Registration and Call for Abstracts Open for Bioc2024

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

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

This list is also available as an RSS feed (devel branch), and RSS feed (release branch)

Package: ORFik
Commit: d2c3b496bac9fca3c3625ea46d211b85878719da
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-27 21:01:01 +0100
Commit message:

 Fix for new config old path
 
Package: ORFik
Commit: 9ab66ab9e7c9a24af467423319c4d883c926d6a6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:54:57 +0100
Commit message:

 All txdbmaker in single function
 
Package: ORFik
Commit: 0c6480f4af4a4e27b4ebf0bd05600222c34976c6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:29:53 +0100
Commit message:

 Wrapped all txdbmaker calls to single function
 
Package: ORFik
Commit: 084462baa832054e869aa9001c41e51455960fc7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-26 19:12:20 +0100
Commit message:

 Cleaned up txdbmaker calls
 
Package: ORFik
Commit: c8b888be8da80ccbaadcf60dbce22ae21f6ff913
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2024-03-21 16:49:57 +0100
Commit message:

 Cleaned up docs for txdb methods
 
Package: edge
Commit: 7c6682a81580f0cfc9a633bf78f1dd3bce6a7bca
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 19:45:58 +0000
Commit message:

 removed snm
 
Package: GeDi
Commit: fe08eaa68cd6cd0fd99a66ed916d76dec151db57
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 20:41:11 +0100
Commit message:

 bump to 0.99.2 to check if the retrieval of PPI/annotation really does take that long as experienced in 0.99.1
 
Package: GeDi
Commit: 4b91380dbda18a9fc30ed3f94038eb3c52deb7ed
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:25:47 +0100
Commit message:

 Merge pull request #18 from AnnekathrinSilvia/bpparam_calculations

Bpparam calculations 
Package: GeDi
Commit: b3734f163d0cf37ae3ad161c6caacc8d80c1e89a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:15 +0100
Commit message:

 updated news
 
Package: GeDi
Commit: d0a2b7905735d5ef186bbf9e9b43b2311d89687c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 19:11:08 +0100
Commit message:

 Bumping version to 0.99.1
 
Package: GeDi
Commit: a146f6ecaf1144a3f129243847bca2374e9f7e6a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:52 +0100
Commit message:

 re-rendered manpages
 
Package: GeDi
Commit: 391701223477f3d4f187605de72c8172622e39ee
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:43 +0100
Commit message:

 homogenizing the content of the BPPARAM entry, cleanup of commented code
 
Package: GeDi
Commit: 422ec80b28ee2d26773912ed9f6074585b1ccce7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:21 +0100
Commit message:

 fixing the tests to match the new API
 
Package: GeDi
Commit: 97043de3c902db9224e2f2250ab9b288cabd0c7e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 18:32:05 +0100
Commit message:

 n_cores + Snow --> Handling directly the whole thing with a BPPARAM object, defaulting to SerialParam to avoid odd behaviors
 
Package: GeDi
Commit: a7d4288dbd2710bc580b92259650f09a52dc8437
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:58:04 +0100
Commit message:

 Switching brutally from Snow to Serial
 
Package: GeDi
Commit: 4d7b21bfcd2b79162f1963bbd23230179821c894
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:13:01 +0100
Commit message:

 * explicitly passing the BPPARAM object to handle gently parallelization
* adding some checks on the method argument and using IC calculations only if needed
* making example reproducible with set.seed initialization
 
Package: GeDi
Commit: a901779533e55808411fd9b9214b6af4bb7a940d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:09:18 +0100
Commit message:

 changing tests run on similarity
 
Package: GeDi
Commit: c3b34bf9d6fcb02128b4121cf755b78c7af3a9f1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-27 17:08:27 +0100
Commit message:

 avoid warning when guessing the separator
 
Package: edge
Commit: b69baf2e02eadfa28187baad097b22326336300c
Author: Andy Bass <ajb359@gmail.com>
Date: 2024-03-27 18:52:41 +0000
Commit message:

 removed snm
 
Package: GeDi
Commit: 3dcdc4d1a9fa5a9cb76c7c6951f024b50410eca3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:50:36 +0100
Commit message:

 removed the .Rproj file - not desired in the built source package for Bioc, but we can keep it locally
 
Package: GeDi
Commit: 8293d7d97a565825baa8f03b86e4e4d937168f60
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:48:11 +0100
Commit message:

 removing CITATION file as there's no DOI yet
 
Package: GeDi
Commit: a03036e1331fcb7ef12d47ff4875bd606e836e61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 12:30:46 +0100
Commit message:

 cache disabled for GHA clear run
 
Package: GeDi
Commit: 5f0b1e0c67d0d025d2d1c29a8be9c6df8a47abd7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:35:19 +0100
Commit message:

 cutting down on examples runtime
 
Package: GeDi
Commit: 9bdd794ce9aaa90bb9d85d22264055da7c1a612f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 10:34:50 +0100
Commit message:

 reducing runtime of the examples - adding explicitly \dontrun{} to each *second* example in long running functions
 
Package: ggspavis
Commit: 380a5edba95e997983bc542a4d35e8cb5ff9382d
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:43 -0400
Commit message:

 version
 
Package: ggspavis
Commit: 8ccae4f707f100ceb290fbcf8024de21cea3b022
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-03-27 14:23:26 -0400
Commit message:

 get feature names from rownames if rowData is empty
 
Package: Banksy
Commit: 8d751508b44cd1b409512e5721a41d881d2ef417
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:08:18 +0000
Commit message:

 Bump version
 
Package: Banksy
Commit: d5edf83fa7ba3d30257a57de157c2272ae4ba76f
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 17:05:39 +0000
Commit message:

 R 4.4
 
Package: Banksy
Commit: c59f67055cc74f3143ec12279ba869709ee7959a
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:37 +0000
Commit message:

 Update docs
 
Package: Banksy
Commit: a469e9dadb33b858986953a795839c244d7af4ff
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-27 16:29:24 +0000
Commit message:

 Add scaling options for reduction methods
 
Package: Banksy
Commit: 86b40563d8358add19bab87b5e4a740a800e4220
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-08 22:56:17 +0000
Commit message:

 Update docs
 
Package: Banksy
Commit: c5ca77b518b227034df468b19415cbeca1b481e1
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-03-06 16:26:32 +0000
Commit message:

 Update README
 
Package: Banksy
Commit: 6ee046a2a714e6395af354d76a6c47a0235ff384
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:22 -0500
Commit message:

 Update README.md 
Package: Banksy
Commit: 091bedcb5dd7b462e85fcae936c2f9122e86dc13
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:37:09 -0500
Commit message:

 Update README.md 
Package: Banksy
Commit: 7305c41e8fad7fd221eecfc9a61d892906cd37fb
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:25 -0500
Commit message:

 Update README.md 
Package: Banksy
Commit: be1140296b8e48eb0251df9e9645d316cd5ab54b
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:36:12 -0500
Commit message:

 Update README.md 
Package: Banksy
Commit: ac5e3118b6e1025125549b40b55c7a2976b8760c
Author: Vipul Singhal <vipulsinghal02@gmail.com>
Date: 2024-03-01 17:35:31 -0500
Commit message:

 Update README.md

updated paper, reviewer file, and tweetorial 
Package: Banksy
Commit: dbda6fde952e65f45409d9bca8e1f821746755cc
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2024-02-18 23:35:33 +0000
Commit message:

 Set R version
 
Package: BiocFileCache
Commit: 19e9ee5be7bc44f7a187d12b4eb31a64f6a56b3f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:59 -0400
Commit message:

 Version bump for file location fix
 
Package: BiocFileCache
Commit: cfb1bd4f6c422ed03b97b902736d55a2180031db
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-03-27 12:38:31 -0400
Commit message:

 Update test file location
 
Package: knowYourCG
Commit: dd12f8af59dc775c7652251ab3212c0b7a0070b8
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:36:08 -0400
Commit message:

 bump to 0.99.92
 
Package: knowYourCG
Commit: 6234dc6fb63814b17bb14a42aef07c72807a8f54
Author: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: 2024-03-27 11:34:26 -0400
Commit message:

 cache data in examples
 
Package: limpca
Commit: 8dce21ad63bd9b5ce2ea3648de3ceed47e519afc
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-27 16:21:14 +0100
Commit message:

 updated code with data2LmpDataList
 
Package: limpca
Commit: 21f904b0a07b32fffce83d3126a7d7203718494d
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 14:38:55 +0100
Commit message:

 lmpData as argument of plot functions
 
Package: limpca
Commit: 2f5f637b2e27a011e62868994d6161f9d50ad8c4
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 12:06:48 +0100
Commit message:

 debugged data checks and test
 
Package: limpca
Commit: 796784d7129242a18215e4a01547326a13342a14
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 11:49:30 +0100
Commit message:

 data check for modelmatrix and plots
 
Package: limpca
Commit: 3e62e4c903c5a693f57613d6489b9953427b923e
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:43:19 +0100
Commit message:

 warning if color, shape are numeric
 
Package: limpca
Commit: 997399fa6abb4d43d7e2625c5ba1f70352932d34
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-25 10:34:47 +0100
Commit message:

 code style, check args pca
 
Package: limpca
Commit: 06bb7a8f1b0590cb1e33d9bed0a305a9da8149a6
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-22 16:54:04 +0100
Commit message:

 lmpDataListCheck, lmpData input of pca fun
 
Package: limpca
Commit: daed6e434d5a9f6d3d6eb61e72523881ae6c7a46
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:37:31 +0100
Commit message:

 updated doc data2lmpDataList
 
Package: limpca
Commit: 3a235d5e6d1588eb58e0c48802c0bb34037e9fc0
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 16:27:13 +0100
Commit message:

 updated DESCRIPTION
 
Package: limpca
Commit: cf6f8e82c25e346d59b979bc575ef966a98c5038
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2024-03-20 15:59:33 +0100
Commit message:

 updated doc
 
Package: scaeData
Commit: 5c742bdbb986fc50ec779c3850fdb3701d894e4e
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-27 15:54:55 +0100
Commit message:

 changed date format; version bumped
 
Package: autonomics
Commit: 9c061acbe9466b90b01ad4592f3b5b181da18108
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 15:53:58 +0100
Commit message:

 Undocument assertions (devel)
 
Package: cypress
Commit: d9a7503412fb84458bc1feb85b3a3144fc2114e4
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-27 10:35:41 -0400
Commit message:

 edit for Namespace

edit the import detail for Namespace
 
Package: scRNAseqApp
Commit: 9f8150a9b2392cd5c4f9445842531d542a4537d0
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 10:04:52 -0400
Commit message:

 Update the description.
 
Package: scRNAseqApp
Commit: 570e9b66b092487139eb84b0de2a9b1eab9fce95
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-27 09:51:41 -0400
Commit message:

 Add a hyperlink to package URL at footer.
 
Package: scRNAseqApp
Commit: ec228eb4500e697eb33e7c1c662edc8af6709934
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-03-21 11:16:43 -0400
Commit message:

 Fix the duplicated rownames.
 
Package: ZygosityPredictor
Commit: 62b1b8c4545251eac79bb8f86ef244b5848b9208
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:53:03 +0100
Commit message:

 fixed illegal version bump
 
Package: ZygosityPredictor
Commit: ee9ee77b3f1a863bf69b235cbf354e0a3a5ce4dd
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 14:50:10 +0100
Commit message:

 fixed final issues via R CMD check and bioccheck
 
Package: ZygosityPredictor
Commit: ce2c073a65c12a282ab1189b16bf1e0cd18cf6e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 13:55:15 +0100
Commit message:

 fixed github issue #5... bumped version
 
Package: ZygosityPredictor
Commit: fe2e2deea32a0ea35176848bae500584e282b9e1
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:07:06 +0100
Commit message:

 code cleanup
 
Package: ZygosityPredictor
Commit: a2310b6f85cf1c99f4a969cadb7093d1375cd5d3
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 12:00:14 +0100
Commit message:

 fixed github issue #6 about global variables
 
Package: ZygosityPredictor
Commit: 8c972269f06d6ba0f099e1334c59718b7a31f09d
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-27 11:30:24 +0100
Commit message:

 replaced global varianbles with internaal environment
 
Package: ZygosityPredictor
Commit: 98c5436e204bdba78ba4d03f5bad0bc72dd3a10f
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 16:50:23 +0100
Commit message:

 replaced gloabl phasing matrices by ZP specific R environment
 
Package: ZygosityPredictor
Commit: 3a4bfda94f4e59c6e6d7dee46c700899dca08c6b
Author: Rheinnecker <m168r@odcf-srv15.inet.dkfz-heidelberg.de>
Date: 2024-03-26 15:45:18 +0100
Commit message:

 moved debugging scripts into seperate directory
 
Package: SPLINTER
Commit: e51bf62185f2b253414196c9edc2c319e511b1cd
Author: dlow <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 21:16:28 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
 
Package: SPLINTER
Commit: 28041e8bb29be96dbdb7fcb07bd18087e1b71e7b
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 20:40:54 +0800
Commit message:

 Update DESCRIPTION

up version number 
Package: SPLINTER
Commit: b34ff81f2264b726b5ae89dd747bf5af1c4c4389
Author: Diana Low <3214561+dianalow@users.noreply.github.com>
Date: 2024-03-27 08:17:10 +0800
Commit message:

 Merge pull request #2 from hpages/master

makeTxDbFromGFF() has moved from GenomicFeatures to txdbmaker 
Package: SPLINTER
Commit: 253d259c9149a18ac52a071009c625a384515e7c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-19 15:32:43 -0700
Commit message:

 makeTxDbFromGFF() has moved from GenomicFeatures to txdbmaker
 
Package: recount
Commit: c61b6727d1c722c89d451a9dac204e22b94130cc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 09:07:20 -0400
Commit message:

 txdbmaker is only available in BioC 3.19, so on GHA I'm now using that version of BioC
 
Package: rawDiag
Commit: 8e57d4b3fde19eeaaef3d7c3817c5b832a722d7e
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:36 +0100
Commit message:

 doc: version bump 0.99.31
 
Package: rawDiag
Commit: d8fa9133b0be5596372065ad618f49f6ef95aa73
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-03-27 13:49:18 +0100
Commit message:

 feat: check if rawrr assembly is working.
 
Package: recount
Commit: 76937504a9766c86b70d5a25c934e868a7434c1f
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-27 08:34:46 -0400
Commit message:

 Ran devtools::document()
 
Package: cTRAP
Commit: 81526c7ce27561c1867d1c7d3a06d82a9943cf1f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:11:15 +0000
Commit message:

 Bump version
 
Package: cTRAP
Commit: eb849fbbb9d169faf576a2d221a589e7650c856f
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date: 2024-03-27 12:10:30 +0000
Commit message:

 Squashed commit of the following:

commit 5b1482190809953077523b1c5d41b94f36cc69fd
Author: Nuno Agostinho <nuno@ebi.ac.uk>
Date:   Wed Mar 27 12:09:59 2024 +0000

    Squashed commit of the following:

    commit 8763bdb8f4634fa30b219ef90ee3d750d44e3e6b
    Merge: ac97834 a177f66
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 12:02:19 2024 +0000

        Merge pull request #38 from nuno-agostinho/dev

        cTRAP 1.20.1

    commit a177f6682dc94367ca67938029f6aa82856d23f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 18:48:06 2024 +0000

        Remove Windows unit tests

    commit bc83be6ce730e3da0280a532fac39b70dcacfafe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:41:41 2024 +0000

        Remove duplicated YAML divider from vignette

    commit 1d91d2f9cbcdb53e44e629cf9556ec51cc50e2a1
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Mar 26 16:58:09 2024 +0000

        Revert package documentation

    commit 31dc532a15a45b21ad329eb9586cd690d03c3bd5
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Mar 26 16:17:52 2024 +0000

        Remove failing unit test

    commit 42dfe5270b115c9ee48d05546d2bf6d50a1def38
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Mar 26 01:57:41 2024 +0000

        Fix spelling

    commit 6bc7321b295b121cf6cb0ca6d274faa8edea0782
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Mar 26 01:55:28 2024 +0000

        Update roxygen docs

    commit b9e3f5fc209c6c1b4e90cf237a465cbf2c86b811
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Mar 26 01:52:01 2024 +0000

        Fix ggplot2 issues

    commit b417cc554e9aa7b10884a90625fc8a04fcd6baba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 01:25:39 2024 +0000

        Fix ggplot2 issues

    commit 807c60eab1986bba655c32cee6080703e674a1e5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 21:42:18 2024 +0000

        Fix unit test

    commit 7d9c082f25947d9f5346beef25219e60315b25db
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 21:32:43 2024 +0000

        Avoid using deprecated `aes_string()`

    commit 1e7f5c87def7545a7f48d70489964d6622ec4662
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 21:06:31 2024 +0000

        Update r-lib/actions in GitHub Actions

    commit 72add994f7b5406d65d258a4cff59ad499759a61
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 21:02:25 2024 +0000

        Fix GitHub action

    commit 4ff0bc6f830baee1c5d533119e377e018c821d90
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 20:58:20 2024 +0000

        Bump version to 1.20.1

    commit 5d7d5a7dc2bfe2b3bc5f1845289bf418795c311d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 20:55:41 2024 +0000

        Fix unit test

    commit ac978340e89da80edce309259999f149e38d4c58
    Merge: 491b0e9 1c3fd8a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 19 16:02:40 2024 +0000

        Merge pull request #46 from nuno-agostinho/license/copyright-to-2024

        Update license copyright year(s)

    commit 1c3fd8a6fabad6c218de2b5fa474540dea15c9c2
    Author: github-actions <github-actions@github.com>
    Date:   Mon Jan 1 03:14:52 2024 +0000

        docs(license): update copyright year(s)

    commit 491b0e9d41ddc313c3deb95b04fe84e9d44bc985
    Merge: 4ed3b2a c865b2c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Feb 15 09:00:59 2023 +0000

        Merge pull request #45 from nuno-agostinho/fix/ci-tests

    commit c865b2c01b2d83bd9aca45719e62ce1b00ea3801
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Feb 13 10:44:09 2023 +0000

        Fix R CMD BiocCheck error

    commit 7a2e95ff264ca501236287678c9cd3c10aa8e40d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 12 21:48:42 2023 +0000

        Avoid CI tests in Windows

    commit 4ed3b2a9a50740e7a7ec6cb80f8e4bb283d6be4f
    Merge: a24e364 e764490
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 12 19:27:17 2023 +0000

        Merge pull request #44 from nuno-agostinho/nuno-agostinho-patch-1

    commit e76449049201d56f61e3e925081f9459bde20cff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 4 09:54:08 2023 +0000

        Remove redundant code

    commit 36cbb26dd354a0fdc07d0d1da723ca01f31351c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 4 09:04:01 2023 +0000

        Include BiocCheck package

    commit c4a4fd8bfc27b60c44c35d7d31e944cbc34fa64b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 02:03:33 2023 +0000

        Simplify R CMD check action

    commit 15c58239e87bee9be34f26e82903b6a87558ffa4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 01:36:36 2023 +0000

        Fix R CMD check in Ubuntu

    commit a24e3645b1bcb741a1aecdd484d3af2fe1573a86
    Merge: 06b81ba b484413
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:54:16 2023 +0000

        Merge pull request #43 from nuno-agostinho/nuno-agostinho-patch-1

    commit b48441387542e0bb8d4ccbec711fa648db82c0cd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:54:08 2023 +0000

        Install cTRAP before building pkgdown site

    commit 06b81ba44b54dc17436c30da558220a39d51b248
    Merge: 2ac559b c42d852
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:11:53 2023 +0000

        Merge pull request #42 from nuno-agostinho/nuno-agostinho-patch-1

    commit c42d8527a29a5bce0b261b767117ad956c4e25e1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:11:25 2023 +0000

        Update pkgdown.yml

    commit 2ac559b91bae2552edd62ac010a1e1f6c89e60f1
    Merge: 11152dc 2930a98
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:00:10 2023 +0000

        Merge pull request #41 from nuno-agostinho/fix/pkgdown

    commit 2930a98888c5f7fb2f7465f4143f33d9aca15264
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 3 00:00:01 2023 +0000

        Fix pkgdown site

    commit 11152dcf64b9e76bf3b2fe89027aaa98ca23b52c
    Merge: 198001e 939e0e3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 2 23:30:32 2023 +0000

        Merge pull request #40 from nuno-agostinho/license/copyright-to-2023

    commit 939e0e31aa726add393c49a7187d5f7bf8d5c533
    Author: github-actions <github-actions@github.com>
    Date:   Sun Jan 1 03:19:27 2023 +0000

        docs(license): update copyright year(s)

    commit 198001e19120eccf303b8c47cd5efdf7409d5f64
    Merge: 574cf69 44dcdc3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 26 00:05:00 2022 +0100

        Merge pull request #39 from nuno-agostinho/fix/gh-actions

    commit 44dcdc3c169707e2fef552979a0046802f2c6c74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 26 00:04:46 2022 +0100

        Fix r-lib/actions branch

    commit 2bffdb68afa835ace35f2e9f1b0e9ac13f6e5918
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Sep 10 15:29:19 2022 +0100

        Fix missing bracket

    commit 046dfe7ea91ff0ad909ef0ecb512cd468730c4f8
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Sep 10 15:27:13 2022 +0100

        Fix header in all interface functions

    commit ca30681dda6b8a93d41827146a148121a1c7ae3c
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Sep 10 15:20:35 2022 +0100

        Raise error if commonPath directory doesn't exist

    commit 90600da71288c4a1bf4e8224555477bf1a0f6d8a
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sat Sep 10 15:12:29 2022 +0100

        Update icon names for FontAwesome 6

    commit 8bfb114b1a9e9de4557cf0294333d08cefb021c9
    Merge: 8337c0c 574cf69
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Sep 10 15:05:16 2022 +0100

        Merge pull request #37 from nuno-agostinho/master

    commit 574cf69ddd383d4af2afaec2b9d84d04199a0b25
    Merge: 33acca5 1d06ca3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 21:55:11 2022 +0100

        Merge pull request #36 from nuno-agostinho/dev2

        Dev2

    commit 1d06ca3f101f331272a8c9ad600b68c9722978ba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 12:07:41 2022 +0000

        Properly import utils functions

    commit bc0ca85345d01eb0c765fd58f9c34cc3babe6f16
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 12:03:33 2022 +0000

        Copy-editing

    commit 65843df5f181103308cf1ceaba3d9260776073f8
    Merge: 68caee3 caadac2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 14 12:02:41 2022 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/cTRAP into dev

    commit caadac20656b3e309d19e5ce30819ba9220c5bc4
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Thu Jul 14 11:45:08 2022 +0100

        Avoid large JSON response from DT

    commit a5b71ebf902c54d0b16219d36b8b4e1d67826e63
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jul 11 17:00:16 2022 +0100

        Add cTRAP version to welcome modal

    commit a3a8f4ba67aec85b00c3f691092d454d99574596
    Merge: 33acca5 0ad8732
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 11 16:39:17 2022 +0100

        Merge pull request #34 from nuno-agostinho/fix/floweRy

        Fix Celery/Flower support

    commit 0ad8732a9f0a8b5022ca306d567a1fd8323cb47b
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Jul 5 23:11:18 2022 +0100

        Bump version to 1.14.1

    commit 330e65c8c01b44872f50ac7bec07c15a6089f142
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 5 22:58:10 2022 +0100

        Update floweRy.R

    commit 33acca5db23d92f23851062f180f56cf6446efe2
    Merge: b4cd38f 668eca3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jun 4 17:49:31 2022 +0100

        Merge pull request #33 from nuno-agostinho/copy-edit

        Copy-edit benchmark instructions

    commit 668eca350a89ec450463d8c4b0984ea873d90e64
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jun 4 17:49:17 2022 +0100

        Copy-edit benchmark instructions

    commit 68caee308a1090457d5d70045ed0302639ac6408
    Merge: f4334d6 b4cd38f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 20 12:11:19 2022 +0100

        Merge pull request #32 from nuno-agostinho/master

        Sync with master

    commit b4cd38f5ac63893e7696bdb839b85a7ebfc8536e
    Merge: 039ad81 bbcde0a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 19 22:59:43 2022 +0100

        Merge pull request #31 from nuno-agostinho/nuno-agostinho-patch-1

        Create devcontainer.json

    commit bbcde0ab0e9874bab2aff64c8e453276fbba762b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 19 22:59:34 2022 +0100

        Create devcontainer.json

    commit 039ad81ca0fbf4a6b68580679efa8388597c1769
    Merge: 369132a 4e06be6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 3 10:34:50 2022 +0100

        Merge pull request #29 from nuno-agostinho/nuno-agostinho-patch-1

        Fix URL to download zscores and checksum

    commit 4e06be682addddd9db0eea1bc0bd371a4f7c8b3c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 3 10:34:42 2022 +0100

        Fix URL to download zscores and checksum

    commit 369132aea8ce5671faa4a91bc355a5557221ccce
    Merge: 8d1dae3 eb40fb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 3 09:57:08 2022 +0100

        Merge pull request #28 from nuno-agostinho/zscores-checksum

        Add CMap zscores checksum to tutorial

    commit eb40fb6664c70a1c0863538f50710f19f526c14b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 3 09:55:13 2022 +0100

        Add CMap zscores checksum to tutorial

    commit 8d1dae3b999f7b846432a30a80371881569bcf6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 14:57:40 2022 +0000

        Fix pkgdown GitHub action (#27)

        * Install missing rcmdcheck package
        * Fix pkgdown missing topics warning

    commit 9a543a2957a9e897d5ad66715409ea22d902f8fe
    Merge: 629ca97 dd2bc24
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 10:28:41 2022 +0000

        Merge pull request #26 from nuno-agostinho/license/copyright-to-2022

        Update license copyright year(s)

    commit dd2bc24c0df29e3724d9525b9eafcc51bf29315d
    Author: github-actions <github-actions@github.com>
    Date:   Sun Mar 13 10:28:01 2022 +0000

        docs(license): update copyright year(s)

    commit 629ca971e1269a3b9c2b80114bc7053a8bffe6d6
    Merge: b112dfb 2a6574e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 10:27:22 2022 +0000

        Merge pull request #25 from nuno-agostinho/nuno-agostinho-patch-1

        Auto-update license year

    commit 2a6574e99c42202394aed063acc9a40050ee95b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 10:27:08 2022 +0000

        Auto-update license year

    commit b112dfb5dc7d2b5a8ffa10a97ef1e44beeaa60de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 16:09:54 2021 +0000

        Update pkgdown.yml

    commit c9ffdc4752f6cb56ee17d492cb192951baccf2cd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 12:21:36 2021 +0000

        Update pkgdown.yml

    commit a26f2a35af1654c751df80cf1b644fcd9d27ae0a
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Dec 27 12:05:53 2021 +0000

        Isolate pkgdown deployment

    commit 6b023df84260d6e5ed645bc9fe1bd5303c6cd26e
    Merge: a4d73d5 f4334d6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:13:55 2021 +0100

        Merge pull request #23 from nuno-agostinho/dev

        Version 1.12.0

    commit f4334d6b02c87324d3c9733b8233d169c2e6fd76
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:13:27 2021 +0100

        Bump version to 1.12.0

    commit 8c2c1e9d2d269578ecde88186d82ed6fd440c1ef
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:07:43 2021 +0100

        Bump version to 1.20.0

    commit 3200dbf2217c0baed54d8ebb75b359710989f750
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 26 00:12:07 2021 +0100

        Update utils.R

    commit 8337c0c80435611159c9d483c2ac96ddfbb1ce29
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 22 10:11:20 2021 +0100

        Include floweRy deps

    commit c70d411f6673947af23b481f6f841cd9b6755fbb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 22 10:03:57 2021 +0100

        Include floweRy code to avoid problems with CRAN/Bioconductor

    commit 20dbe5a3c37c285505a5558fbe2c709e09a18c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 18:05:10 2021 +0100

        Update cTRAP docker

    commit 81ef21c8623291175d17abb74de685597783dfdd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 17:52:35 2021 +0100

        Fix suggest (rather than import) biomaRt

    commit a91a5d7f1437ab5254b35a15e74824f759b77b8c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 17:46:37 2021 +0100

        Include biomaRt functions and floweRy

    commit 5079a4d40b2c7617178eaa09db1c228a11539460
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 17:26:51 2021 +0100

        Change task state to "Not found" if not in Celery/Flower queue

    commit 2a7d40d6578144a69b6abe98c5201dd90c081016
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 16:22:38 2021 +0100

        Fix issues with R CMD check

    commit 7878eacc615e47f9cb2c32c007536217e8dc0a45
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 15:49:42 2021 +0100

        Include optional packages in Suggests

    commit 6c5e4ffe72c113dce136229ad1f70b5c7fd82c09
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 15:23:29 2021 +0100

        Fix error when setting app data

    commit efba905dd59c8e3c40221d30af059d9ba7e65cd4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 15:23:10 2021 +0100

        Fix issue with unit tests

    commit 773ddbe4b191f72d26080081585544da8ff661f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 11:48:06 2021 +0100

        Remove biomaRt dependency

    commit e339c0be3905076449b03461a81c7a1ed426ffc6
    Merge: c955b51 b1d13bd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 11:37:57 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit c955b51dd98d2c6e75decf2fd55bdfecc0e3aecc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 21 11:37:31 2021 +0100

        Avoid using biomaRt

    commit b1d13bda9fe99655813aa7d69bdf917bc8a0fdd9
    Merge: a28be42 951d1b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 19:15:55 2021 +0100

        Merge pull request #24 from nuno-agostinho/master+dev

        Fix crash with shiny 1.7.0

    commit 951d1b1aa8ab5776da72e12fca282aae19045048
    Merge: a4d73d5 a28be42
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 19:15:17 2021 +0100

        Merge branch 'dev' into master+dev

    commit a28be425f5a0894b0fdb62f0bb56bfb5c8580bf5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 19:13:57 2021 +0100

        Remove biomaRt from imported packages

    commit d79addfe2d25e7f10da17ec7b6855840f7bb11cc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 19:08:47 2021 +0100

        Reformat NEWS.md based on current releases of cTRAP

    commit 4ff1f98ee38276301c29afa06c4baf5ab073ebdd
    Merge: 1904325 05228eb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 17:02:50 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

        # Conflicts:
        #	NEWS.md

    commit 190432585cfa751142f766d5079aa150b1783822
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 17:00:46 2021 +0100

        Improve drug set enrichment interface and many other UI improvements

        - All drug sets are now shown and available to automatically download
        - Loading indicator shown while loading a new drug set
        - Hide "leading edge" column of drug set resulting table
        - Reduce internal usage of data for UI components (all data-dependent content should go through server logic)

    commit f70f297a09af3829603adea0433dbd8dc57b212a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:47:29 2021 +0100

        Revert (meta)data viewer design

        - Alert if no dataset is loaded/selected

    commit 757429cc13f457e70ca2e377fd9ab825157b1982
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:42:55 2021 +0100

        Fix "loaded" not showing after loading CMap data

    commit 9a28fbea3cd124b68e62bf7b7ef73e31bb81bdbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:38:25 2021 +0100

        Fix error when visiting tables containing expected datasets and there are no data

    commit 05228ebcae479822b395f3ff872b32283a1d32e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:38:25 2021 +0100

        Fix error when visiting tables containing expected datasets and there are no data

    commit a82df9c41b1af142e8461468fd4e3d9ce4ad13bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:28:26 2021 +0100

        Render dataset tags as labels to easily identify them

    commit 7f912c622545bf48fa4143f2058b27c41bbfc378
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:20:22 2021 +0100

        Exclude expected datasets from total datasets

    commit eda8c173857ff9a55f0f56328b232a71de7fcc5e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:15:11 2021 +0100

        Load session via qs or RDS

    commit 250bf7381c2613306ad81f1d0cb16752a082b919
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 16:12:11 2021 +0100

        Fix dataset comparison plot crash with too many zeroes to estimate density

    commit 0e605c4713f13fe4ff5d80ae34926b785f784680
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 18 20:45:00 2021 +0100

        Use qs instead of RDS for data storage

        - Change data URL for cTRAP's pre-processed data
        - Load drug sets
        - `cTRAP()`: save data session in qs
        - Use qs in remote files

    commit b97ee0dae11466189e41613c6cf6e311fcd1f5b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 12:06:19 2021 +0100

        Fix usage of string (instead of logical) values for rankSimilarPerts variables

    commit 8810269ab7c71d3767d317b5a1899ca6c58ed7d4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 12:05:40 2021 +0100

        Fix rankSimilarPerts table showing targeting drug results

    commit 1606e1516e693b39a8b3d6bfb1d5894f3a6eb529
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 12:04:15 2021 +0100

        Fix showing "Running" for tasks that were "Received" but still not running by Celery

    commit 3262f4711e85be075fbf861ca673c0404520404c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 12:03:47 2021 +0100

        Fix not being able to save variables in current environment

    commit 46cf2250fcfe05f3a0d2912951ac3dd35d87248e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 12:02:24 2021 +0100

        Add link for datasets in table to their plots

    commit 8eff3db34c3651da5ddb251785baa188bc0fc2eb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 12 11:56:01 2021 +0100

        Avoid updating task if not found in Celery task list

    commit 5d793bc71acd408b1a971f66aa1a09b5011068a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 11 16:31:09 2021 +0100

        ENCODE data table: hide unneded columns by default and revert interface changes

    commit 344af914d843bd05f919a6e76727d55f02348422
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 11 16:30:08 2021 +0100

        Predict targeting drugs in global UI

    commit 2e778382e51e8d3afb6339927c766c1fa9c95978
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 11 12:16:29 2021 +0100

        Improve appearance of Celery task status

        - Minor code copy-editing

    commit d354cabf36e765b75a747905f6d9d8bc59483458
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 7 18:35:00 2021 +0100

        Check if output files from Celery tasks are ready to be loaded

        - Update state of tasks

    commit e0070053ec9e1772fe0518a34feb7d0f5c7f7711
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 7 16:00:31 2021 +0100

        Create dummy "expected" dataset in data to be replaced with final results from Celery

    commit 01c5e16189c765bd05c8eb07fcc07eaae81298b9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 7 15:59:08 2021 +0100

        Allow to create new session after initial screen

        - Clean existing data when creating new session

    commit 054ab44740d6b4740a7d40a60de7a41ef55d138b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 6 17:20:54 2021 +0100

        Minor code copy-editing

    commit b5978d0e8768c8212ae130c113004cf486b5bf77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 6 16:13:51 2021 +0100

        Fix issues with R CMD check and other minor issues

        - Improve Celery task
        - Allow to set custom path for ENCODE data
        - Properly pass port/host options to runApp
        - Fix expiration help text not showing

    commit a4d73d5d323558f549e71996bd018d0c42ed442b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 17:37:32 2021 +0100

        Fix issues with R CMD check

    commit 6021a2108fe80f9779aabb4f3db10e30734bcac8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 16:51:23 2021 +0100

        Fix crash with shiny 1.7.0

    commit e3770847ce1103615a36e0971e5f3f4fbb157ddd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 19:51:40 2021 +0100

        Add support for Celery/Flower

        - Copy-edit code

    commit 2575b40195ecf07b23afbad796de039413c0a669
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 18:07:19 2021 +0100

        Fix issues with shiny 1.7.0

        - Avoid using generic positions when modifying Shiny objects

    commit 126693015d385fc8ff87de13503a85c17342c2a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 27 15:55:05 2021 +0100

        Minor improvements

    commit 0f71a81edc453ca3f5749919b6b99ddbcc13ac68
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 23 16:52:32 2021 +0100

        Automatically save session and load datasets in directory

        - Automatically load RDS data from session directory every 5 seconds
        - Automatically save RDS file with elements in session when:
            - Adding new datasets from UI
            - Loading a session from a RDS file
            - Loading data from session directory
        - Notify when loading new datasets
        - Show some progress bars for slower operations
        - Add loading status in navigation menu
        - Copy-edit UI text

    commit 962b39625f91ada7e37f2467981380c4172f6e39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 20 16:34:24 2021 +0100

        Improve usage of Shiny modules

    commit 9997935764cb9f47ae07ee2915ed897cc6fd0c7f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 9 01:13:15 2021 +0100

        Add UI for similar pertubations ranking

    commit a8d93436ed6dc79c8321316299e3c1d5c0ef15a7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 8 12:21:50 2021 +0100

        `cTRAP()`: new global interface

        - Support sessions
        - Increase file size upload limit

    commit d92e061c61d53cf3ef4e19a378a1f3bf133ba31f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 21 13:59:02 2021 +0100

        Add benchmark instructions

    commit 9a9c269452d86cb57547247d398fadbea9a7a527
    Merge: 914320a 64ce211
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 21 13:48:22 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit 914320a1a0d504b763330f27bb6cb048279136f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 21 13:48:15 2021 +0100

        cTRAP benchmark

    commit 64ce211a8881cadaa68021c9d39c48707206a380
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 18:20:26 2021 +0100

        Update Dockerfile

    commit fd376e9af77d6ad0225b1656eff2aa5d50984f11
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 13:43:48 2021 +0100

        Fix biomaRt usage warning

    commit 3a10760b2a5252e939564a5bc807feda16b4cf91
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 12:41:30 2021 +0100

        Remove biomaRt dependency

    commit 415cce93af74aff20edd42d2423ab0e68c683dee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 12:21:57 2021 +0100

        Bump version to 1.10.1

    commit e3ad90412bbfcb69aff984061b12aa388050b461
    Merge: ec324aa e031783
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 12:21:13 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit ec324aad00d1438a8b4dac224eb86405032fab6a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 12:20:56 2021 +0100

        Use AnnotationHub instead of biomaRt to convert gene identifiers

    commit e0317832519a4073df6c3dc6a8a59e5d8758f9bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 11:03:04 2021 +0100

        Push Docker images to DockerHub also

    commit 5e05ac9333072fc8d0fe913814be9bde1333cdad
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 2 21:30:03 2021 +0100

        Update docker.yaml

    commit 829e9cca6ff32903272ef78d287f1671eda065e3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 22:04:21 2021 +0100

        Fix Docker install instructions

    commit cad6f8ac82bce4fab45f7b6207be33b0340656e5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 21:08:33 2021 +0100

        Add Docker install instructions

    commit 22332e7b785b916cabff5afba66c5adac6823224
    Merge: 6848808 9a37355
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 18:01:12 2021 +0100

        Merge pull request #22 from nuno-agostinho/master

        Update docker.yaml

    commit 9a373551c46965464a85764475ab0247130bdb5b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 18:00:38 2021 +0100

        Update docker.yaml

    commit 6848808f7edb3afa161d62e6e51e262167980b64
    Merge: c46c25c 7cc03d7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 19:22:58 2021 +0100

        Merge pull request #21 from nuno-agostinho/master

        Update dev from master

    commit 7cc03d7c0bdd84fb9874d871000dc51d42640f99
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:19:41 2021 +0100

        Update R-CMD-check.yaml

    commit faa40bbaf0b2b32f1a395d875cb52857e479a665
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 17:54:49 2021 +0100

        Update R-CMD-check.yaml

    commit e8fe1b639ee3cb002b27bbd588fb719efbabbb1d
    Merge: 9f8a667 c46c25c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 14:56:13 2021 +0100

        Merge pull request #20 from nuno-agostinho/dev

        Dev

    commit c46c25c4d7de299d95209b68283b584d012e6a42
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 20:12:33 2021 +0100

        Fix issues with R CMD build/check

    commit 37b8db7c46f85fc8d854168b2126d2ef72b97153
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 19:35:40 2021 +0100

        Fix issues with R CMD build/check

    commit 262b0338b3a1ee940f7c99926b930dfddb862d87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 18:34:00 2021 +0100

        Bump version to 1.10.0

    commit df87aa5fa829e3e7c0cbdcdb8830a156a0a4c653
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 18:31:03 2021 +0100

        Ignore .DS_Store

    commit 29fd6a70ae3383955dd9f3004b9df0733259f666
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:10:55 2021 +0100

        Minor improvements

    commit d96b0c24d63dc9e8f0fb338f7b09d12ca50bb9ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:09:56 2021 +0100

        Improvement to graphical interface

        - Allow to compare different datasets
        - Allow to click-and-drag points to filter the table

    commit 0107097a7258b6484219e537a08de05b7bfc42fc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 23 15:39:36 2021 +0000

        Update available columns and plot using user-selected one

        - Minor copy-editing

    commit 123ad6b23c9869623f2b8b03268d6cf20d927b39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 23 15:34:07 2021 +0000

        Fix wrong element used in vignette

    commit 672c95bae3d280f53921f9e90244fbf54c341780
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 23 15:33:31 2021 +0000

        Improve data plotting in `launchResultPlotter()`

        - Show tables below specific plots
        - Allow to drag-and-select points in plot to filter table results
        - Minor code improvements

    commit 696fc29ae4bd16e9d785fbef4250072b2fea5f94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 23 15:23:25 2021 +0000

        Improve `launchDiffExplorer()`

        - Add proxy table
        - Copy-edit code

    commit 75e74597b3e32cf8add1a1cee0bdb92a9005eee0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 23 15:18:18 2021 +0000

        `launchCMapDataLoader()`: fix issues with CMap control perturbations

    commit c200c2c4fbbbc6f4e7e6567ff0904669897e73ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 18 18:28:04 2021 +0000

        `plotTargetingDrug()`: Fix warning regarding missing values

    commit 4f40b17fcdf9e56a8d5ae08c3400d14e3d281c08
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 18 18:26:52 2021 +0000

        `launchDrugSetEnrichmentAnalysis()` major fixes

        - Correctly match compounds like in CLI
        - Correctly use sorting column when plotting

    commit 7caf66c0a8d542a8ef4c47abd9f013c4fa6573de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 18 18:20:38 2021 +0000

        `launchCMapDataLoader()`: add bubble plot of CMap perturbations

    commit 82ab28bab7c76eb152adb8a965dfb3e1cdf2e884
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 17 11:06:29 2021 +0000

        Improve `plotTargetingDrugsVSsimilarPerturbations()`

        - Fix highlighting of plot points depending whether drug activity is directly proportional to drug sensitivity
        - Add rug plot
        - Copy-editing of code

    commit 8252cb92e4fb685146cb130ef61ebab2442b27ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 17 10:46:47 2021 +0000

        Rename first column's name of the resulting table to `descriptor`

    commit be66eb8b118705a839199e62c9cb2f589160405c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 17 10:37:38 2021 +0000

        Improve handling of HDF5 data for expression/drug sensitivity association

        - If argument rows/cols is NULL, load rows/cols according to rownames/colnames of the first argument
        - In verbose mode, print number of columns and rows to load
        - Close all open HDF5 connections (avoiding warnings of open connections)
        - `plotTargetingDrug()` now supports loading HDF5 data to plot
        - `plotTargetingDrug()` labels now avoid showing missing values

    commit 6085cc136ad7b9687141092c612b17857f04750f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 15 15:40:24 2021 +0000

        Fix wrong labels when plotting `targetingDrugs` objects

    commit d82f293c59e124d56f1bb363290434b8ec08db8a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 11 20:41:39 2021 +0000

        Subset custom objects by column when only passing one argument

        - Slightly improve performance of cmapR functions

    commit 4d759cbf2204e517c64b7287f99cb70ea4a6197e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 11 15:21:44 2021 +0000

        Avoid explicitly showing NA in plot labels

    commit fda582a6a8ffb95f5a9b4918e4f6af5f4120e074
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 9 11:40:37 2021 +0000

        Persist selection of other elements when selecting another perturbation type

    commit 06e8ddd96ddc5a082e1b7002ab669f3c3f4b0338
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 8 18:03:58 2021 +0000

        GUI: Load multiple CMap perturbation types at once

    commit 38040682df3c47845d0579c157dc607d3de9f917
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 26 19:51:33 2021 +0000

        Improve graphical interface for drug set enrichment analysis

        - New launchDrugSetEnrichmentAnalysis() function
        - In DSEA, change "pathway" to "descriptor"
        - Word break long strings as needed

    commit c8f6aa94f514c7ba006c7d0d2e8b5bbe7d54c34d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 9 18:15:03 2021 +0000

        Allow to change chunk size and copy-edit documentation

    commit 7a993f3781fb0db386e48d1f7ea8bd2352e9d684
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 25 18:41:22 2021 +0000

        Increase optional message verbosity

    commit d6ff29bb96cca3f94c3d7b48b2a0595d5672fe0e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 25 15:36:42 2021 +0000

        Small changes

    commit 296f9b21a6ab7e6c145681a6b3e688cfeb7ef5a6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 22 15:21:07 2021 +0000

        Chunk data columns based on chunk size of 1 GiB or less

    commit b1aa07819210ea261d29453478196326310a66a6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 21 14:44:44 2021 +0000

        Fix GSEA scores affected by lower number of loaded genes

    commit f932ea5d44deffca2121056c56662c287c6d90ed
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 21 09:41:04 2021 +0000

        Add tibble to Imports

    commit 2e08d24aeaf36326610a037d7f593f87f1d2792f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 21 01:06:12 2021 +0000

        Reduce `predictTargetingDrugs()` memory footprint

        - Load and process NCI60 gene expression and drug sensitivity correlation matrix in chunks (by giving specific rows and cols to load)
        - Save NCI60 correlation matrix in HDF5 format to allow fast data subset loading
        - Read attributes from HDF5 file without loading data values themselves into memory
        - Load data for intersecting genes only (instead of all as previously done for CMap z-scores data)

    commit 1c8ecaccb56b6c4e0430c28a0668c3b022463e44
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 7 14:51:57 2020 +0000

        Improve drug set enrichment analysis

        - Allow to set key columns to match compounds between datasets
        - Use same internal algorithm used to match compounds in `plotTargetingDrugsVSsimilarPerturbations()` and refactor code
        - Fix bug where trying to convert non-numeric values to numeric for key columns
        - Reorganise code

    commit 3c51a4f3589ecef46eed25cf40071b45a508f403
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 2 14:54:07 2020 +0000

        Fix issues with missing values

        - Fix setting names when there are missing values
        - Fix error when there is a low number of non-missing values

    commit 741776aece429d4112a977841899fd2c742ec406
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 2 11:14:29 2020 +0000

        Directly set metadata conditions on preparing CMap perturbations

    commit dc5fa2ce2580020b0f9cd9333bf19212da1400a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 15:46:13 2020 +0000

        Include example of differential expression for dev scripts

    commit d1359242c97ff231649711baa4a98cfc83378660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 15:45:21 2020 +0000

        Test differential expression for cystic fibrosis dataset

    commit 52179075912d5da67012e2ca5dea3ed68b315193
    Merge: 5539163 e8ce386
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 15:43:07 2020 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit 5539163151801106be162eee7cfc42bf01bbca57
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 15:42:52 2020 +0000

        Include parallel package

    commit e8ce38686b6fba8f52414c5b60ef046bb71e7833
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 14:31:55 2020 +0000

        Update R-CMD-check.yaml

    commit 00f1d40522afb63633568117755ae1e0f6cc6de2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 13:48:46 2020 +0000

        Include fastmatch in packages and ignore TXT files

    commit 562bf2ef9e152ec61a6df001d32b4485f679e245
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 13:25:01 2020 +0000

        Set drug set size and max set number from numeric columns

    commit e16e3826ebe39baf7d1bdb42a764075e2bda6808
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 13:20:14 2020 +0000

        Import fgsea

    commit 73236f2258ba7ed922618cf69e2aeeb300a13d49
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 13:19:10 2020 +0000

        Allow geneset sizes of 0

    commit 1d2f2e35713ce91043fdfae751ca3206c9adfd75
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 24 12:12:30 2020 +0000

        Support multi-threading

    commit 9f8a667e364e8779ebdbffe8ecae292274afd2bb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:33:55 2020 +0000

        Fix setting environment variable

    commit 0d8d3e536657e56ec2b40df2f3e789e35f0d4955
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:05:22 2020 +0000

        Avoid bioc-devel while R-devel is not available

    commit 35b93f85e99b888d30df27e4b7fb7871a847d338
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 20 10:03:07 2020 +0000

        Fix non-proper function usage

    commit cec61881dc51bde97a736519c86c2534384824d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 20 00:39:43 2020 +0000

        Fix usage of non-imported external function

    commit 001788fce6e94e3f3db01e503b779277fa4aa223
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 20 00:18:15 2020 +0000

        Fix original column order when comparing data by chunks

    commit 1f35b4689fb80bb79dc5362557afe3ca4cb4d7f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 19 17:45:33 2020 +0000

        Fix original column order when comparing data by chunks

    commit c34566c79909b64a0f0735c91e62e32d28a604f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 19 15:19:57 2020 +0000

        Fix error when using pre-loaded z-scores

    commit d106ee19eee70028d6f55f6ab2441f7daf8a179e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 19 14:39:41 2020 +0000

        Reduce redundant loading of CMap z-scores

    commit 093c1b9fd73d7a5bc83fc02d1af4548ac3fa1560
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 18 12:51:55 2020 +0000

        Fix drug sensitivity script

    commit b13ee45bff3d41fa2684376d191658fb7905567c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 18 12:50:38 2020 +0000

        Speed up GSEA-based score calculation

    commit 15229dd8dd812057c551446ed776ce348074e427
    Merge: c29a84b dd8aedf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 30 11:10:21 2020 +0000

        Merge pull request #15 from nuno-agostinho/dev

        cTRAP 1.8

    commit 7311d8f6320810184ad6edcbd5287cc765af127e
    Author: Unknown <unknown@example.com>
    Date:   Tue Oct 27 18:41:26 2020 +0000

        Improve compound descriptors

        - Fix compound names and information in NCI60 3D descriptors
        - Replace 99999 with missing values in all compound descriptors

    commit 79caf31461b919e5bfa38c35e8573fe354e1438b
    Author: Unknown <unknown@example.com>
    Date:   Tue Oct 27 18:37:16 2020 +0000

        Test multimodality of drug descriptors

    commit dd8aedf59ed85b0f21fd9cffc76a4d0c38cdf004
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 23 17:57:16 2020 +0100

        Fix issues in R CMD build/check/BiocCheck

    commit 27deee0e974cb02f4adcf1159470eb02006c2918
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 22 19:24:59 2020 +0100

        Include more useful dev scripts

    commit 91a27d6a05acfc81fe86cd9475e169dd74ec7287
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 22 19:19:49 2020 +0100

        Create evenely-distributed sets for numerical drug descriptors

    commit a237e3ceab189650b2c75bbab639389ee669f057
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 12:18:47 2020 +0100

        Add graphical interface functions

        - `plotTargetingDrugsVSsimilarPerturbations()`: automatically look for matching compounds in multiple columns of both datasets
        - `plotTargetingDrugsVSsimilarPerturbations()`: allow to manually select columns on which to merge datasets
        - `downloadENCODEknockdownMetadata()`: Save ENCODE metadata to a RDS file
        - Include dev folder

    commit 354b26559df96eacd7e68004486cbfd9dbd3791f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 12:18:29 2020 +0100

        Simplify tutorial

    commit c29a84b546e5ac163179103683fdd3505fb7c246
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 19:50:47 2020 +0100

        Fix pkgdown install

    commit 979d873bb0fdf0b7354a0997ac52a10f741881da
    Merge: af82d42 d21bb4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 18:01:33 2020 +0100

        Merge pull request #14 from nuno-agostinho/dev

        Bump version to 1.6.1

    commit d21bb4eff0ff60e05406a418420fd6372f2efbc1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 17:58:57 2020 +0100

        Bump version to 1.6.1

    commit af82d42bc129829053e13729e53c494d2a5b2292
    Merge: d6be0a1 15d0584
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 17:41:20 2020 +0100

        Merge pull request #12 from nuno-agostinho/dev

        1.4.1

    commit 15d058469022db03170b5a51b6db7ea388ae6255
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 17:39:45 2020 +0100

        Remove TODO list from NEWS

    commit f2e860079ef46ec66133c82f20d2807132ecaebb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 15:24:42 2020 +0100

        Fix issues with R CMD check

        - Suppress ggplot2 warning on using vectorised argument in `element_text()`
        - Document `title` argument in `plotComparison()`
        - Correctly import other package's functions in the needed functions

    commit 02e4600768009ed437ee006949cb0db61f4caa25
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 12:45:23 2020 +0100

        Fix ranked genes in compact GSEA plots taking too much space

    commit 558fa3fdf53e3607dccf42916280ae8750d3bcc1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 12:44:56 2020 +0100

        Show first/last values of ranked genes in GSEA plots

    commit 6bf5556bbf7e0150fec2a6420acc815673d0d597
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 12:12:52 2020 +0100

        Fix legacy code in GSEA plots for targeting drugs

    commit 4855a2440ff2d37470fea98e3c24ae952f753ea1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 17 12:02:30 2020 +0100

        Set plot title when using `plot()`

    commit c17360b9f12a5039f871b7f85460c6d8199b0b87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 16 21:04:24 2020 +0100

        Fix GitHub Actions badge

    commit 771d5f80711a98aa487f259284e582e2e993072d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 16 00:42:36 2020 +0100

        Fix Docker name

    commit 98adb199687028c130eadb4e08045eae43f75f87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 16 00:38:07 2020 +0100

        Fix Docker name

    commit 8176d8520e08ca6cf807a3fdc8c351fb4b65dfa9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 15 10:56:36 2020 +0100

        Use latest Bioconductor docker

    commit 5373a8f410a3dc7ad7633b75b64c4f8207994945
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 14 13:16:04 2020 +0100

        Fix R CMD issues and copy-edit documentation

    commit c413a30097af999ac085b7b4fec5e012318f382d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 14 12:26:29 2020 +0100

        Use GitHub Actions

    commit 95a2082c07f2260f0065ec4949a25e8017af6aa8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 14 00:36:03 2020 +0100

        Copy-edit documentation

    commit 0a502918ff6a81765409eab7bca69e7a538bd2b4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 14 00:34:57 2020 +0100

        Preserve original order when converting results to table

    commit cf9672fe0b928c13ec7f01ca868175cc4d761b32
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 13 23:33:03 2020 +0100

        Fix changes related with ENCODE metadata

    commit 5b651b89b28dd9e46d3c163e66bb19eee5b1eb12
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 13 18:21:21 2020 +0100

        Plot GSEA of multiple perturbations

    commit 9f1a17d3a26680ecf313183cbbd0dacf1a534f6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 4 14:38:22 2020 +0000

        Generalise as.table for referenceComparison objects

    commit d9e041576608c50169ac06a6f20bb00355a402b5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 2 15:52:09 2020 +0000

        Fix warning when trying to read average cell line perturbations in z-scores file

    commit 636d48b0f3a3ebd1b6caddde4c76db5b52eca0f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 27 10:24:42 2020 +0000

        Replace WCTS for WTCS as appropriate

    commit bd4d1283ca180fc09f72ac84aeb47c5f38cbdbaa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 27 10:24:10 2020 +0000

        Improve `as.table()`

    commit c7db4e3aabadcb647d63e8ebe2f47eb1a8545fc8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 10:57:20 2020 +0000

        Fix truncated warning

    commit 6b1fcb5ab0192e3c63b60497f5a2ca9c5b74a56a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 10:39:19 2020 +0000

        Include genesize for custom geneset

    commit cdc7084b96397885700865c9d58600de99398f58
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 10:32:27 2020 +0000

        Copy-edit function documentation

    commit bed21e5b6d99640e67dffee67ed2a489f4b6f339
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 24 18:04:00 2020 +0000

        Allow to set different gene set size for top up- and down-regulated genes

    commit 9f9d106bfad5ff484451e6374e4bd509ec4852dd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 24 18:00:14 2020 +0000

        Fix plot of CMap perturbations not showing enrichment score (ES) parts

        - Same behaviour as performed in 1.4 release

    commit 068a47115c258e87040bcdf167d13d1e7a8cd633
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 24 12:01:11 2020 +0000

        Copy-edit NEWS, tutorial and function arguments and documentation

    commit f18993e7f36cec3b83929b0f059d1de6a8e077ec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 24 11:57:31 2020 +0000

        Allow to directly input zscores data when plotting

    commit ac12716ad641682ce802027c77379812ffc1a58e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 18 20:36:59 2020 +0000

        Test enrichment of custom gene set and plot targeting drug results

        - `plotDrugSetEnrichment()` now returns a list whose names are drug set names
        - `plotMetricDistribution()` now supports only two or less gene hits
        - Copy-edit messages and function documentation
        - Copy-edit tutorial (e.g. resize figures)

    commit 24113a82d8c745c33dddef4859dd633d9dd98e64
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 11:40:33 2020 +0000

        Use Linux and bioc-release for later build stages

    commit b50e74d5974eb67596912175c899268ef36b14f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 10:03:42 2020 +0000

        Use Linux and bioc-release for later build stages

    commit df4e68061c2edccf853fecf04fda7aa5bdbe9520
    Merge: 8de1337 8f8d794
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 3 19:02:07 2020 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

        # Conflicts:
        #	.travis.yml

    commit 8de133703ac1825ebcdab314fc006734a9b2d812
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 3 18:59:32 2020 +0000

        Fix warning from config file

    commit 8f8d794c7b0db2e8ff601a438f0d9cf0e80bc6f0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 3 18:59:32 2020 +0000

        Improve Travis CI automation

        - Include macOS support
        - Include pkgdown site deployment
        - Remove warnings from configuration file

    commit b2a95c4cab07fbaf823fe8ffc9b20d4ca4ff6e9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 3 18:35:06 2020 +0000

        Spell checker support

        - Fix documentation misspells

    commit d22ff7beae561d379670dd20fe0f0b94f97f0964
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 3 16:18:08 2020 +0000

        Create pkgdown site in GitHub pages, improve Travis CI and include spellcheck

        - Copy-edit function documentation
        - Improve Travis CI stage builds
        - Add spellcheck

    commit ef1067736d0ee89555b5eb51dc19ad53f7ebb4dc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 17:54:47 2020 +0000

        Update NEWS.md

    commit 38b1f974d82d699aacfff0295ef229f54cc3487a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 17:54:25 2020 +0000

        Improve function documentation

    commit de89b2d261b69000f0af28c3d7bdd42d64c948ec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 17:54:01 2020 +0000

        Copy-edit tutorial

    commit 32bee1170040822ec99e8f5f629a031e7bc7df98
    Merge: 48e97d0 d6be0a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:44:31 2019 +0000

        Merge branch 'master' into dev

    commit 48e97d03ffa40e5d5e3177eb7ea75c0df2ffc6fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:35:51 2019 +0000

        Bump version to 1.4.1

    commit d19c22d3d34e5a91a2d0820fbeb2ad7467fe1b5e
    Merge: ac9661f cae2411
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:34:25 2019 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit ac9661f915d3836fd3e90129cd25099b1e6fa39c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:34:07 2019 +0000

        Improve tutorial

    commit 07d5ee48b3d4037ba0467eaeb9301d73f0816261
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:32:41 2019 +0000

        Copy-edit CMap-related console messages

    commit 310a2808e9a112531fc3420a6d8c2613947f9e2f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 18 11:29:10 2019 +0000

        List available gene expression and drug sensitivity associations

    commit d6be0a17fdb10c53295059bd02101585a4f5bd95
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 11 23:12:14 2019 +0000

        Fix Dockerfile

    commit 86a58282c2ee7120f0cd8d572b2b9ac7777e37fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 11 22:44:16 2019 +0000

        Bump version to 1.4

    commit 2d9a9f466e4642372c96d814f576c1209eca8777
    Merge: 08457c7 cae2411
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 11 18:43:09 2019 +0000

        Merge pull request #8 from nuno-agostinho/dev

        cTRAP 1.4

    commit cae2411c020a59c1259fc5834b23fc56e58ab207
    Merge: 28a6eec 5ee5dd4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 28 16:15:35 2019 +0000

        Support Linux+Mac CI in Bioconductor release+devel

    commit 28a6eecc51d8ae0aa5fd27deb0346bfd08426e18
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 28 16:14:48 2019 +0000

        Fix downloading binary data in Windows

    commit 5ee5dd4700e111e642438d3f5c9885833ddf4629
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 28 11:42:23 2019 +0000

        Support Linux+Mac CI in Bioconductor release+devel

    commit 84e2e1433d7a7cd30aeb35078cf5dd550f909899
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 25 18:52:53 2019 +0100

        Fix issues with downloading CMap data in Travis CI

    commit b90ae9dd86751972aca421ccb08d04e80938d8bf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 25 18:33:48 2019 +0100

        Update NEWS date

    commit 7525748033c6f1c7be98cef1c0ba8410d6cd80c6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 25 18:33:39 2019 +0100

        Include rmarkdown for CI builds (specially Travis CI)

    commit 65c85f6d1c858222ff9c614fcab418d24b0b161a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 25 18:24:12 2019 +0100

        Fix R CMD build/check issues

        - Fix 80% of non-runnable examples
        - Fix ASCII characters on cmapPerturbationsCompounds

    commit 2e2b53c0231b6a91c271e6519aa8c5c0bb4a7cb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 21 16:38:44 2019 +0100

        Minor changes

    commit 757381cf607f160b405e2e2c11ee087aa2a7d16f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 9 14:45:26 2019 +0100

        Remove two depencies

    commit 7c66c201823f67f3af56c2088ccf886e40b84d65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 8 18:57:15 2019 +0100

        Load missing library for unit tests

    commit 5bed9e16fecaa4eb694f21a73eba1dc53f87c9ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 8 18:56:42 2019 +0100

        Improve vignette

    commit 72c2067fe07bd2a882255db35585fc2b1596e94b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 8 18:55:59 2019 +0100

        Improve function documentation

    commit d57c21c079c815b4bb7a402a8658da3d899fc46a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 8 18:55:00 2019 +0100

        Update links to download CMap data from GEO

    commit 87722655caab4617fc48f1920a89ee78bc94ea6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 8 18:10:39 2019 +0100

        Add recommended biocView

    commit e554ddfbdce8a1b9b85c0d25a4a9dcdf678ef7c6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:24:26 2019 +0100

        Fix downloadENCODEknockdownMetadata not returning metadata

    commit 5759fe66f37a42e24b81e1bc5d5c65ce1bc811ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 30 17:11:18 2019 +0100

        Improve gene expression and drug sensitivity correlation

        - Add dataset versions (GDSC 7 and CTRP 2.1)
        - Use -AUC values instead of AUC values for NCI-60 drug activity metric (so it is directly proportional to drug sensitivity)
        - Allow to state whether drug activity metric is directly proportional to drug sensitivity or not

    commit cf0959616b89e8a4114dead4fa9b555c8806af78
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 16 15:14:10 2019 +0100

        Improve drug set enrichment analysis

        - Add support for 2D and 3D CMap descriptors
        - Improve name of drug sets
        - Improve compound matching between drug sets and data of interest by using respective metadata and compound information (when available)
        - Improve unit tests
        - Scale number of breaks in metric distribution according to number of ranked elements
        - Add title of drug set in use for GSEA plotting
        - Minor code copy-editing

    commit 3e715b3722af09f03f2815cad800e8244d41e6ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 16 15:04:29 2019 +0100

        Add Dockerfile for Docker images

    commit 58568ef4e0bcbe36b0d68b6c42691ca6cba45bc3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 7 18:49:49 2019 +0100

        Set dataset version for expression-drug sensitivity associations

    commit c27a88121a3207a903248aaab7c717fd08743069
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 6 18:09:38 2019 +0100

        Fix R CMD check issues and export loadDrugDescriptors

    commit 982ea9eb5fb2cb49f3a0b3264b7cebb5ae73c8e5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 6 14:52:32 2019 +0100

        Fix unit tests for CMap perturbation ranking

    commit 4501e94f3145eb24fd28dd1a0126d8902d74101c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 5 17:06:59 2019 +0100

        Cross-reference functions in function documentation

        - Fix issues related with R CMD check
        - Copy-edit function documentation
        - Organise code
        - Export function convertENSEMBLtoGeneSymbols
        - Import missing packages
        - Add alias to rankSimilarPerturbations()

    commit 7757ace30681980d06f1a978f2b517cb44fb477c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 5 16:12:21 2019 +0100

        Analyse drug set enrichment

        - Prepare drug sets based on a table with compound identifiers and respective descriptors
        - Test drug set enrichment
        - Copy-edit plotting code
        - Copye-edit NEWS
        - Add in tutorial

    commit 4c046303daeb691003c0068d665868d787c1c911
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 18 19:05:31 2019 +0100

        Predict targeting drugs based on drug sensitivity data

        - Export function ot convert ENSEMBL to gene symbols
        - Stop if no intersecting genes are found
        - Improve vignette, including demo of new features
        - Copy-edit documentation
        - Include compound information in cmapPerturbationsCompounds
        - Sort results based on rank product's (or other method's) rank

    commit ba77e3d317930f5d68c04ace6038c26512690009
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 11 16:41:33 2019 +0100

        Fix literal NAs in compound metadata

    commit ba1d86c7247971e1e428a58d17fb27846b7a831a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 11 15:42:27 2019 +0100

        Include information on mean perturbation scores in metadata

    commit 26e3fac3c3c415b4d00bb78e2d3da93af90b1115
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 11 15:40:39 2019 +0100

        Fix missing imported functions in use

    commit d069d66202b934f9c165ef2175c3fa8ecbd4f764
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 11 15:30:13 2019 +0100

        Fix classes of demo datasets

    commit 4628cf9d089e9cdaa03156140c607ae4e5705e60
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 10 18:28:42 2019 +0100

        Improve chunk loading of CMap perturbations

    commit cf749415989dee9b638a4e54eea0797131321850
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 9 10:50:41 2019 +0100

        Improve function names related to perturbation comparison

        - Rename "compareAgainstCMap" with "rankSimilarPerturbations"
        - Rename class "cmapPerturbations" to "perturbationChanges"
        - Rename class "cmapComparison" to "similarPerturbations"

    commit 0b0f6ad901c23edb84a7c84c2e7a4c0dc49ab0e6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 8 17:32:47 2019 +0100

        Fix error when trying to calculate the mean for cell lines with no intersecting conditions available

    commit ab423c3de86d8ed88947fefe8e24c97ec2751721
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 8 17:31:58 2019 +0100

        Include rank product's rank in tutorial

    commit 0b6da8578f1c4b4d41e5dacf093c318fb69a1ea9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 1 13:02:30 2019 +0100

        Clean up CMap perturbation comparison code

    commit 6d25ad9a1a24f2dcc1343b9537aa3580bcb42753
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 26 16:41:20 2019 +0100

        Calculate rank product's rank

    commit 23b9fb4f5a0740e8fcf36a13cf15ff6a2334d1c4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 21 14:20:08 2019 +0100

        Display summary of laoded perturbations after running `prepareCMapPerturbations()`

        - Copy-edit NEWS file

    commit 59d9a8a2f8fde407802edb91dc6998b3d2c42516
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 21 14:18:52 2019 +0100

        Assign missing values to identifiers of summarised perturbation scores

    commit f94100f38f13a107611278bf844202436efa6a8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 10 20:22:28 2019 +0100

        Fix R CMD BiocCheck issues

    commit dff63d9cdf524b874ee52caaa9b2d6659aee29f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 10 20:10:43 2019 +0100

        Update R dependency

    commit f303096f18b5d0f7de0d136aa94960ad97993f5c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jun 8 15:35:31 2019 +0100

        Allow cmapPerturbations to load z-scores directly if preferred

    commit c704ba04f1b87ee70955b23e65765ffcb77c2715
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jun 8 15:06:28 2019 +0100

        Unfix assembly filtering (ENCODE API issues)

    commit 8a61a6dac408133574ea32f48bdb73c0adebe67f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jun 8 14:38:14 2019 +0100

        Ask to download CMap perturbation z-score file if not found

    commit 2b02ea9d41a7e506552d91783cf4ffcacc24f084
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 6 14:18:30 2019 +0100

        Fix ENCODE metadata downloading a table of missing values

    commit 4fcdbc6ac4af450a68189b49c2e5bfa8eb0d3e43
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 6 14:18:03 2019 +0100

        Improve plot unit tests

    commit 48a780e5656e7bcf6652b70579101c8f1c5aa503
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 6 13:06:47 2019 +0100

        Perform correlations on all filtered perturbations

        Faster than by cell line, as previously done

    commit fd761a6c3dfdbd947aadd77b0dbb1f83a383d385
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 6 13:05:25 2019 +0100

        Fix getCMapPerturbationTypes not correctly showing control perturbations

    commit 3769bd9d96e7f13cb9c8353e7146781bbe446734
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 3 15:49:43 2019 +0100

        Fix bug when comparing differential expression profile against a single CMap cell line perturbation

    commit 29482d92b4ac9b15d7d8533e1646dc3a1fe5e20d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 30 17:21:53 2019 +0100

        Decrease RAM requirements by loading chunks of CMap z-scores on-demand

        - Instead of loading CMap perturbations, prepare its attributes and save its filename for loading chunks of data on-demand
        - Modify compareAgainstCMap() and plot() functions to load chunks of CMap perturbation data on-demand based on its filename
        - Copy-edit code and comments

    commit 76de2f694e81034583cac38b624f19c61a1b77b5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 27 17:07:38 2019 +0100

        Improve loading of compound information

        - Significantly improve time taken to aggregate compound information from both drug and sample files
        - Allow to use real filename of either the drug or sample file
        - Show filepath of file to load

    commit 6dae1ab66bcf6fac3936f11ccb1d5b3fda8087a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 23:39:55 2019 +0100

        Rename vignette filename

    commit 80bb53ed9d971f595596622a1081e95160a5bb75
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 23:18:57 2019 +0100

        Fix NEWS

    commit 17f45db3513a62f79268503c6e654686fe0628fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 23:08:16 2019 +0100

        Update version number

    commit 44daf6e0a677b48b9ae4c92b90f1aba811b1cb7b
    Merge: b965ee5 a1f9059
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 23:01:12 2019 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/cTRAP into dev

    commit a1f9059dc26b518b8df58c1ccdee867446e0cf2e
    Merge: b94b605 08457c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 18:49:18 2019 +0100

        Merge branch 'master' into dev

    commit b965ee509e7f7d496cbf601445fe3b854d50324c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 18:34:21 2019 +0100

        Fix R CMD check issues

    commit b94b605dd8a8da7fce168589cb5fcc1b15cfa37c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 22 18:19:45 2019 +0100

        Colour scatter plot based on cell lines for cmapPerturbations objects

    commit 23b06b7ea10184fd5c98d0a1f5af45a3ec7fc573
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 21 17:24:29 2019 +0100

        Update tutorial

    commit 3a38efd31d8f25b8402fea8ceed6f4d60213a399
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 21 17:01:47 2019 +0100

        Fix issues with R CMD check

        - Add unregistered dependencies to NAMESPACE
        - Update data to avoid non-ASCII characters
        - Update, copy-edit and simplify code to get example data
        - Copy-edit code, documentation and unit tests

    commit 2ed1521104ef25d7b5eb7a223ed697bc1ea76d9a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 18:16:18 2019 +0100

        Include missing packages and sort them

    commit e5303e6f5653b664e22d9ddc7eed0aab87888db0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 18:09:45 2019 +0100

        Parse CMap identifiers

    commit 869b31018d31f88865a8512ad1c0dd16d34f01e0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 17:50:07 2019 +0100

        Test plotting non-ranked perturbations

    commit 2c53a62fdd40ad9e72b64a71bd63b881a6d991f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 17:24:29 2019 +0100

        Increase verbosity when (down)loading data

    commit 31dd24dd0f384d8b8b2bbee7c0d42e2c6475f99e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 17:23:40 2019 +0100

        Plot non-ranked perturbations when plotting a cmapComparison object

    commit a88f650421fc2e87a58c936c11a673372cee8242
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 20 17:20:49 2019 +0100

        Improve compareAgainstCMap function and copy-edit

    commit ffd96f0f8aec576e771ad309d4d653e90b410d1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 7 18:48:27 2019 +0100

        Improve plotting and add unit tests

        - Warn if cmapComparison object was not run with a given method
        - Automatically select 'spearman' as the default method

    commit 14481989b5d90a5c7df50810c319a768c2310133
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 7 16:49:17 2019 +0100

        Fix bug when comparing against CMAP using only one method and fix test units for compareAgainstCMap

    commit b1a696a6baa3309e71a41c8fb4d26dd7af5bb3f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 7 15:25:25 2019 +0100

        Minor changes

    commit cb43cf05a2cc8c067ae792cece3bcd06dbb695b2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 7 15:24:13 2019 +0100

        Rank similar perturbations based on individual cell line

    commit af2df9a36d2ba2d87ce84ff1f515bcff4428d0ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 6 16:00:18 2019 +0100

        Fix non-exported function

    commit 32e11baed4197cc32c0dfb91c3b4f424bee3bbb1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 00:08:12 2019 +0100

        Fix issues with plot testing and copy-edit NEWS

    commit 98ef9aaafaa244e7fa24373bd37f6591296c7aec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 00:07:16 2019 +0100

        Update tutorial vignette

    commit a7a601e4468d162f959e789e46cf3a8279d6d890
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 00:04:37 2019 +0100

        Improve plotting functions

    commit 164d88c4bc28b69f43cbe29eb18148853fc88d6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 00:02:23 2019 +0100

        Update demo datasets

    commit 9022435dfcbe49f289212136c52598c140ea4adb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Apr 29 11:17:11 2019 +0100

        Improve compareAgainstCMap

    commit 76ccfefb02a67d4ef05c57a7181a6a280225f362
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 25 13:52:49 2019 +0100

        Improve metadata retrieval and helper functions

    commit 54a413f5446d03e6d2cf257f5b1b4a75a48622c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 23 12:53:49 2019 +0100

        Improve metadata integration from CMap

    commit 189be68657ce74be29eacbb561e96993cc470a1d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 23 12:43:41 2019 +0100

        Download and load multiple genes and cell lines from ENCODE metadata

    commit 78fb7cc6111da544f4b1a8d72cf86a278cae70a2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 23 11:52:37 2019 +0100

        Improve performance of handling cmapPerturbations objects

    commit 36c533c0c34684372a4616ca5a88dec8a828a62c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 23 11:49:49 2019 +0100

        Update .gitignore

    commit 355cda028c6cb1f6ad7c8571e09ccaf0cc879fc9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 18 14:37:28 2019 +0100

        Replace instances refering to L1000 with CMap

    commit db34dcb0e9acb4185cd344e1b6c2bb2710de5bdf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 18 13:43:54 2019 +0100

        Minor changes

    commit 5e8cda2ea1d5023a9d73ff1ef7644740c2a421b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 18 13:43:13 2019 +0100

        Rename function names containing download to load

    commit 907b20f7722d0eee74a3e1c6047fbff64be5a8e5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 18 13:23:43 2019 +0100

        Update .gitignore

    commit 69c59c2e07286dab54f54ff0bb2d309edbcb24ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 30 17:30:12 2019 +0000

        Major changes

        - Improve plotting with new plot types
        - Update function documentation
        - Update vignette

    commit e127a0badad7195a01b9170e36dafc537e4b286d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 5 15:59:42 2018 +0000

        Update and copy-edit the tutorial

    commit 8746c644e85b278500c2ec8d92c826b78752c52d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 5 15:57:00 2018 +0000

        Update function documentation

    commit b97b1020fd32bbb70e25b08333b855182e9c37e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 5 15:55:00 2018 +0000

        Improve comparison performance when testing for correlation

    commit 65e0cce55becbd4f62f604c811c458f8bde98d60
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 17:53:13 2018 +0000

        Create l1000perturbations object with associated metadata and functions to edit said object

        - Correctly set name of perturbagen types when comparing against CMap perturbations
        - Avoid calculating the mean across cell lines if only one cell line is provided when comparing against CMap perturbations
        - Automatically order results when comparing against CMap perturbations
        - Update internal datasets
        - Update .gitignore

    commit 08457c7b836670c6080c04fd92755d4dd15ac376
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 15:56:15 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit ec346fc5fbd6d68305f6b0431f9cee2d2ab04dce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 27 15:52:27 2018 +0000

        Replace instances of -666 in CMap data to show up as missing values

    commit 45be6754e1e9648bafbcb0867de428444f234ffb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 21 15:45:26 2018 +0000

        Update NEWS and bump version number

    commit 309bde4c6c90f9429c358961b6e7ac18fadf5451
    Merge: 1d0814a fc66327
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 12 15:47:59 2018 +0000

        Merge branch 'master' into dev

    commit fc663279c4dc280cd44c193787b2056aa2c7a2e0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Nov 11 18:23:17 2018 +0000

        Fix comparison against CMap perturbations using GSEA

    commit 1d0814a3081d779545246c3376812f2114fde713
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 17:43:27 2018 +0000

        Include BSD3 license for cmapR

    commit ecb24ebeb47ea27b5fb71e7b911f4de0bf59b923
    Merge: 2611ec8 74e338b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Nov 4 17:43:40 2018 +0000

        1.0.1

    commit 74e338b39bb0a4bcbe872f2a0f19e46b181cfa43
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Nov 4 01:37:17 2018 +0000

        Suggest biomaRt to build vignette

    commit daf0ce22ee2e2978cd82f4ce6a925c530ed1e401
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 15:15:27 2018 +0000

        Fix issues with duplicated gene symbols

    commit 6b880aa0864a5bcca9e54b1fb17eeb4199e0f7c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 14:57:07 2018 +0000

        Select p-value adjustment method when performing correlation analyses

    commit 72da59d442564046f8923a4fd953169ec3c26be9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 14:40:35 2018 +0000

        By default, show CMap perturbation types except for controls

    commit f8387e863ef814685c8ad07d71c59eb469968bf0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 14:39:23 2018 +0000

        Update NEWS

    commit d1e7a94c57ef85978231bad2aa4fa0eee9f77411
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 14:32:27 2018 +0000

        Fix obsolete function calls in function documentation

    commit 9697b622f232a35d1f4f8bf3a3f05d5e803ff9b5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 14:32:07 2018 +0000

        Remove "_t" from column names from the results

        The t-statistic may or may not be used by the user

    commit 7d301bfb02af285f1947535c2776745a23c8e4a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 13:40:24 2018 +0000

        Remove biomaRt dependency

    commit bcf9769b0c64d89ffd090abe5cececd653ea5c16
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 13:07:22 2018 +0000

        Update title, author names, version and README

    commit 9b56c207c74cc02ee0c0441d734fde98f16e9328
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Nov 2 13:05:28 2018 +0000

        Hide non-exported functions from reference manual
 
Package: CATALYST
Commit: 462b12173c6fde7a88b13887ba8c181e1360577a
Author: HelenaLC <helena@crowells.eu>
Date: 2024-03-27 10:53:43 +0100
Commit message:

 unit test & docs fixes
 
Package: multicrispr
Commit: 5aadbd37f2c2eebc4762c7a40923164738e5a3d1
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:52:56 +0100
Commit message:

 Eliminate assertive.sets (in devel)
 
Package: multicrispr
Commit: 549f0f55a8ac0417aae261dd6859e43b2c2f6257
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:20:35 +0100
Commit message:

 Eliminate assertive.numbers
 
Package: iSEEindex
Commit: 853cbfbf11f5d70fa0d13a9e67e63bc862796425
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-27 10:24:05 +0100
Commit message:

 Fix docs (#58)

* Rerender documentation

* Update to recommended format for package documentation

* Version bump 
Package: iSEEu
Commit: 7961e3f45aac1e7d2d8d20eaf2dcd3a8ddb8711f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 15:11:47 +0100
Commit message:

 Extra docs vignette markdownboard (#116)

* adding documentation for two additional panels - already in the codebase, just not highlighted yet in the vignette

* adding screenshots, created via appshot on the app objects

* newer roxygen version

* manpage re-created

* udpated news

* version bump, 1.15.1

* updating GHA to use latest Bioc devel version 
Package: multicrispr
Commit: 85551536efca2bea7bb24f7100eb0a9003a900dc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-27 10:04:42 +0100
Commit message:

 Eliminate assertive.files (in devel)
 
Package: SingleCellAlleleExperiment
Commit: bf86234a4900285d0856d77017f355812f71f9df
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:18:38 +0100
Commit message:

 version bump, incorporating changes made related to the review process in scaeData
 
Package: SingleCellAlleleExperiment
Commit: ab4eb864823e2e25b8ce2bb9911f38fea1625c5f
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-27 09:12:23 +0100
Commit message:

 deleted pkg-level man page; ready to version bump
 
Package: SingleCellAlleleExperiment
Commit: f372be377c8812d5a083e7a9f2c7388a3bdb1b27
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 13:23:27 +0100
Commit message:

 added R 4.4 in Description/depends; made a note in NEWS for changes made related to the scaeData review; ready to bump version
 
Package: SingleCellAlleleExperiment
Commit: 8f306448be842ea1ba8dbdc97e0b69f114eb948b
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-26 12:16:23 +0100
Commit message:

 changed read in for the lookup table; updated all examples/tests/vignette according to new read in; deleted example_test parameter in read_allele_counts() function; added package level man page (currently colliding with SCAE-Constructor)
 
Package: SingleCellAlleleExperiment
Commit: f4bfddc169d2da0f29c0600d1e122ebce17b6dd1
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2024-03-22 12:01:56 +0100
Commit message:

 added installation section to vignette; removed .Rproj file; made some codestyle changes across all files containing code
 
Package: FLAMES
Commit: 94fa129d3ba7b2e4a3580bb53a134d667383d0c0
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-27 16:29:08 +1100
Commit message:

 update ssw
 
Package: Rsubread
Commit: e5b232195e2f4507bc592386f601f71d8435b293
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2024-03-27 13:20:56 +1100
Commit message:

 removed a big that having very few reads written reversed in BAM output from cellCounts.
 
Package: SingleCellExperiment
Commit: 69aa3c7203819385ecdf640eaa84302bf739373d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-26 17:43:09 -0700
Commit message:

 Minor docfix.
 
Package: SingleCellExperiment
Commit: 8407934af979927c31c073bac1ad4ea07bbd16db
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-27 01:32:09 +0100
Commit message:

 Check for NULL metadata when returning a matrix from *Pair() functions (#74)

This auto-fills the sparse matrix with TRUE values, just to avoid outright failure. 
Package: IgGeneUsage
Commit: 309f5468c974d4fd795ef5ec43213fe14cc6ea41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 23:50:43 +0100
Commit message:

 update of case study 5
 
Package: EpiTxDb
Commit: d628bc86814af06628ae7cdf409cf8576254749f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:25:19 +0100
Commit message:

  Changed config after default branch rename
 
Package: Structstrings
Commit: 351ac7c49a97db0f0dbceda03367b4ce13c33a85
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:23:32 +0100
Commit message:

  Changed config after default branch rename
 
Package: Structstrings
Commit: 46abcd101da164a1c3e83284ca2fa89dff89d53a
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:59:25 +0100
Commit message:

 Update README.md 
Package: tRNAscanImport
Commit: 1ac7921d0e6cf00c27a1dd2af3d94f24549246b5
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:18:42 +0100
Commit message:

 Changed config after default branch rename
 
Package: tRNAscanImport
Commit: 716afc5f429adaa1b75fa78b1c3f2966e954053f
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:14:04 +0100
Commit message:

 Update README.md 
Package: tRNAdbImport
Commit: da09c4c9f8a434a76d0afa1e78680edc3c579ca3
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:17:19 +0100
Commit message:

 Changed config after default branch rename
 
Package: tRNAdbImport
Commit: 3c637daf5b24da4ebf04626f1086f1941bfba5e2
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:13:43 +0100
Commit message:

 Update README.md 
Package: tRNA
Commit: eaf74ae73343fc4d18297340de507373886e2052
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:13:49 +0100
Commit message:

 Changed config after default branch rename
 
Package: Modstrings
Commit: d020ab16a6d18a6eaab09756a2a4e1b4c6e0a0cb
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:10:57 +0100
Commit message:

 Changed config after default branch rename
 
Package: Modstrings
Commit: 25dd0b47c603b404e530b90e9f6588a4c09fe553
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:01:12 +0100
Commit message:

 Update README.md 
Package: RNAmodR
Commit: edc8dbf321f830eedb956866fb03eb4b8ad59cc9
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 22:03:09 +0100
Commit message:

 Changed config after default branch rename
 
Package: RNAmodR
Commit: 184805de98b17de5e47f1128288e09e8094385cb
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-26 21:55:25 +0100
Commit message:

 Merge pull request #28 from hpages/master

Replace GenomicFeatures::makeTxDbFromGFF with txdbmaker::makeTxDbFromGFF 
Package: RNAmodR
Commit: 51dcdb43dd5de26b21fadfb71082a098fdb60d35
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:15:39 -0700
Commit message:

 Replace GenomicFeatures::makeTxDbFromGFF with txdbmaker::makeTxDbFromGFF
 
Package: RNAmodR
Commit: 7423101b1bc54a90a81f9af074308e78e1f99a79
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:21:43 +0100
Commit message:

 Update README.md 
Package: scaeData
Commit: b6a053d22fcdd73ffa2f5b5d89aeff9ae86c3215
Author: AGImkeller <89422241+AGImkeller@users.noreply.github.com>
Date: 2024-03-26 21:39:18 +0100
Commit message:

 Merge pull request #4 from AGImkeller/bioc_review

Revision per Bioconductor's feedback 
Package: scaeData
Commit: 1dd32f26cf9eb175fc5e8fc7d05616007b2961b8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:11:09 +0100
Commit message:

 updating the GHA to reflect the newly added dependency, to be picked (for now) from github
 
Package: scaeData
Commit: 4dc73463a83f68c732bf5d2654a1a3430c567865
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:38 +0100
Commit message:

 version bump, 0.99.3
 
Package: scaeData
Commit: cf4073a556517ba1e6ad495c5b1844299a115925
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:04:27 +0100
Commit message:

 edited News with latest changes
 
Package: scaeData
Commit: 99a11f497f14a9a801d581a17dde330f8d69d00a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:02:22 +0100
Commit message:

 adding SCAE as suggested dependency, and indenting a bit the lines of the DESCRIPTION file
 
Package: scaeData
Commit: c68cde6845cc59ebe84e5d3f6b57daca2903aa26
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-26 21:01:08 +0100
Commit message:

 evaluating the last chunk now, to allow a full end-to-end run
 
Package: scaeData
Commit: f59bb236a4774881418cd7d8a53936175f74f2ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:20:52 +0100
Commit message:

 explicitly reporting LICENSE.md in .Rbuildignore
 
Package: scaeData
Commit: 5e0fd32efd174032c979d6c390bafd405cc107a0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 23:15:33 +0100
Commit message:

 Adding also Matrix as suggested dependency, as it is also used in the vignette
 
Package: scaeData
Commit: 330a97d84d9e63d0da6915198009c69a3a468885
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:45:07 +0100
Commit message:

 few adjustments in the vignette last chunk - still need some fixes if we want that to be fully eval'd
 
Package: scaeData
Commit: b901e3c298b9cd9ed1ab23e8cd215ca7c8c65345
Author: Ahmad Al Ajami <ahmad.alajami@kgu.de>
Date: 2024-03-25 22:05:44 +0100
Commit message:

 updated the vignette per bioc reviewer's feedback
 
Package: scaeData
Commit: 5bd68f1a6bc0c79eacd6b6767b19f6e0f9efae7c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:31 +0100
Commit message:

 adding rendered manpage, with correct aliases (scaeData/scaeData-package/scaeData-pkg)
 
Package: scaeData
Commit: 22467c6f8622983e003cdae797ce2748eeea0565
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-25 22:02:00 +0100
Commit message:

 adding pkg-level documentation, as suggested in the review
 
Package: splatter
Commit: ea842a225ba46ed365deddd590eea56c88e61543
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:18:58 +0100
Commit message:

 Update NEWS and bump version
 
Package: splatter
Commit: ed1afeaee603f10d92272194c170110500731ff3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 21:09:59 +0100
Commit message:

 Minor fixes from BiocCheck
 
Package: splatter
Commit: 8614ad6c181b3b0034ae181ce9075a9c5cd2dee5
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:53:25 +0100
Commit message:

 Only ask to install dependencies when interactive
 
Package: splatter
Commit: 9472e2fcaa29253ce5d0d19ca370372182dc6b32
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 20:50:23 +0100
Commit message:

 Add @keywords internal/@noRd to function docs
 
Package: splatter
Commit: 81cf3e7b0da6235e474527427a498e98f8113882
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 17:58:31 +0100
Commit message:

 Restyle code

Use something more modern/sane with styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
(and some adjusting)
 
Package: splatter
Commit: 31a986716ad397df127d563eb0443c3e01807e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:44:01 +0100
Commit message:

 Update DESCRIPTION

Add GitHub usernames and Bioconductor URL
 
Package: splatter
Commit: 411b3faebc22848da564d6b228545841e175b366
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:38:13 +0100
Commit message:

 Replace package man page with usethis auto page
 
Package: splatter
Commit: ceac288173349048f831ed3e11a55a45eb156d76
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:36:39 +0100
Commit message:

 Bump roxygen version to 7.3.1
 
Package: splatter
Commit: bd62c5906a72681b95861152f7c1401b45106e92
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:35:05 +0100
Commit message:

 Specify expected warnings in tests

Removes unhelpful output
 
Package: splatter
Commit: 7b8b13c3613cfd992519392896a7df7399c2c8ea
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:22:31 +0100
Commit message:

 Properly sink output in scDDSimulate() when verbose=FALSE
 
Package: splatter
Commit: 0454898d63cc7f1a2ed5c45e5726029f063b8ba0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:54 +0100
Commit message:

 Set verbose=FALSE in tests for scDDSimulate()
 
Package: splatter
Commit: 1fb0eff93f4bb8099cd572b18c02501e03377aad
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-26 14:17:27 +0100
Commit message:

 Properly sink output in BASiCSEstimate when verbose=FALSE
 
Package: rRDP
Commit: 80028da1529d2a76862bd81f41cdd570f0f7ded2
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:17:20 -0500
Commit message:

 Upgrade to RDP 2.14.
 
Package: rRDPData
Commit: 973e13232d3f5b7448fd86fef5bb6e43ae816510
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 15:02:00 -0500
Commit message:

 updated man page.
 
Package: MGnifyR
Commit: 60c01d2b09cfa9ffe86228e528b1389a7cf27104
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-03-26 20:51:26 +0200
Commit message:

 Update vignette
 
Package: MGnifyR
Commit: f52572187eca6430a614da13ee64dca62c76acc2
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-26 20:31:56 +0200
Commit message:

 Final changes for Bioc submission (#40)

* up

* up

* Fix links in ?MGnifyR

* up

* up 
Package: VariantAnnotation
Commit: 038a3fc1a8da381a39bd542b2340578b264b4525
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:53:04 -0700
Commit message:

 The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
 
Package: BSgenome
Commit: 96ff87f2d9963d2fb41bedd6a030294a3696fa4f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 11:46:31 -0700
Commit message:

 The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
 
Package: MGnifyR
Commit: d6bb555d18119eeb093bf67ad0d292355fe6fd95
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-21 13:47:30 +0200
Commit message:

 Add findingpheno acknowledgement (#39)

 
Package: MGnifyR
Commit: 8e2080f5bbeffbb9550778f9ecdab8ce44949bf0
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-20 16:03:18 +0200
Commit message:

 Enable GHA for mac and win (#38)

* Enable GHA for MAC and WIN

* up 
Package: rRDPData
Commit: 5d7bf939382a928846d13c985492ee5944b80e35
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 13:18:18 -0500
Commit message:

 Update data to the RDP Classifier 2.14 released in August 2023. Added fungalits_unite, fungalits_warcup, and fungallsu.
 
Package: DegNorm
Commit: 2e3e9c950849869289b8651f8c735aba4774cff5
Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2024-03-26 13:17:24 -0500
Commit message:

 txdbmaker correction
 
Package: recount
Commit: fea8aa399f4cdb39051720e83e8b0022e6605203
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:48:49 -0400
Commit message:

 Use GHA with BioC 3.18
 
Package: recount
Commit: 08104fbaf45183caced5c3f957d59a424eee2627
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:44:57 -0400
Commit message:

 v1.29.1 -- bump version after merging https://github.com/leekgroup/recount/pull/24 by @hpages. Thank you!
 
Package: recount
Commit: 60d0e5e2e1b74cadde290b714eb0ba212ea3eddc
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2024-03-26 13:42:05 -0400
Commit message:

 Merge branch 'devel' of github.com:leekgroup/recount into devel
 
Package: recount
Commit: 4d918700995a73fc30de187e2a88660733925450
Author: Leonardo Collado-Torres <lcolladotor@gmail.com>
Date: 2024-03-26 13:41:51 -0400
Commit message:

 Merge pull request #24 from hpages/devel

The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker 
Package: recount
Commit: e95d6fb01d8f9509cf36a136ccfa141ea34d8bc5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-26 10:31:05 -0700
Commit message:

 The makeTxDb*() functions have moved from GenomicFeatures to txdbmaker
 
Package: rRDP
Commit: 924e72780c20d105602f55c83139f4096cb04926
Author: Michael Hahsler <mhahsler@smu.edu>
Date: 2024-03-26 12:31:50 -0500
Commit message:

 We use now Roxygen and markdown.
 
Package: smartid
Commit: b958720e44be896b1973d826243de7bb47565b2b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 04:07:22 +1100
Commit message:

 Add package:: before colData to avoid no visible function.
 
Package: smartid
Commit: 03dc19f19f2b09eb884f4ac2eee86d05a08fb40d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:52:01 +1100
Commit message:

 Include package.R file to avoid undefined function.
 
Package: smartid
Commit: e6ba0364123a2682ece357ca279565b63476fdc4
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:32:08 +1100
Commit message:

 Removed un-used commented codes and update vignette.
 
Package: smartid
Commit: 892a8f38a6add7898d5f53b386326b5c011e4457
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 03:02:00 +1100
Commit message:

 Remove un-used codes and use && instead of & in condition.
 
Package: smartid
Commit: 34bf266e44ce38b9db19152538357871b75e4243
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:55:33 +1100
Commit message:

 Fix metadata slot problem.
 
Package: smartid
Commit: 470b22fbe50c3fc465e97ded002b920c54184f85
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:25:19 +1100
Commit message:

 Use 4 spaces as indents, replace accessors @ with functions.
 
Package: smartid
Commit: 3002a02250d6be1f2645f843b1beea950624c610
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 02:00:55 +1100
Commit message:

 Replace sapply with vapply and add drop=F in [].
 
Package: smartid
Commit: baa33a1774b46b4d13c8eda8c0599f630c24c0a8
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:59:38 +1100
Commit message:

 Replace print with show.
 
Package: smartid
Commit: 751531f514cb6c67098aa9e484e377e28123711d
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:43:16 +1100
Commit message:

 Styler and spell check.
 
Package: smartid
Commit: 02d615d785e5be88f6087b156263b225f2e69eaa
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:17:13 +1100
Commit message:

 Update bioc-check yml file.
 
Package: smartid
Commit: cdd877d3575baabdd447ed8044a169bccf99d7f3
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-27 00:13:41 +1100
Commit message:

 Update vignette and bioc-check yml file.
 
Package: smartid
Commit: ec25f84216708d507d315f3906b638f65d79340b
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 23:37:46 +1100
Commit message:

 Bump R version to >= 4.4 and update vignette and function details.
 
Package: CytoMethIC
Commit: f2d0383bb99f7f41757ee06fcc6eaad86e5cc7f4
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:56:23 -0400
Commit message:

 update NEWS
 
Package: CytoMethIC
Commit: 91f81855fbda9a57f0b73ae28db898afd1d419b2
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:16:02 -0400
Commit message:

 bump to 0.99.26
 
Package: CytoMethIC
Commit: 2fe98f309e7641eb5f8e625c811d907074beb28a
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-03-26 12:15:06 -0400
Commit message:

 Review 1 Changes
 
Package: CytoMethIC
Commit: 7c292c9fcd4048cc617f5dd25aef79f735a9cd10
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-03-25 13:11:37 -0400
Commit message:

 minor, message omitted
 
Package: TCGAbiolinks
Commit: 2cfe182595da1bcff32446caf525f096dbe54863
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:40:05 -0400
Commit message:

 Minor code style changes
 
Package: TCGAbiolinks
Commit: 3f5efb99525e6fc0925331db989081f178ab97e8
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2024-03-26 11:36:07 -0400
Commit message:

 Removing dnet from package as it is not available in CRAN.
 
Package: QFeatures
Commit: f1e56d1dc830586388113327b62a383154978a00
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:14:32 +0100
Commit message:

 load more data (not lazyLoading anymore)
 
Package: QFeatures
Commit: 415ba77b8748c1ce7a23495527a172cd23208177
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 16:10:01 +0100
Commit message:

 load necessary data (not lazyLoading anymore)
 
Package: QFeatures
Commit: af5f841ace1e24916b72a80c394b11e40ece7c82
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:58:59 +0100
Commit message:

 minor fix based on BiocCheck
 
Package: QFeatures
Commit: cc42c7ab4493b63c2e9306604aa368b5cd566677
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:53:25 +0100
Commit message:

 udpate unit test
 
Package: QFeatures
Commit: c703655e67ead820b04aa0111dc007b7a579ac02
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-26 15:38:19 +0100
Commit message:

 fix as.vector() - closes issue #203
 
Package: QFeatures
Commit: 21f74a8ba049fa53fc5fda549fdb9f4ae64dbc75
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 21:02:03 +0100
Commit message:

 update notes #1199
 
Package: QFeatures
Commit: b0b8c9a2a5c728ee4dacb6a4c1810824cf8dd7b7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-03-07 06:57:55 +0100
Commit message:

 add notes from issue 199
 
Package: cypress
Commit: 3c8ef7de9f097bcda0cd5925cee0a864f802a4ba
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-26 10:24:49 -0400
Commit message:

 edit for vigenette

edit for csDE
 
Package: multicrispr
Commit: 125c9082bbd264e8a98c9698319f451cdf1ba344
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 14:27:39 +0100
Commit message:

 R CMD check Fixes
 
Package: multicrispr
Commit: 08b95964bcd8d659aec85d9c28cb4ba1633d7afd
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:59:45 +0100
Commit message:

 R CMD check Fixes
 
Package: multicrispr
Commit: 63f75879aff31a9d0fc18e0b121935a006209dcc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-26 13:39:30 +0100
Commit message:

 Eliminate `assertive.base`
 
Package: mia
Commit: ecd661f43b39cc2e087534d21d475e69e6f8a944
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-14 10:26:38 +0200
Commit message:

 getExperimentCrossCorrelation and SampleMap (#504)

 
Package: mia
Commit: aa1d488af9981075d52f4a5805d86e0419447690
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 15:25:59 +0200
Commit message:

 getPrevalence, NA values (#486)

 
Package: mia
Commit: 6a356cd826d45aa5dc9a3b9cf0cbcff795a9de41
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-05 12:25:10 +0200
Commit message:

 cluster: fixes (#477)

 
Package: mia
Commit: 5f18f82539aa191e226033637c9008cf2b05aabe
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-04 16:42:03 +0200
Commit message:

 Add pages to pkgdown (#500)

 
Package: mia
Commit: 45544f3a4823f8b4af32dcf6dafc3dedeb98fe58
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-03-04 15:51:12 +0200
Commit message:

 Deprecate taxonomyTree and addTaxonomyTree (#496)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: TuomasBorman <tvborm@utu.fi>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi> 
Package: mia
Commit: 1269d9c6a3b70c1e8323748c6a4bc0a780510f77
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-03-01 21:48:03 +0200
Commit message:

 loadFromMetaphlan: support taxonomy-named column (#499)

 
Package: mia
Commit: d159f74430cdf193ec3dca25f1c56a3ee2b4b672
Author: Himmi Lindgren <137785061+himmil@users.noreply.github.com>
Date: 2024-02-28 11:14:27 +0200
Commit message:

 New arguments for perSampleDominantFeatures (#479)

Co-authored-by: Leo Lahti <leo.lahti@iki.fi> 
Package: mia
Commit: be6bcbd1711d31bb9ae731edc2e6abb625823310
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-02-26 14:16:12 +0200
Commit message:

 Fix splitOn bug (#495)

 
Package: mia
Commit: 97b01b62cf9ad820bc7d2ec659783f6b8bb56c3a
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-21 18:17:15 +0200
Commit message:

 agglomerateByRank fix: empty ranks (#493)

 
Package: mia
Commit: 61f2d16cbf6dabf90a8c2435d057937b35220eed
Author: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>
Date: 2024-02-19 11:55:52 +0000
Commit message:

 Clarify pseudocount argument (#490)

Co-authored-by: artur_sannikov <artur.sannikov96@gmail.com> 
Package: mia
Commit: 4d1a093aa937a9c66d60d56445328ff05c47e580
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-02-13 12:32:43 +0200
Commit message:

 agglomerateByRank: agglomerate tree fix (#487)

 
Package: mia
Commit: 2d0c38d47c2ad5b7cfc4bf9f890d07cd6c3488b6
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-01-30 16:09:58 +0200
Commit message:

 loadFromMetaphlan: support for strain level (#485)

 
Package: rGREAT
Commit: 70a34fb23aed6f5534930ab59f1383e01e4057b9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:28:29 +0100
Commit message:

 positions are enforced to be integers
 
Package: rGREAT
Commit: 18de7beca19a01008272679e7b57fbe5d6f25a92
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:20:19 +0100
Commit message:

 remove o/so files
 
Package: rGREAT
Commit: de671d63755bf7dadd39b7fa5799fe7567b48d79
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 10:19:21 +0100
Commit message:

 use try() to wrap seqlevelsStyle() to get rid of the error
 
Package: gDRstyle
Commit: ebeb99a552c9ba4d02c4dc659827d3e45707bd34
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-03-26 09:21:39 +0100
Commit message:

 Merge pull request #79 from gdrplatform/add_as_cran_flag

feat: add support for running `R CMD CHECK` with `--as-cran` 
Package: gDRstyle
Commit: c7d5c6b2c003eeaadc31c8ac9d7c54c367327017
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:56:51 +0100
Commit message:

 chore: update gititnore rules
 
Package: gDRstyle
Commit: cb983a9530f0e485abf61bdc64158a8fda35f200
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-26 06:53:00 +0100
Commit message:

 chore: udpate deps
 
Package: gDRstyle
Commit: 80b265ad54caa764ab1fd07371a8124c35de5fb1
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-03-25 18:30:49 +0100
Commit message:

 feat: add support for running `R CMD CHECK` with `--as-cran`
 
Package: simona
Commit: fe29f94c0ed1a4f47205a259346fa6f882a495fa
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:43 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: simona
Commit: b250510d53dde1f934e0209b08bbcd752b281c08
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-03-26 08:58:28 +0100
Commit message:

 update docs
 
Package: simona
Commit: 764a58bad0a119b93f565d37dcdfc934f185b5ab
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-29 11:07:54 +0100
Commit message:

 add 'alternative_terms' argument in create_ontology_DAG()
 
Package: simona
Commit: 6a1aeef188fe5fff9b8a88db2a48c44a63526081
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-27 20:30:55 +0100
Commit message:

 update website
 
Package: DAPAR
Commit: 642f0cdd44111903d4ad219f0fe274ec43026d12
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 08:14:40 +0100
Commit message:

 Delete limmaAnalysis2.R
 
Package: DAPAR
Commit: 11fd87c516f99835b354e358084aed18969a09c8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:25:07 +0100
Commit message:

 Delete R/limmaAnalysis2.R 
Package: DAPAR
Commit: 76f854364bd7b4e644e562b1674b867b7691a31f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-03-26 04:21:53 +0100
Commit message:

 Update limmaAnalysis.R 
Package: SpatialFeatureExperiment
Commit: 9e6586feba5b93638c8ca6dcb7d9660c1ac6f2ae
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2024-03-25 22:10:26 -0700
Commit message:

 Temporary fix
 
Package: smartid
Commit: fe762f19636d6ada24f4faf01a45b4815d404203
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:49:47 +1100
Commit message:

 Fix note for no visible binding variable.
 
Package: smartid
Commit: a72ecd64066d968857f8fcf68689636fb51ef85f
Author: Gene233 <chen_jj97@163.com>
Date: 2024-03-26 15:33:43 +1100
Commit message:

 Added test for gs_score function and bump version.
 
Package: tidytof
Commit: 4fce362df3f0193b14f263a4788dc2ab0f711bf9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:26:06 -0700
Commit message:

 increment version
 
Package: tidytof
Commit: 6a6be801a470b222158e868b6f947d5cb53bc6aa
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 21:05:10 -0700
Commit message:

 update tests
 
Package: motifTestR
Commit: d7f3201b529d06381089a0ea91619054426877dc
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-03-26 13:34:15 +1030
Commit message:

 Added script references in man pages
 
Package: IgGeneUsage
Commit: d43cb097c073d428546aeed99c946a38e7084bb1
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-26 04:22:39 +0100
Commit message:

 update bugfix in paired analysis
 
Package: cypress
Commit: 65260e797f6afbbacd58a5d61808ed2f49e9868d
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 22:20:53 -0400
Commit message:

 update for bpparam

update for new item bpparam
 
Package: matter
Commit: b32a112d9d5a4780c80541b53eb130f28f0b1b67
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:11:06 -0400
Commit message:

 v2.5.10 bump
 
Package: matter
Commit: 1b7c35a9402e1fe8a05312eae720a044e84a9fb9
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 22:10:10 -0400
Commit message:

 mi_learn()
 
Package: matter
Commit: f6626a51694bb7a9fa9a1f380c2e9d5a7bedf0d1
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 19:26:47 -0400
Commit message:

 mscore()
 
Package: matter
Commit: 29df2313a810ad231e910efc6cc0a2e8a6e692dc
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-25 17:20:39 -0400
Commit message:

 sgmix()
 
Package: matter
Commit: a365b2bf958ace0386526377447e1596b9bf3508
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-24 21:27:11 -0400
Commit message:

 nscentroids()
 
Package: matter
Commit: fe7e7886bb08b7ebf43fce01825be84caf7e263a
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-22 21:43:13 -0400
Commit message:

 pass verbose to distfun in fastmap()
 
Package: matter
Commit: 65eb8a972841fe5fd71e1c1dc3933938330914da
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 14:40:38 -0400
Commit message:

 rowscale()/colscale() set corresponding attr to NULL when center/scale=FALSE
 
Package: matter
Commit: 8e021e370f838f07b606ba809bde075ccfaecd81
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-22 12:16:40 -0400
Commit message:

 vectorize predict.pls() over k
 
Package: matter
Commit: 0fb32e66534a57ff74a60f196c557eaee77d7f1c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:59:12 -0400
Commit message:

 rm nchunks arg from predict.pls
 
Package: matter
Commit: 707c317ff9cfd96204dfeeb7c41900f376a41a4f
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-21 21:05:45 -0400
Commit message:

 add nchunks arg to prcomp() and pls()
 
Package: matter
Commit: 4e3b25d97f548d1c7ee3fc30872134839e8442ae
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-19 15:04:42 -0400
Commit message:

 fix issue in simspec()
 
Package: matter
Commit: b7d76ceec98555fd3d7b2837c73a7ac8805f62bc
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-18 13:04:44 -0400
Commit message:

 export linear_ind() and array_ind()
 
Package: matter
Commit: c961d7008aef888f41c84388f6ce150032e7d283
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 23:04:39 -0400
Commit message:

 v2.5.10 fix potential infinite loop in binpeaks()
 
Package: matter
Commit: 9e24dc625a9c4bf65bda52da129682f945adbc89
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-17 20:57:38 -0400
Commit message:

 v2.5.10 remove duplicate peaks in findpeaks_cwt()
 
Package: matter
Commit: a0d2c5fc3f83cc1a79a04bbc9f862a9720416784
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 20:45:40 -0400
Commit message:

 v2.5.10 update estres() arg tol.ref => ref
 
Package: matter
Commit: ef637de8d4f14348c99a077e4d211bd39dc9e4d2
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 16:55:01 -0400
Commit message:

 v2.5.10 peakheights() + bug fixes
 
Package: matter
Commit: eeea9a5b1c7ea8c97a1c02c8164a28a3e480e739
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-16 12:39:35 -0400
Commit message:

 add peakheights()
 
Package: matter
Commit: 0d86ffda4a01a84e343dc51181bfdebf9a40aa4c
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:22:17 -0400
Commit message:

 reorder approx interp codes
 
Package: matter
Commit: d538c891325071f77537b532c2ec4096424f7bc8
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:07:51 -0400
Commit message:

 fix as_tol() again
 
Package: matter
Commit: a7a716a9bc1343c90333946486c9a02c97517746
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 22:04:53 -0400
Commit message:

 update as_tol()
 
Package: matter
Commit: 98e01e21b4a0a8958a550d4eddbb08fb2e38967e
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2024-03-15 16:15:26 -0400
Commit message:

 rename some variables
 
Package: matter
Commit: 273666ff07ad20bf2aa7def7a948ed84c58dd2c0
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2024-03-13 16:00:35 -0400
Commit message:

 v2.5.9 fix outfile write order in chunk apply functions
 
Package: standR
Commit: 23da1fae3c6a97c1b07301a793568239418443c5
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:04:03 +1030
Commit message:

 i Please enter the commit message for your changes. Lines starting
 
Package: standR
Commit: 5b386298917e7b2d6b325903a07b4209075ea2aa
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-26 10:03:21 +1030
Commit message:

 fix bug in citation page
 
Package: M3Drop
Commit: cced8b74275e96bcef3f5c7680840a353f7b44c8
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:22:33 -0400
Commit message:

 fixed scater version compatibility
 
Package: M3Drop
Commit: 928dc1662cf8c54c44f8b63500524356a7ebccdc
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 18:10:41 -0400
Commit message:

 Remove old scater support
 
Package: hdxmsqc
Commit: cfddc4754bdb6d90bb597d78ee267451bd8222ab
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 21:51:08 +0000
Commit message:

 updated NEWSs vignette describes how to pefrom quality control for
 mass-spectrometry based  hydrogen deuterium exchange experiment.
 
Package: txdbmaker
Commit: 971331726b80d8d7109b7e9f9436935fc0651c60
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 15:04:20 -0700
Commit message:

 update TODO
 
Package: IgGeneUsage
Commit: 936fed9832a4a25b117df2508993877322c2279f
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 22:48:49 +0100
Commit message:

 update before more serious tests
 
Package: txdbmaker
Commit: 09fe795bb3c622b2139a9044e634a6bd71682f59
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 14:48:03 -0700
Commit message:

 remove markdown from Suggests (not needed)
 
Package: AnVIL
Commit: 40451868ee43d9fbe1baaa28f9f88277d321e6c5
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:28 -0400
Commit message:

 version bump 1.15.9
 
Package: AnVIL
Commit: a24698b30e2bc6f8c32c5d212459666321a88597
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 17:43:14 -0400
Commit message:

 use assertions from BiocBaseUtils
 
Package: tidytof
Commit: 2f40d01f461bd9c25eeb3d5520672e1430f104c5
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 14:30:51 -0700
Commit message:

 update tests/dependencies
 
Package: pathview
Commit: 24250b848480afb1935540479d7ff56b6b4c6427
Author: Weijun Luo <luo_weijun@yahoo.com>
Date: 2024-03-25 17:38:52 -0400
Commit message:

 version 1.43.1
 
Package: M3Drop
Commit: 0c58f40baa90f678af2c9444ec2711fb01833fb9
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-25 17:26:09 -0400
Commit message:

 Update Version & Date
 
Package: BloodCancerMultiOmics2017
Commit: d6eaa9ce29a3eda24ff9d25de7b0c7b492b84365
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:43:18 +0100
Commit message:

 version bump in devel
 
Package: BloodCancerMultiOmics2017
Commit: 9d4a88533c0be5e00e5e3b53d8542dbddeaa538c
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2024-03-25 21:40:48 +0100
Commit message:

 bug fix: change guide-box to guide-box-right
 
Package: GenomicAlignments
Commit: 3479ba78b0b99ec5a496adf1044f7e1cc72bf18e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 12:52:40 -0700
Commit message:

 minor edits + version bump
 
Package: GenomicAlignments
Commit: 5410f9c597a250b73d2490bad316ff1eaba924b5
Author: Halimat Chisom Atanda <66901562+Chisomgold@users.noreply.github.com>
Date: 2024-03-26 05:47:57 +1000
Commit message:

 Convert WorkingWithAlignedNucleotides from Rnw to Rmd (#22)

Co-authored-by: jwokaty <jwokaty@users.noreply.github.com> 
Package: ASpli
Commit: 6ffebd3c49c75f240d416cc8942ef4a5b8d4bba4
Author: achernom <algo107@gmail.com>
Date: 2024-03-25 16:16:15 -0300
Commit message:

 update version numbering
 
Package: ASpli
Commit: 06d26e863ea59ef1c3a071c9640f989fed599afc
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:47:26 -0300
Commit message:

 Correct some glitches on man/*Rd docs
 
Package: ASpli
Commit: 87346eab659f0e957629ccf367fb85b4c6eb72f1
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:15:33 -0300
Commit message:

 update package version and date
 
Package: ASpli
Commit: 6f08d3d62184d69acafc1e1ed9c53ecfbd72ea8c
Author: achernom <algo107@gmail.com>
Date: 2024-03-22 16:12:43 -0300
Commit message:

 correct package version comparison to correctly build vignettes
 
Package: ASpli
Commit: a1395d7ec01452da5d16a659afe8d2e840a7f43f
Author: achernom <algo107@gmail.com>
Date: 2024-03-20 15:43:55 -0300
Commit message:

  makeTxDbFromGFF() has moved to the txdbmaker package, so now call txdbmaker::makeTxDbFromGFF()
 
Package: tidytof
Commit: 61551d4000427c17aa32241bab71277b0a3f9c57
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 11:37:10 -0700
Commit message:

 increment version
 
Package: tidytof
Commit: e7d05e4a31a8f9f89585731aaa79f5364aeb9530
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 10:44:40 -0700
Commit message:

 update testthat.R
 
Package: hdxmsqc
Commit: 2d035bfea50d9d4c6bd55b81bb6cf044601ecc3e
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:32:40 +0000
Commit message:

 more documentation
 
Package: hdxmsqc
Commit: 48f2e9562fec18801ec9c979f673e260dd96486a
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-03-25 18:30:32 +0000
Commit message:

 package updates according to review
 
Package: saseR
Commit: a4790cd45151b53fb5dfe72da7b6847e4d4a47e0
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2024-03-25 19:19:34 +0100
Commit message:

 add binGenome functions from ASpli
 
Package: cypress
Commit: b58203237a3f73063eacd4cc3f24033c163e1470
Author: Shilin Yu <sy597@georgetown.edu>
Date: 2024-03-25 13:59:59 -0400
Commit message:

 edit for comment

oding modified in compliance with BioC requirement.
 
Package: IgGeneUsage
Commit: 451f61add5d6e7be308fb27edf72d7fae04eff3e
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:41 +0100
Commit message:

 new models commited
 
Package: IgGeneUsage
Commit: 898ffacbcda76ca4e9642170f3dfda8d86092fb7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 18:49:10 +0100
Commit message:

 paired analysis integrated
 
Package: BASiCS
Commit: cc133767c2f35ee840b875545e2121a84e2341fe
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2024-03-25 17:34:38 +0000
Commit message:

 bug fix in subset method
 
Package: BSgenomeForge
Commit: a8380e769627939467c6f25bae7d0c0ef0d28ea7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-25 10:20:08 -0700
Commit message:

 make vignette compatible with rmarkdown 2.26
 
Package: tidytof
Commit: b2ea3cfa2377dd71fa59a30398817b2128349e5e
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:57:01 -0700
Commit message:

 increment version
 
Package: tidytof
Commit: 01685cc50d8ea79f917fe7bb069ca3658e548680
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 09:56:20 -0700
Commit message:

 update docs
 
Package: BiocCheck
Commit: 77fa12d556ced823f4312934e1a8ee95f2be2c2e
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:05 -0400
Commit message:

 version bump 1.39.27
 
Package: BiocCheck
Commit: 1b5a10fabe9ac54aa0c4fec4b468acd75fb1fb27
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-03-25 12:48:00 -0400
Commit message:

 avoid system call and use devtools::build
 
Package: ZygosityPredictor
Commit: 4fced5261740705d7c43a6c04564e2a0a9d6eeb2
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-25 17:38:58 +0100
Commit message:

 fixed build errors
 
Package: tidytof
Commit: b16165c8783c681995cd08f362e428df3aab9fe8
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:08:42 -0700
Commit message:

 increment version
 
Package: tidytof
Commit: e6f17a10c56ba3ffd7789ef98b265433436d4847
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-25 08:07:55 -0700
Commit message:

 update docs
 
Package: GrafGen
Commit: e7c0db1939f26daa375fbb27145a631c4b2234a4
Author: wheelerb <wheelerb@imsweb.com>
Date: 2024-03-25 11:49:50 -0400
Commit message:

 changes for review
 
Package: funOmics
Commit: 3bf724321d1f467149f43fa1a86cc2d710a14ae9
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:53:36 +0100
Commit message:

 UPDATE: vignette, DESCRIPTION v.5
 
Package: IgGeneUsage
Commit: 15ebf37ee22bdbca00967bb4365d1c39a02f46cb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:52:22 +0100
Commit message:

 update data generation
 
Package: IgGeneUsage
Commit: 9c56201ee92df58d7b1ec02585e7f313ad9ae713
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-25 15:33:53 +0100
Commit message:

 updated vignette to include data on analysis with replicates
 
Package: funOmics
Commit: 2020c21f798a4995983d697a99338a92039142ec
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:52:21 +0100
Commit message:

 UPDATE: add processing comment to vignette
 
Package: funOmics
Commit: 362f742cde6aa746070c25e45c494893e032a85e
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 15:43:01 +0100
Commit message:

 UPDATE: vignette from branch master to devel
 
Package: M3Drop
Commit: 5f314bfbade4e60d5b33940b10933ae5f18f0aff
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:48:46 -0400
Commit message:

 Properly fix PearsonResiduals Example
 
Package: M3Drop
Commit: 40da566dd2b192e5bef16867af39ac7b0f235ff7
Author: Tallulah Andrews <tallulandrews@gmail.com>
Date: 2024-03-22 14:41:27 -0400
Commit message:

 Fix Pearson Residual Example
 
Package: funOmics
Commit: d35bb2b7084b6343eedd5040c4d9c25503c0505c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:54:18 +0100
Commit message:

 UPDATE: DESCRIPTION & README from branch master to devel
 
Package: funOmics
Commit: e900a3df88713b6df8aeb772a8e486cd40f1e1f7
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 14:22:37 +0100
Commit message:

 FIX: Updated NAMESPACE
 
Package: zellkonverter
Commit: a64ff2d45173575ccdd83625df9b4077448a7dee
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:20 +0100
Commit message:

 Bump roxygen version
 
Package: zellkonverter
Commit: 52f0583cf919880b2f80a74112980917a7d03810
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:50:00 +0100
Commit message:

 Update WORDLIST
 
Package: zellkonverter
Commit: 24efa6a832fc75a89767ce2f75ce8b0a72a874b7
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:47:33 +0100
Commit message:

 Add environment for anndata v0.10.6
 
Package: zellkonverter
Commit: e8202deefea4d4452ba7fe01ca7c55026065b26c
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 13:05:08 +0100
Commit message:

 Improve warnings when converting matrices fails
 
Package: zellkonverter
Commit: 5834f30f072529d95add4d8ddefa7608ee84e577
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-03-25 12:56:14 +0100
Commit message:

 Correctly handle use_hdf5=TRUE with newer anndata

Class of the matrix read by Python is different

Fixes #114
 
Package: BioNERO
Commit: 5de1a416daf0f8ddae3b161cbe64f4681e9322e1
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:54 +0100
Commit message:

 Version bump in devel
 
Package: BioNERO
Commit: bea1a817518d345c3b325910dd33a17907c17975
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2024-03-25 13:39:24 +0100
Commit message:

 Added exp2gcn_blockwise() + increased unit test coverage
 
Package: escape
Commit: 99fed6482d39477cbff92171849cf68c067da5c9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-03-25 06:24:52 -0500
Commit message:

 silencing some tests
 
Package: multicrispr
Commit: a2e2370e1f0ec179529b23b41841e31754818959
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-03-25 12:05:37 +0100
Commit message:

 removed obsolete file `00_properties_has-dims.R`
 
Package: funOmics
Commit: 4bf583b2abc61369e685f08eafe48b994e269e5c
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:14:29 +0100
Commit message:

 UPDATE: update functions.R in branch with get_kegg_sets()
 
Package: funOmics
Commit: dd0ae6f72f27a115bca712ee33ea86279a545711
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 11:13:55 +0100
Commit message:

 UPDATE: update functions.R in branch with get_kegg_sets()
 
Package: PIUMA
Commit: 0b48fe985e1c92ce255cb8bfc21e68aaca0869c9
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:48:56 +0100
Commit message:

 0.99.6 BioC review
 
Package: funOmics
Commit: 3e963097488647c3c067f9bd34814de5650858bb
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:46:01 +0100
Commit message:

 FIX: un-ignore man/ documentation
 
Package: funOmics
Commit: 323db5fdd9ea82a9b336d943008b628ab159299b
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:43:42 +0100
Commit message:

 FIX: un-ignore man/ documentation
 
Package: funOmics
Commit: e7b15bd312400e3ec980cb4be6c815e086a82ebf
Author: elisagdelope <elisa.gdl95@gmail.com>
Date: 2024-03-25 10:20:37 +0100
Commit message:

 UPDATE: DESCRIPTION version
 
Package: PIUMA
Commit: eeb78895a59ddf16b898caf11b2176b73ecaef07
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2024-03-25 10:19:03 +0100
Commit message:

 0.99.5 BioC review
 
Package: Repitools
Commit: cf61279df20d622a2e736c9b190040a40d7cdea9
Author: Mark Robinson <mark@imlssherborne.uzh.ch>
Date: 2024-03-17 22:03:03 +0100
Commit message:

 ported a few things from Ringo
 
Package: decoupleR
Commit: 68bf5f61dbc5bcb6aa87d27896205e97a9ffb5be
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:34 +0100
Commit message:

 Bump version: 2.9.5 → 2.9.6
 
Package: decoupleR
Commit: 3fe7322e85d41d7c11e41957555f8b88cd27b55a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:38:28 +0100
Commit message:

 `test get_progeny mouse`: removed bypass on build servers, since the slow_doctest issue has been addressed in c1485180
 
Package: decoupleR
Commit: ea4ecbb11bc36ce407806dbb645f95063a997f26
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:31 +0100
Commit message:

 Bump version: 2.9.4 → 2.9.5
 
Package: decoupleR
Commit: c1485180d09a486a6125a93fdb2b7be19e1608f4
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 12:22:13 +0100
Commit message:

 disable OmnipathR slow doctest bypass
 
Package: decoupleR
Commit: 41d18b6c394b4cbb4e693a096413a0b2c3f68993
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:52 +0100
Commit message:

 Bump version: 2.9.3 → 2.9.4
 
Package: decoupleR
Commit: 41706b28a86fa12d5bb638190b85ee979198da8a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:47 +0100
Commit message:

 docs rebuild
 
Package: decoupleR
Commit: cf951afe98188ee4833fd07548c3ef901972d59d
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:41 +0100
Commit message:

 namespace updates by roxygen
 
Package: decoupleR
Commit: f085045fbe71d8f7264566deea326435c71cb842
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:28:25 +0100
Commit message:

 `test-gsva`: `minsize = 1` instead of 0
 
Package: decoupleR
Commit: 73df90bfe86f6bd6dd86654db4cd7ac68f233684
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:27:27 +0100
Commit message:

 `ulm`: use `tidyr::pivot_longer` instead of `reshape2::melt`; fixes R CMD check warning; + coding style
 
Package: decoupleR
Commit: 712e1863c5b1f344d2e21971cd8419a739e3a1ec
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:26:21 +0100
Commit message:

 `mdt`: updated to new `dplyr` API (`reframe`); fixes deprecation warning; + coding style
 
Package: decoupleR
Commit: 589a7650b05aac7754c85e40ff955b3ad2fbc8dd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:24:19 +0100
Commit message:

 `aucell`: updated to new `AUCell`/`BiocParallel` API, fixes deprecation warning
 
Package: decoupleR
Commit: 7dbd1156d1db084b9f2840884a6b1f06f1d31adc
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:51 +0100
Commit message:

 `gsva`: restored column order
 
Package: decoupleR
Commit: fdc1c22de6ecfc817bc8c3c7a9e5a6d874dda06f
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:22:32 +0100
Commit message:

 `gsva`: warn if `minsize == 0`
 
Package: decoupleR
Commit: 4ee8ac65da319dc968f006be7373dd12c766d7e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 13:45:41 +0100
Commit message:

 `run_gsva`: typo
 
Package: decoupleR
Commit: d623008d9d5a5f1677717d30c8cbff153296def8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:40 +0100
Commit message:

 Bump version: 2.9.2 → 2.9.3
 
Package: decoupleR
Commit: f1eae69259c21949295c8e8144fb59b7bc18656a
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 00:09:30 +0100
Commit message:

 do not import `GSVA` functions, it is suggested dependency
 
Package: decoupleR
Commit: cb3cdea89621e23784ce902a6583e07006d6fde9
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:30 +0100
Commit message:

 Bump version: 2.9.1 → 2.9.2
 
Package: decoupleR
Commit: 9498daae02ed4b0ea153f8b614aca24330cafe08
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 17:47:23 +0100
Commit message:

 `run_gsva`: updated to new `GSVA::gsva` API; fixed: `minsize` arg had no effect
 
Package: decoupleR
Commit: 26d6fed9fa19298e7977857b3e41d99b82896b50
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:56:25 +0100
Commit message:

 import `cor` and `pt` from `stats` in `.ulm_analysis`
 
Package: decoupleR
Commit: 50fe673f90cf42e2df5ffb22de36e194705747d8
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:52:48 +0100
Commit message:

 `tests/progeny-mouse`: disable on BioC build servers
 
Package: decoupleR
Commit: 11cde41c61bb0ad12a8217e2e6042d25bc2bd597
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 16:44:24 +0100
Commit message:

 `rbuildignore` removed `inst/doc`
 
Package: decoupleR
Commit: 79f24fe83703c0b9e7537fd88b76c027a9bbc3c2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:57 +0100
Commit message:

 Merge branch 'master' of github.com:saezlab/decoupleR
 
Package: decoupleR
Commit: c0ea29d354c868b7383485c2cbc2682097a77a84
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:13:48 +0100
Commit message:

 added bump2version config to rbuildignore
 
Package: decoupleR
Commit: ea34746e834996a1171d65a3b610fd722f4e08e4
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-02-20 14:43:45 +0100
Commit message:

 Updated readme
 
Package: DMRcate
Commit: 86df50bb8de4abe3aa040b75b94d7eb76eacc0d5
Author: timpet <t.peters@garvan.org.au>
Date: 2024-03-25 15:43:16 +1100
Commit message:

 DMRcate_2.99.4
 
Package: standR
Commit: b20520e18e4dfa80cb7a554b493f88fd2f9b2429
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:41 +1030
Commit message:

 version bump
 
Package: standR
Commit: 0755f5ae72bd18f3d1aedc84a663db63d1651545
Author: ningbioinfo <ning.liu@adelaide.edu.au>
Date: 2024-03-25 15:01:04 +1030
Commit message:

 add citation document
 
Package: tidytof
Commit: 59311df58335792ec13076a2a913db09d6ebc5c9
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 21:11:35 -0700
Commit message:

 increment version
 
Package: tidytof
Commit: fadf8982b18829fa4818ddba60a9efbc67c7e05d
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:39:01 -0700
Commit message:

 update docs
 
Package: tidyFlowCore
Commit: 0ede10bcc13c669fa02bbdedc851e49add9ed342
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:28:32 -0700
Commit message:

 increment version
 
Package: tidyFlowCore
Commit: 035f0343a4175c0e7e81e37c7a0570e8a26e5279
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 20:06:13 -0700
Commit message:

 Update docs
 
Package: tidyFlowCore
Commit: 238c4c4fd34f0b775c7d463b7924e9f1f2e159ea
Author: Timothy Keyes <keyes.timothy@gmail.com>
Date: 2024-03-24 19:46:20 -0700
Commit message:

 Delete tidyflowCore.Rproj 
Package: tidyFlowCore
Commit: 6305790efc339ca002e74b361e2f63098c026bcf
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-03-24 19:43:34 -0700
Commit message:

 remove unneeded files
 
Package: beachmat
Commit: a8fcb49857cd2a3745357b0dc51862e10962c712
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-24 18:22:27 -0700
Commit message:

 Initialization no-ops when supplied with an external ptr.

Downstream functions can call initializeCpp without worrying about whether
initialization has already been performed on the input.
 
Package: FLAMES
Commit: 16383263f35824d46c3502cbf4cbfa8756de30d5
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-21 10:23:30 +1100
Commit message:

 fix find_variants docs
 
Package: FLAMES
Commit: 29de37b374499cfed9e3de2425e5153e8388f801
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-21 10:18:33 +1100
Commit message:

 Merge branch 'devel' of https://github.com/OliverVoogd/FLAMES into youyupei/devel
 
Package: FLAMES
Commit: 1847f1575f76124c026757428b37e28aa3f28fbb
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 23:14:54 +1100
Commit message:

 fix gff not found error in quantification-only mode
 
Package: FLAMES
Commit: 4f9249190e886d5f49d6114047ef6e16f37b9c81
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-20 16:20:43 +1100
Commit message:

 update sc_mutations
 
Package: FLAMES
Commit: 40f1ae2b73e94ad22d6daaff6e63626acb6c5fbd
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 11:35:11 +1100
Commit message:

 move txdbmaker to suggests
 
Package: FLAMES
Commit: efbc6842b94bef22e3dfaeef2c36d555521eadd8
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-20 10:41:55 +1100
Commit message:

 use annotated transcript for quantification if there is no isoform  discovery result
 
Package: FLAMES
Commit: c2b1ff091b21dd2753a7ad951491138ebc3846ba
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:34:21 +1100
Commit message:

 Merge branch 'devel' of https://github.com/OliverVoogd/FLAMES into youyupei/devel
 
Package: FLAMES
Commit: c4017e4a73086e0f7cc3eb6d8baaf6d67704c3e2
Author: youyupei <youyupei@gmail.com>
Date: 2024-03-19 11:28:39 +1100
Commit message:

 update BLAZE to v2.2.*
 
Package: FLAMES
Commit: 2c531603e6f4b7e3451591e4e569fc975335a987
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:53:55 +1100
Commit message:

 misc: docs
 
Package: FLAMES
Commit: 4e02489cc7b5a92f2e5ca8ccfea0188ea9204823
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-19 10:25:13 +1100
Commit message:

 misc: docs, imports
 
Package: FLAMES
Commit: 9b36c0437484f1156c552ed96169505d92827aa9
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2024-03-18 20:01:35 +1100
Commit message:

 add find_variant
 
Package: FLAMES
Commit: e2cc3aca586284239fd4ef47fff640041bec47fe
Author: youyupei <youyupei@gmail.com>
Date: 2024-02-20 16:46:31 +1100
Commit message:

 add option to disable novel isoform discovery in bambu
 
Package: ZygosityPredictor
Commit: 8ecce1bbb2b6c10ee33f57556c8649e0f3dbfe07
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 22:12:51 +0100
Commit message:

 improved debugging
 
Package: ZygosityPredictor
Commit: a8f475cabc9782ef8795c0a292f29e75531fc40b
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:22:38 +0100
Commit message:

 fixed github issue #1... deviating chromosome annotations chr1 - 1
 
Package: ZygosityPredictor
Commit: 4424799b584504b0e34c4d6bbf539ac94b732eba
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-24 17:03:04 +0100
Commit message:

 fixed github issue #2... character tcn column
 
Package: ZygosityPredictor
Commit: 54b3e27b850aeb573bccf0de16e1b1594b71da67
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:27:42 +0100
Commit message:

 moved external debugging script into repo
 
Package: ZygosityPredictor
Commit: ed0dc64170c0e6640f47851e0cd8e5f7b05e0b58
Author: Rheinnecker <m168r@odcf-srv16.inet.dkfz-heidelberg.de>
Date: 2024-03-07 18:17:22 +0100
Commit message:

 included debug functionality
 
Package: bettr
Commit: c4fe4cd19105ba2d7c7022a64e16637dcaefa76e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:31:19 +0100
Commit message:

 Merge pull request #23 from federicomarini/add-stop-button

Add stop button 
Package: bettr
Commit: 75aae77de7508e05814b788fc502883cf72be43f
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 17:10:49 +0100
Commit message:

 Add button to close app and return data
 
Package: bettr
Commit: a4452006de66be5c8ab9ccfc61c6ca7428777026
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:35:51 +0100
Commit message:

 Bump version
 
Package: iCOBRA
Commit: 4c15d3ba9ba019ded7986852307c76cc6ce9e2aa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:06:43 +0100
Commit message:

 Add 'Close app' button to close the shiny app
 
Package: iCOBRA
Commit: 4c7234dbd1d9eb8b5bac2ac710199219144999d5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 16:00:26 +0100
Commit message:

 Bump version
 
Package: alevinQC
Commit: db44b143a1a87c959a1e96dcf74a04f212388dac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:56:46 +0100
Commit message:

 Add 'Close app' button to stop app and export data
 
Package: alevinQC
Commit: 40ac72e2333aaef603ed2dc062ef160ed4b74349
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:54:44 +0100
Commit message:

 Update package documentation format
 
Package: alevinQC
Commit: 5b3842ca3b8c46782381183362bb21ce208cedd5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 15:53:51 +0100
Commit message:

 Bump version
 
Package: GeneTonic
Commit: 6e695297b8a4f39c0bc3dd61d66e27211f5446ce
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:43:09 +0100
Commit message:

 forcing installation from source (?) for ComplexUpset to make it work
 
Package: GeneTonic
Commit: b4e8db05bd5a099c4408505302633b3b41aa8c17
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 14:14:42 +0100
Commit message:

 manually forcing the required version of ggplot2
 
Package: GeneTonic
Commit: 3cf6deb48ea1e96e03f76b67b52837ade2730d44
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:54:26 +0100
Commit message:

 version bump, 2.7.3
 
Package: GeneTonic
Commit: f836789aef94b28e2efb592ef9b65cf8e2e2f965
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-24 13:53:41 +0100
Commit message:

 back to deplyoing from macOS instance
 
Package: GeneTonic
Commit: 2fde72c320d29d14a86982f2a3587766d64b7353
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-21 15:45:53 +0100
Commit message:

 disabling the tooltip-based help
 
Package: GeneTonic
Commit: fa536afd472131cbcf79157b8d071c3c91240f61
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:46:25 +0100
Commit message:

 deploying (temporarily?) from the ubuntu-latest config
 
Package: GeneTonic
Commit: 481b29c35ed6294e3c76d8da7fb6a11850705d3a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-03-18 16:41:14 +0100
Commit message:

 updating GHAs to match with new branch names, should enable auto-deployment
 
Package: ClustIRR
Commit: c3e5e40ba2775aea3030bb80f4435430bf5ac508
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 15:14:49 +0100
Commit message:

 commit vignette and man fixes, version bump -> to devel
 
Package: ClustIRR
Commit: 7bca6efa2828bbf3d3aab66f16e86ecd1f36fae5
Author: Kai Wollek <kai.wollek@stud.uni-duisburg-essen.de>
Date: 2024-03-22 16:06:45 +0100
Commit message:

 fixed some tests
 
Package: ClustIRR
Commit: 42277e35ba8e4c5384e506566c854148b032eb2f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 16:20:52 +0100
Commit message:

 simplification
 
Package: ClustIRR
Commit: 5dc115580f399f7a555749018419721a7c7e1af1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:42:25 +0100
Commit message:

 bugfix, clones with duplicated CDR3 excldued from graphing, now added
 
Package: ClustIRR
Commit: 4d3806654453b3accfbe110472ce905aecc30729
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-15 15:41:43 +0100
Commit message:

 vbump
 
Package: ClustIRR
Commit: c8956bc39d1efe6e111b4eaf245fb112a2b894ec
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:53:23 +0100
Commit message:

 Merge branch 'main' of github.com:snaketron/ClustIRR
 
Package: ClustIRR
Commit: fcbe614ab48a668118232d2a50e4b9461bf8dc3a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:51 +0100
Commit message:

 bugfix in global_clust -> double normalization when computing ncweight
 
Package: ClustIRR
Commit: ccdec582ddf561d36902c6509362f12eb569b294
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-03-04 21:52:10 +0100
Commit message:

 version bump
 
Package: ClustIRR
Commit: 75eac9fa130d135afe0c9c6436ea56c07db26498
Author: kaozkai <freibeuter69@freenet.de>
Date: 2024-03-04 16:30:04 +0100
Commit message:

 - added sentence about ClustIRR not clonotyping / clone_size column to vignette
- fixed small typo in README
 
Package: ClustIRR
Commit: 99f2991a83a7da011bdadae4b2a19e2f9b11b499
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:47:42 +0100
Commit message:

 merge
 
Package: ClustIRR
Commit: d823f57cdc048d5fc0f6b2bc87997adbfa1c8c01
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:44:52 +0100
Commit message:

 before merge
 
Package: ClustIRR
Commit: 71fa206b4584d4056c83347290ca0ad90437a29c
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-02-26 11:32:04 +0100
Commit message:

 naming bugfix 0.85 -> 0.8
 
Package: ClustIRR
Commit: c9db5f096402f95a2494b2bdc4439d7fb8636e54
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-01 11:23:00 +0100
Commit message:

 change: input are clones, not clonotyping within ClustIRR, this is the job of the user and here are plenty of algorithms for this (e.g. consider the clonotyping caveats of BCRs -> we should not compete here)
 
Package: ClustIRR
Commit: 3b05a075a1be0aa4b220d82c3a6107307d0b5fef
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:29:09 +0100
Commit message:

 minor bugfixes
 
Package: ClustIRR
Commit: dd36c3b624de9534eee9101f96ff6d7e5051e247
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 14:17:58 +0100
Commit message:

 init
 
Package: ClustIRR
Commit: e030823b5413cef29234d5aeb9b6e23201912025
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-26 13:54:31 +0100
Commit message:

 version parameter removed
 
Package: ClustIRR
Commit: 1d31dd1b761f4efce5510ffba19e7556fe35d838
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:24:15 +0100
Commit message:

 version bump
 
Package: ClustIRR
Commit: 6542d463cc096c19892934f11ebcb408a7e40c59
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-21 18:23:52 +0100
Commit message:

 minor doc fixes
 
Package: ClustIRR
Commit: ef39c060dcf389823d218e7ac8b457e984fec25f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-18 16:04:42 +0100
Commit message:

 0.85 -> 0.80
 
Package: ClustIRR
Commit: 9460abc84503044d62fa9bb5b5b2c2a35c392a56
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 22:38:58 +0100
Commit message:

 0.9->0.85 simplification thr.
 
Package: ClustIRR
Commit: 355f199573414d4521b050034e361a3438aa75a2
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:46:32 +0100
Commit message:

 bugfix
 
Package: ClustIRR
Commit: b35d2c303ab6047b1a6d6203bb5f5d37778ce593
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-17 17:34:41 +0100
Commit message:

 distance normalized by max len
 
Package: ClustIRR
Commit: a995e553e0c3f843dff8e6b93d615997aa947567
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:46:12 +0100
Commit message:

 version bump
 
Package: ClustIRR
Commit: a4409a5065cce89b095465d791641f581cc73923
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:45:22 +0100
Commit message:

 Last bugfix
 
Package: ClustIRR
Commit: 618a465357270e0f5f8873e894cf1b05983fc1e0
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:24:12 +0100
Commit message:

 first round of bugfixes
 
Package: ClustIRR
Commit: 93d47c6ebfa69a386bde86935661a3f6c0cf6d63
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:10:47 +0100
Commit message:

 moved function
 
Package: ClustIRR
Commit: 9a2e722b5f5a25dec55f5711d7e37d4afd8b4ccc
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 15:07:53 +0100
Commit message:

 same changes about core region added in the intergraph computation
 
Package: ClustIRR
Commit: 86984b3d6c463d288f6ec8cebb18186b6da61cad
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:17:04 +0100
Commit message:

 more clear description of global_clustering
 
Package: ClustIRR
Commit: c0b9df1a2ef0bd977ee843079d867e6a2a7b12bf
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 14:12:31 +0100
Commit message:

 4th column added to get global -> cweight -> core weight
 
Package: ClustIRR
Commit: 4e15fd5b4bc65c7a1b47b4e69cf9c4abd219fcde
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-16 13:54:17 +0100
Commit message:

 adding global clustering of the core
 
Package: ClustIRR
Commit: 52014f5aa63e3f1fff21ae15fb040746c235dd46
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 17:19:47 +0100
Commit message:

 80->90% similarity global threshold
 
Package: ClustIRR
Commit: 352d8dc71bb9e48c70499e9b4bd90f326b7c97a8
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 14:03:19 +0100
Commit message:

 fixes of minor issues, documentation and namespaces
 
Package: ClustIRR
Commit: 7c443a66091f82d366987b543bc94433e6061ae7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-15 11:38:29 +0100
Commit message:

 vignette updated
 
Package: ClustIRR
Commit: 710c72829bb27b9236bc8e30f2de6d29b406ddfc
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-15 10:33:42 +0100
Commit message:

 problem with global graph removed
 
Package: ClustIRR
Commit: da9bd21fa71f74e2442774b5b3be3467b18667aa
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-13 12:08:51 +0100
Commit message:

 graph new attributes
 
Package: ClustIRR
Commit: f31da369df806aee1aeb6ebf870e7a4d7c70e4db
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:54:13 +0100
Commit message:

 minor adjustments of weight scaling, making global and local comparable
 
Package: ClustIRR
Commit: e070410909284197ec2f38cfa62444d5687d23d7
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 11:44:18 +0100
Commit message:

 more bugfixes and optimizations
 
Package: ClustIRR
Commit: 1c2fc8bd6f5ba0ee689c0460978c18071f61f69d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-10 10:37:51 +0100
Commit message:

 minor plotting bugfixes
 
Package: ClustIRR
Commit: 2d79eec284680b0cfce71f21ce94cb1828a0e94b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-01-10 00:14:23 +0100
Commit message:

 bugfix and graph joining fixed
 
Package: ClustIRR
Commit: 30e1d908351420192336eb83c6ba860412ecbe78
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 20:53:13 +0100
Commit message:

 joining graph fixing
 
Package: ClustIRR
Commit: 46171b8c9c5432676796397a3d87acd289adda4f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 15:10:11 +0100
Commit message:

 weight -> -b62
 
Package: ClustIRR
Commit: e5f430564fea88e8c8ad6f834b0f1f3f92fd7944
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:19:30 +0100
Commit message:

 minor mistake redone check
 
Package: ClustIRR
Commit: 66fbbf61d0f8c4c674520310cee1a76fefe39ff5
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-01-09 12:15:23 +0100
Commit message:

 updated global_pairs input and a new (hopefully smarter) global clustering strategy
 
Package: ClustIRR
Commit: 375ac7f747c31a8ff194d5019db8da051b1bea0a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-22 12:35:08 +0100
Commit message:

 speedup, cores reconsidered
 
Package: ClustIRR
Commit: 8b5ab8ee140881042310799e583d54429a5ab684
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 15:34:43 +0100
Commit message:

 speedup
 
Package: ClustIRR
Commit: 5587fb284c7529c3765ddf8703e19c64a5ca4b87
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:32:10 +0100
Commit message:

 bugfix
 
Package: ClustIRR
Commit: 13a1aed38375ec174c8465a051771906aedb0238
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:20:03 +0100
Commit message:

 get_graph and get_joint_graph fixes and doc update
 
Package: ClustIRR
Commit: b116317bc041cae7361f891ebcbc3e7317a483b8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-21 12:19:29 +0100
Commit message:

 version bump
 
Package: ClustIRR
Commit: 170f18e38ac0ba5c49031d2edd814930de81ad69
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-19 10:41:20 +0100
Commit message:

 get joint graph message updates
 
Package: ClustIRR
Commit: 01e4e60952c3d129567f0eafb73ffaa4b8f1c46b
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:25 +0100
Commit message:

 update last chapter
 
Package: ClustIRR
Commit: 607bf2d91325f14a85e9359a7448fc6249cd9d14
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:53:16 +0100
Commit message:

 small bugfix, if df_e has no values
 
Package: ClustIRR
Commit: f1ea24417a28dd4b827ed6856b698af14aff6560
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:44 +0100
Commit message:

 bump
 
Package: ClustIRR
Commit: 1b897b517d4ce94aacf9cdd0d1bb1e6efba8d737
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-17 22:28:29 +0100
Commit message:

 update vignette intro
 
Package: ClustIRR
Commit: 07338c0cdd66a48c79388ed8114929479e497763
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:05:51 +0100
Commit message:

 bugfix, tests next
 
Package: ClustIRR
Commit: 285460084d439b300025b17521393c9e5da0083f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-16 09:00:37 +0100
Commit message:

 more bugfix
 
Package: ClustIRR
Commit: 467a6fa37840107859c7a130139813cf2aed047c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-15 15:56:28 +0100
Commit message:

 all bugfixes done except for cols, next
 
Package: ClustIRR
Commit: 860a00a2497d3f7930cd4a0bf1850a0c35301d1e
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:48:51 +0100
Commit message:

 prelim version, more bugfix come tomorrow in graph-building part
 
Package: ClustIRR
Commit: 0f08d1a8cb269817c1a1940cfd9744f39ee9a98b
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 21:18:17 +0100
Commit message:

 bugfix chain
 
Package: ClustIRR
Commit: a102fed518b97e6b3f51f05d863519339fabe7a3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-12-14 20:10:28 +0100
Commit message:

 version back to ok
 
Package: ClustIRR
Commit: 7690b59e52d22ad26151130c1193ace0b3b70d49
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:06:45 +0100
Commit message:

 version bump
 
Package: ClustIRR
Commit: 460f0315648a11154cb8c2084408ca34b1026f68
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-12-14 20:05:07 +0100
Commit message:

 bugfix and massive speedup for graph joining
 
Package: ClustIRR
Commit: 04d19b8f1d6397b0d7ba802887c5b363f4b577c8
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2023-12-13 17:09:39 +0100
Commit message:

 Update README.md

Fixed reame 
Package: ClustIRR
Commit: 081908e07f68fd371c9ebe53de56844d9ccaa2de
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 17:04:04 +0100
Commit message:

 updated vignette
 
Package: ClustIRR
Commit: c5d558a4d3cd595dec5d15d26d6eefe709b2db84
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-13 16:54:59 +0100
Commit message:

 how to join multiple graphs together
 
Package: ClustIRR
Commit: d1cfe316f36d0c3c6c66344d41f22cc1d14fdb41
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-12-08 16:04:24 +0100
Commit message:

 joining many clustirr object now possible
 
Package: OmnipathR
Commit: 582735943c63e64aeaf52a0cb7ad0733ff4bcbd7
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:18 +0100
Commit message:

 Bump version: 3.11.9 → 3.11.10
 
Package: OmnipathR
Commit: e9ef4a8c3a24b85042c21b6f5f56b5d6ae2c16bd
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-24 13:31:11 +0100
Commit message:

 forgot to rebuild the docs after 442cb77
 
Package: alevinQC
Commit: 9025674817b081d22a6df79317b97eac59bd0617
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:56 +0100
Commit message:

 Catch messages in unit tests
 
Package: alevinQC
Commit: 7fb51cc532c08bdeae6251f72760ef33969801cc
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:43 +0100
Commit message:

 Expand chunk options in template
 
Package: alevinQC
Commit: be2068eda827093579d3ebe884544aa8fac9fa91
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 10:19:21 +0100
Commit message:

 Version bump
 
Package: iCOBRA
Commit: 6a7e2a95ae9c2350cc01409372f5fca74d5e498c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:57:47 +0100
Commit message:

 Merge pull request #7 from csoneson/fix-gha

Replace deprecated tidyverse functions 
Package: iCOBRA
Commit: f1a2cc118bfa96d62d3a04a7f3e2356a02312c7d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:41:28 +0100
Commit message:

 Update results (rounding differences)
 
Package: iCOBRA
Commit: a095ab12baa26b7ea7f06b1e511deaf94b4ca1ed
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:40:16 +0100
Commit message:

 Catch expected warnings in tests
 
Package: iCOBRA
Commit: 748753413afebb9f7a16f0ddc6112caaad56e6a7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:39:57 +0100
Commit message:

 Replace deprecated aes_string, use linewidth instead of size
 
Package: iCOBRA
Commit: d67fa73fa2e3e3d07b34ee217511bbb2ebb159c2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:29:34 +0100
Commit message:

 Add warning expectation to test_app
 
Package: iCOBRA
Commit: c081586ae0add1ecabe60b0ea857d415301d72ac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:27:49 +0100
Commit message:

 Add tests for get_keeplevels
 
Package: iCOBRA
Commit: 0bb29754142654906f99c1361a8d662c893ecad5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:09:23 +0100
Commit message:

 Replace deprecated dplyr functions
 
Package: iCOBRA
Commit: 58784a9f5c1df190be10033ea50d330e354bc479
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-03-24 09:06:48 +0100
Commit message:

 Bump version
 
Package: EpiTxDb
Commit: 821fd21d97be545a3570d216c33350a2e2a41c80
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:48:14 +0100
Commit message:

 Fixed making EpiTxDb from RMBase

 
Package: EpiTxDb
Commit: 8129305e62d75a0902532909f46b949d57e88634
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:47:13 +0100
Commit message:

 Update DESCRIPTION
 
Package: EpiTxDb
Commit: 34638d4904babb40994a7786bb93d162a10f0d5c
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:23:07 +0100
Commit message:

 Fixed RMBase loading and update RMBase data dictionary
 
Package: EpiTxDb
Commit: 461e99a357e852e050d3c63a6fcfb31ff116332f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:22:16 +0100
Commit message:

 reversed order of importing txdbmaker and GenomicFeatures
 
Package: EpiTxDb
Commit: 1419ef691740a13ca7593d3fb80310bfd34141f9
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-18 22:22:09 +0100
Commit message:

 Update README.md 
Package: tRNA
Commit: 2cc567ee5095164308b5e1a97a2a4ca4c9eabdf6
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-24 01:46:09 +0100
Commit message:

 Fixed warning from upstream ggplot2 chnages
 
Package: tRNA
Commit: 2e08d8bc66e9186c6e1c1aacea5f577d63b1db6c
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:12:29 +0100
Commit message:

 Update README.md 
Package: alabaster.ranges
Commit: 773a02a93c50bfe2554ce094e6b1fe9bee497fbc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-03-23 17:03:15 -0700
Commit message:

 Added badges to the README.
 
Package: alabaster.ranges
Commit: 6e6acfd5108b62d06e5937b4a8cdbca4598c19e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-01-26 22:54:50 -0800
Commit message:

 Updated the GitHub action to use BioC image and packages.
 
Package: IgGeneUsage
Commit: 231b901411698e03b8d4e960f000078c734d3518
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-24 00:12:01 +0100
Commit message:

 minor checks and version bump
 
Package: Modstrings
Commit: 603cb4674c0b6ded4c35de2b63d9ee710511112f
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:57:57 +0100
Commit message:

 Update GitHub Action config
 
Package: Modstrings
Commit: d27b32f6cbbbb49bf043443be91522c73542b646
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 22:56:55 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Modstrings
 
Package: Modstrings
Commit: 84fb6b7541e724c6a8cfdd71a3e75699f6242eda
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 23:06:31 +0200
Commit message:

 Update README.md
 
Package: Modstrings
Commit: 5a73d389a6d0c7bd2aa27b191aaa732cddc4d4f1
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:54:10 +0200
Commit message:

 Update R-CMD-check.yaml
 
Package: Modstrings
Commit: 01bc40ab7a09d36d2c32a6750a014f78137575a4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:25:06 +0200
Commit message:

 Update R-CMD-check.yaml
 
Package: Modstrings
Commit: 18bd46ae67f76bbdbb949f618f40ec780bf5819e
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:22:43 +0200
Commit message:

 update to GitHub actions
 
Package: Modstrings
Commit: b32a9803d165264980217ffa7a0bd3499a8d6438
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:20:36 +0200
Commit message:

 Update R-CMD-check.yaml
 
Package: Modstrings
Commit: 503abd0a494bdd8a661b9dd1aec851c24de15fcd
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2022-08-13 22:16:21 +0200
Commit message:

 Update R-CMD-check.yaml
 
Package: tRNA
Commit: 12e627b193af2df3cf1211f95bdea16551924e54
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:07:14 +0100
Commit message:

 Update GitHub action config
 
Package: tRNA
Commit: c1705c640019dfe8ff039342216b62d3409c1502
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:06:24 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/tRNA
 
Package: tRNA
Commit: f50bc835e38ea71246b80b605ba91dcf5df24ab0
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-01-17 21:01:28 +0100
Commit message:

 Update NEWS
 
Package: tRNAdbImport
Commit: d86b30d8ab59468a8e4c92bede2e9acd684c6ee2
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:09:56 +0100
Commit message:

 Update GitHub action config
 
Package: tRNAscanImport
Commit: 4ac8f8618c22219ad6407dec2b0bf677b20a84f4
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2024-03-23 23:11:28 +0100
Commit message:

 Updated GitHub action config
 
Package: IgGeneUsage
Commit: 8f96632dd7d95f9caaebb28b89b903cbdff1530d
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2024-03-23 22:44:09 +0100
Commit message:

 minor bugfixes
 
Package: IgGeneUsage
Commit: 1bbb804bf2593f66de608cb5d790abdbefcf545a
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 23:00:25 +0100
Commit message:

 bugfix in theta
 
Package: IgGeneUsage
Commit: 6247dc07574a9511e764dd88558fd36a159eb5d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 17:39:56 +0100
Commit message:

 prior alpha ~ normal(-3,3)
 
Package: IgGeneUsage
Commit: fa486a46da0ee62498fa5144e2e416c7088a5d19
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:16:29 +0100
Commit message:

 update rng
 
Package: IgGeneUsage
Commit: da979c8ae14ac2dc378c4dc424c269f80818a459
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:15 +0100
Commit message:

 improved rng
 
Package: IgGeneUsage
Commit: 579590413bb7da13575590af5544668e90c3f7e1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-14 15:14:04 +0100
Commit message:

 bump
 
Package: IgGeneUsage
Commit: a563d95d074ee474e78ee37e252f40752670eec1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 22:20:53 +0100
Commit message:

 now with bugfixes
 
Package: IgGeneUsage
Commit: d07e56909319edf38360884e4b0f46c03127cb9c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:08:13 +0100
Commit message:

 makevars deleted, do we need?
 
Package: IgGeneUsage
Commit: 0cb285e2e52b2977a6a6953579f6063a688b779f
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:46 +0100
Commit message:

 vignette and namespace update
 
Package: IgGeneUsage
Commit: b0fd0998cc70840d7e4e543f82ded06932e21fc3
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:28 +0100
Commit message:

 update replicates model
 
Package: IgGeneUsage
Commit: 5152e25a9a1b27cb39f89343ec170e8b6c2be067
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:07:01 +0100
Commit message:

 update replicates model
 
Package: IgGeneUsage
Commit: ce25381b3e1d7fb2bc115765ab06432df70aafa8
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:06:47 +0100
Commit message:

 update replicates model
 
Package: IgGeneUsage
Commit: afc593796dbd3a2b5cb51b0bb2dfd457cb74b8f9
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-11 18:05:59 +0100
Commit message:

 update replicate model
 
Package: IgGeneUsage
Commit: ee0167f87f86ea37e7873c3ca07fbea525fc5813
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2024-02-10 22:25:35 +0100
Commit message:

 model for replicate analysis -> stub
 
Package: IgGeneUsage
Commit: 2696ac30581353c3a7cf3203c5da392e262b486d
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2024-01-22 09:45:57 +0100
Commit message:

 Merge pull request #13 from andrjohns/array-syntax

Update deprecated Stan syntax 
Package: IgGeneUsage
Commit: cf6b83ba44ad3f2a2a4ccc0b65a1ee5a6616f7bf
Author: Andrew Johnson <andrew.johnson@arjohnsonau.com>
Date: 2024-01-19 19:07:52 +0200
Commit message:

 Update deprecated array syntax
 
Package: IgGeneUsage
Commit: 288af7a1c44e90701ed467b5cd9187787ba8f0ea
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-22 18:11:41 +0100
Commit message:

 model simplified
 
Package: IgGeneUsage
Commit: 812313a18813d9233421f8063c0e82038dd8212c
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-19 20:05:06 +0100
Commit message:

 new phi, kappa, ppc, var recovery
 
Package: IgGeneUsage
Commit: 55b3c037c3193d51aabc20f79869fc1fb443c7d1
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-13 16:22:05 +0100
Commit message:

 minor change
 
Package: IgGeneUsage
Commit: fcb8af905dab7f052241ff7912ce8520d6bc8fcb
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2023-11-04 14:05:04 +0100
Commit message:

 merge Description with bumped version
 
Package: IgGeneUsage
Commit: 30e200cac2c09502d41f3527d7f267dc13c040fd
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-04 00:48:11 +0100
Commit message:

 pmax fix
 
Package: IgGeneUsage
Commit: 77cd6a11d3923787aa164b22e703898d1769313d
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 15:04:10 +0100
Commit message:

 Minor change in GU model
 
Package: IgGeneUsage
Commit: 722d417f4bc3f6774292d5062baca079aafad946
Author: sktron-vm240 <simo.kitanovski@uni-due.de>
Date: 2023-11-03 14:37:44 +0100
Commit message:

 fix GU model
 
Package: IgGeneUsage
Commit: d8219065f9b21721a2c116c4fbff7f4f77efa2e2
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 11:36:27 +0100
Commit message:

 version bump, bugfix in GU analysis
 
Package: IgGeneUsage
Commit: af66f9dd326edfe41756acbfd7acab17b3164114
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-03 09:44:18 +0100
Commit message:

 More prior changes
 
Package: IgGeneUsage
Commit: bf4bc80109515cddf9282e39b2de7eebf0c88a88
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-02 12:27:56 +0100
Commit message:

 minor prior changes in model
 
Package: IgGeneUsage
Commit: e36a85c936a1704ca7e08f48c558b959bbb80838
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-11-01 19:43:12 +0100
Commit message:

 model upgrade
 
Package: IgGeneUsage
Commit: 456b3b5bca132c26bd11593d861c3d4afae1d94f
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:51 +0100
Commit message:

 version bump
 
Package: IgGeneUsage
Commit: dd6926a5fd481f1b3ab12926e1e5f627d00992ae
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 20:06:35 +0100
Commit message:

 minor updates, 1st  push after release
 
Package: IgGeneUsage
Commit: 570c4f1ef72a693c218aab61025cbd8cf523ec59
Author: sktron-vm240 <simokitanovski@gmail.com>
Date: 2023-10-30 19:12:09 +0100
Commit message:

 first push version 1.16
 
Package: Biostrings
Commit: d13154e5013363a568d983ff26e483e6c77fb007
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:57:19 -0700
Commit message:

 more cleaning/reorganization of the TODO file
 
Package: Biostrings
Commit: 41955d99621065a36f910f848b00621ca7bfe89c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:22:06 -0700
Commit message:

 More cleaning/reorganization of the TODO file

Some items moved to pwalign's TODO.
 
Package: pwalign
Commit: 2b7411d477361523de4c3336e0973c7efb81225e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-03-23 12:15:10 -0700
Commit message:

 add TODO file (all items taken from Biostrings's TODO)
 
Package: tximport
Commit: 7b1fbe4bffc98c21e891a37c5a0e1751a85045ba
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2024-03-23 13:58:58 -0400
Commit message:

 experimental support for oarfish
 
Package: OmnipathR
Commit: bbbfae5a6c7341f4c490772555de3e5ac6bb18a5
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:37 +0100
Commit message:

 Bump version: 3.11.8 → 3.11.9
 
Package: OmnipathR
Commit: 442cb7767bbf54b68efddad4873c63f44e6160e2
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-23 18:34:29 +0100
Commit message:

 `_PACKAGE` sentinel for roxygen: finally getting it right
 
Package: OmnipathR
Commit: 812514458909a784315e3d01dd85c86429463368
Author: deeenes <turei.denes@gmail.com>
Date: 2024-03-22 14:09:17 +0100
Commit message:

 updated years in code file headers
 
Package: edgeR
Commit: 8cb63a65c2e65f7e25bfa92b72d26c41a6c3beb7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-03-23 22:21:34 +1100
Commit message:

 edgeR 4.1.19
- voomLmFit will now extract exprs from an eSet object but with a warning message.
- voomLmFit.Rd help now refers to SummarizedExperiment rather than ExpressionSet.
 
Package: ggtreeSpace
Commit: 020060b9e96169a3fdb27e828a709883058eb22f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 16:00:42 +0800
Commit message:

 for bioc
 
Package: ggtreeSpace
Commit: 0d0a41ce11ad2dcd0cd41b8b72e2a3b6ddb5eb65
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-03-23 15:58:03 +0800
Commit message:

 update vignette and licence