit message:
Update pb_filterNA function to handle NULL pbf_name; update docs the vignette for clarity on missing data handling and normalization steps.Package: proBatch
Commit: 942639d22a043149b2eaa9df6d55a1391a8a8ba2
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 16:38:03 +0200
Commit message:
fixed plots missing and testsPackage: proBatch
Commit: c92761553efae2306207d56c48c34693943cc4f8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:52:35 +0200
Commit message:
fixed missing helpers df testsPackage: proBatch
Commit: 8d2f9f4132cf96e3a249e9896c05e9aa91d57e1d
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-21 15:49:32 +0200
Commit message:
Review added missing values plotsPackage: proBatch
Commit: 5276084041a5cd930f758cb7434764bb6c967738
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 23:43:36 +0200
Commit message:
missing values tables from QFPackage: proBatch
Commit: bb7f2df7cae8e9022958c6279f71cb91add4f209
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-19 17:06:50 +0200
Commit message:
added missing values info operationsPackage: proBatch
Commit: 9a762564d131e471f59e51c85dec11967c1bc0a3
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:21:54 +0200
Commit message:
updated wide_diagnostics for pbf objectsPackage: proBatch
Commit: 2b01d199d2dc8e5c884cb7cce7cce66bc23aba0a
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 16:13:37 +0200
Commit message:
updated pca plotting for pbfPackage: proBatch
Commit: 112883e16beac5389f2f7d194f063930f136f021
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 13:55:18 +0200
Commit message:
added plots from "fast" logs from operationsPackage: proBatch
Commit: be633f5a2efbf219acefe272cd76ed1e417c4f5f
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-18 11:19:47 +0200
Commit message:
minor fixes in PBF logsPackage: proBatch
Commit: 7aef1aaf77eaa7c7168cb4a1730d431ad4a21455
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 16:35:40 +0200
Commit message:
update show in pbf classPackage: proBatch
Commit: 9f0d53de1e9230dbc27624cd848b4800dddedd49
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 14:35:50 +0200
Commit message:
updated log and chain structurePackage: proBatch
Commit: c4a3191a69e05366a8f3d099ef65c70e0658bd50
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 13:10:55 +0200
Commit message:
added pbf support into initial_assesment funcsPackage: proBatch
Commit: d3706c1a95d9f3a0cbdc6c606f17ba46002167c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-12 11:43:48 +0200
Commit message:
fix a bug in metadata df creatid in pbfPackage: proBatch
Commit: 60bf2cbf865e99b7eb3bf56e50a259b01c7106ee
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-10 16:34:52 +0200
Commit message:
added levels links into PBF classPackage: proBatch
Commit: 028d6d513f13414276c91c94c1a93773490326c8
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 15:38:43 +0200
Commit message:
added E.coli test dataPackage: proBatch
Commit: eaac342ba499686b181d68c777bc21f79b298dc6
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-09-08 13:53:06 +0200
Commit message:
probatch class addedPackage: proBatch
Commit: eb84dbeecfd444abf1edaeb60a2b1723b54cb493
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 21:16:16 +0200
Commit message:
updated ProBatchFeatures classPackage: proBatch
Commit: 7ca01b19eb1d5f07eb1bfcac243c63db7efda282
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-27 16:49:36 +0200
Commit message:
probatch classPackage: proBatch
Commit: 80a37c5b1c8c396277fa42671790e8f960580707
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-08-25 23:47:35 +0200
Commit message:
added new TMT datasetPackage: proBatch
Commit: c08551a124b7713ec57bc0abecfa831411ec9c18
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-07-02 21:00:44 +0200
Commit message:
vignett updated (citation autoformatting added)Package: proBatch
Commit: 368b93c5afff61d4d7e25d96b26c89de5f00c5a5
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:16:26 +0200
Commit message:
typer checks, added tmp files ignoresPackage: proBatch
Commit: 7185ee849f7ea3f12de59064cdf90e47e074b79c
Author: Yuliya Burankova <15180672+Freddsle@users.noreply.github.com>
Date: 2025-06-23 00:14:31 +0200
Commit message:
Merge pull request #1 from Freddsle/warning_fixes Warning fixes, refactoring, typo fixes, and minor bug fixes.Package: proBatch
Commit: 810fb31e358610e4302d351290640a821563da65
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-23 00:10:58 +0200
Commit message:
Refactor feature level diagnostics tests to include warnings for missing values; update vline_color handling in plots.Package: proBatch
Commit: 7bb7c6ddc8e6e2cc44bc6cc98d2907b632eb3644
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:57:13 +0200
Commit message:
Fixed warnings in proteome_wide_diagnosticsPackage: proBatch
Commit: 011a2f1deac144b5c6397acf7ca930e04d4f559c
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 23:18:37 +0200
Commit message:
Add tests for normalize_data_dm to verify offset handling; include example_sample_annotation in hierarchical clustering testPackage: proBatch
Commit: 15fa176137bbf368ca6a4d84012b5ae347393590
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:58:34 +0200
Commit message:
Refactor plot_boxplot function (remove default NULL for sample_annotation); Added in log_transform_dm call in normalize_data_dm offset parameter. Adjust save_ggplot call position in plot_PVCA.df function. Added tests for adjust_units.Package: proBatch
Commit: 2356af3be10374c7753649bdbffa0f9c291da139
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:50:28 +0200
Commit message:
Fix typos in documentation in feature_level_diagnostics.RPackage: proBatch
Commit: 93ce5ebea36ec5dd212df9477aedad8afc18fe75
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:47:20 +0200
Commit message:
Improve fit_nonlinear function warnings and handling of insufficient data; added rle_func testsPackage: proBatch
Commit: b26eae34ddf96b4e183044c7c79331678dfa54c1
Author: Yuliya Burankova (Freddsle) <burankova.y@gmail.com>
Date: 2025-06-22 22:35:13 +0200
Commit message:
Refactor documentation in date conversion functions for clarity, improve error messages in fit_non_linear, and enhance tests for rle_func and fit_nonlinear behavior.
</div> </div>