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GIT Logs

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

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Package: DMRcate
Commit: 8bc91ce9eafd29a563845e49058f73681d9e0c40
Author: timpet <t.peters@garvan.org.au>
Date: 2023-12-05 14:49:52 +1100
Commit message:

 DMRcate_2.17.1
 
Package: DMRcate
Commit: f582bdd59f962a6f33c8b3f57946102f415c9ca4
Author: timpet <t.peters@garvan.org.au>
Date: 2023-12-05 14:39:41 +1100
Commit message:

 DMRcate_2.17.1
 
Package: flowWorkspace
Commit: 0137cfce2b58a80b32b676fcd2c2621ee78e2457
Author: mikejiang <mike@ozette.ai>
Date: 2023-12-04 17:37:47 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: edcd9f56f8a08bb600e7f20a1943269ef964a701
Author: mikejiang <mike@ozette.ai>
Date: 2023-12-04 17:37:22 -0800
Commit message:

 Merge branch 'devel' into hotfix/update-according-to-latest-scales-package
 
Package: flowWorkspace
Commit: 11218c9f8dcd79b7a12e30dc66c5957ae25560bf
Author: mikejiang <mike@ozette.ai>
Date: 2023-12-04 17:32:11 -0800
Commit message:

 update transformerList constructor according to the latest scales package
 
Package: seventyGeneData
Commit: e23ad37dae385b08e5a31b32491257804a971878
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 17:13:45 -0500
Commit message:

 chore: update news
 
Package: seventyGeneData
Commit: 44bfd102c6745e2986e1a5a5362032123c0de133
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 17:00:49 -0500
Commit message:

 fix: typo in description version
 
Package: SWATH2stats
Commit: 27b62c25cdc37aab68332b5c5bafbfce66da27c1
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2023-12-04 22:53:37 +0100
Commit message:

 version bumb in devel
 
Package: SWATH2stats
Commit: ba06f69a04c9e633d28bfa9561d08d3e64de3826
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2023-12-04 22:53:04 +0100
Commit message:

 bug fix: added https to biomart command
 
Package: timeOmics
Commit: 8be9984ab036731f39d8a678d3134f9923235c46
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2023-12-04 16:05:37 -0500
Commit message:

 fix summary and documentation
 
Package: timeOmics
Commit: 916e024cd549ea57fdce2bdad8b7573cb7ec4184
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2023-12-04 14:01:22 -0500
Commit message:

 Version bump
 
Package: seventyGeneData
Commit: da3d65f25ca33154c5e6adb95eca651363380501
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 12:33:42 -0500
Commit message:

  chore: version bump in devel
 
Package: seventyGeneData
Commit: 83c9c19675ed74c6f51b23822805005444eeba0d
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 12:32:41 -0500
Commit message:

 fix: remove extdata on project root
 
Package: timeOmics
Commit: 26cc303995ea74771fe03f961b62bbd36c01ab20
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2023-12-04 12:31:19 -0500
Commit message:

 Version bump
 
Package: scMultiSim
Commit: fce57e6db2800ec00ccbb4a8f8cd561ae6e549c6
Author: Hechen Li <lhc199652@gmail.com>
Date: 2023-12-04 12:16:36 -0500
Commit message:

 Fix build errors
 
Package: seventyGeneData
Commit: 12fc11c4f256c239349051fafb5454e3573c1fbc
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 11:45:02 -0500
Commit message:

 feat: version bump in devel
 
Package: seventyGeneData
Commit: a5fe39884666f129259fb13548d3f18d5d1a8117
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-04 11:18:28 -0500
Commit message:

 feat: initial implementation of new data generation workflow
 
Package: distinct
Commit: 780b1ee910002dc7cb00f467bd5a44bd6a046217
Author: SimoneTiberi <simone.tiberi@uzh.ch>
Date: 2023-12-04 15:31:25 +0100
Commit message:

 C++17 Updated
 
Package: distinct
Commit: 6ce135d8c3dd13294e39e9531d65fdc8f05172e3
Author: SimoneTiberi <simone.tiberi@uzh.ch>
Date: 2023-12-04 15:26:40 +0100
Commit message:

 C++17 Updated
 
Package: biomvRCNS
Commit: b4ca43375c460c4f97e3a48a92e35c1c64c103eb
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2023-12-04 07:52:03 -0500
Commit message:

 Undeprecate
 
Package: TargetSearch
Commit: 770e170d66dede75833e8d5f04565977ab7f17f3
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2023-12-04 11:58:20 +0100
Commit message:

 Fix: RI corrected binary format compatibility

RI files generated with TargetSearch after 2.4.0 allow for empty
spectra (ie, no fragments). This is incompatible with earlier
TargetSearch versions, so we remove such spectra before passing
them to the C code.
 
Package: CDI
Commit: 618de3d6d3f922917427f00c7a2d322be6b11c3f
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2023-12-04 18:49:30 +0800
Commit message:

 minor
 
Package: IntOMICS
Commit: 48cfe7128a579597ce676a1432b10469f660d2bf
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2023-12-04 10:41:40 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
 
Package: IntOMICS
Commit: 0cd11480361eb9e40c0fa1057633caea3e8757d9
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2023-07-05 11:55:04 +0200
Commit message:

 missing log GE values
 
Package: katdetectr
Commit: f6ee5827291722abf06c8e0ca2615a3638fbff12
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-12-04 10:36:27 +0100
Commit message:

 fix merge
 
Package: katdetectr
Commit: 21ad57c228a235278e3211c08b63df8e8ec1a4bf
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-12-04 10:33:39 +0100
Commit message:

 version bump
 
Package: katdetectr
Commit: c6392fa2cdbc5e5b4d6cd7e9960cbd3e74fb9201
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-12-04 09:39:56 +0100
Commit message:

 update rainfallplot with correct pyrimidine classification of substitutions
 
Package: katdetectr
Commit: 95601611764ed82ca0b331fbd93ec3c7d053302e
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-11-30 09:32:41 +0100
Commit message:

 Update README.md 
Package: katdetectr
Commit: e0b1c166984790f2b6e88c55200a3ed37023543f
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-11-30 09:31:01 +0100
Commit message:

 Update README.md 
Package: katdetectr
Commit: 89170771d8c9e0bd2a971cf0d60c6bcc27043d7a
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-06-12 09:05:25 +0200
Commit message:

 merge
 
Package: katdetectr
Commit: 20e327b620f46aa93f16f2f8deaaab4099330fb3
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-06-12 09:04:00 +0200
Commit message:

 remmoved additional parameters settings section from vignette
 
Package: katdetectr
Commit: 4062df517c50619f4d34aeee8a45af3afaa82ac4
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-03-24 16:20:58 +0100
Commit message:

 Update README.md 
Package: katdetectr
Commit: e5143a7e936cc776f5e696fd3c09099836942a33
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2023-03-24 14:52:31 +0100
Commit message:

 Merge pull request #3 from ErasmusMC-CCBC/devel

fix reading of synonymous variants in .maf files, git issue #2 
Package: DSS
Commit: 4815d830122bbc774dc8121c0babe465f8d9204a
Author: Hao Wu <haowu_sz@outlook.com>
Date: 2023-12-04 14:05:44 +0800
Commit message:

 add edgeR as suggested package. Minor change in callDMLto avoid NA
 
Package: scMultiSim
Commit: 41e5ec655fb519ca4f9654e7d07ef1dc53d9937f
Author: Hechen Li <lhc199652@gmail.com>
Date: 2023-12-04 00:32:27 -0500
Commit message:

 Remove unnecessary imports
 
Package: scMultiSim
Commit: 752dc5deea772088564811a10af43d3c87a6f46a
Author: Hechen Li <lhc199652@gmail.com>
Date: 2023-12-02 21:51:16 -0500
Commit message:

 Use seq() when possible
 
Package: scMultiSim
Commit: 47c9094fbba32e1fae745634978018bc186d97b3
Author: Hechen Li <lhc199652@gmail.com>
Date: 2023-12-01 11:59:48 -0500
Commit message:

 Add more comments
 
Package: tidybulk
Commit: 2ae63e699d5486a38141d72bed52c12ee7a26b17
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-12-04 13:52:37 +1100
Commit message:

 fix dependency
 
Package: tidybulk
Commit: 512a534bb3bc6e933a78ebbfa1bfaea6d2f6cb38
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-11-17 17:48:56 +1100
Commit message:

 Merge pull request #303 from stemangiola/de-no-forking

De no forking 
Package: tidybulk
Commit: 7e55e53dac48ef644d843801b4292e24c73fa05e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-11-17 17:42:16 +1100
Commit message:

 Merge branch 'master' into de-no-forking 
Package: tidybulk
Commit: 85fc3139f204819b0b89854515fb8f250ef6604d
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-11-17 14:55:44 +1100
Commit message:

 fix vignette
 
Package: tidybulk
Commit: aaf4bb17a742c50b170350f2021e64ea77149643
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-11-03 20:26:24 +1100
Commit message:

 version UP
 
Package: tidybulk
Commit: d3b743896aaf3500b4ea58f2e8fd45acc5add597
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2023-11-03 20:26:02 +1100
Commit message:

 add argument to avoid forking
 
Package: MetaScope
Commit: 25cb53c99441ae753691d1a07bd8dc42cd95a1ef
Author: Aubrey Odom <aodom@bu.edu>
Date: 2023-12-03 20:43:57 -0500
Commit message:

 Amend --local option in filter_host and update location
 
Package: SurfR
Commit: faed2c0a277c7cd6bee1c4b03773af8e4f8b8d89
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-12-03 20:15:32 +0100
Commit message:

 bumped the package version v0.99.36
 
Package: SurfR
Commit: 1b72992535cd355cb521dafc0bcddaf9d03f88bf
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-12-03 19:55:44 +0100
Commit message:

 bumped the package version v0.99.35
 
Package: SurfR
Commit: 1f8236e24bc767e588644695889d21644a0c6c85
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-12-03 19:34:48 +0100
Commit message:

 bumped the package version v0.99.34
 
Package: SurfR
Commit: ef1dc75cbf3f000c6cef2ec5753e0307311f25bd
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-12-03 18:38:56 +0100
Commit message:

 bumped the package version v0.99.33
 
Package: cleaver
Commit: 1b9155e2023b75e506d58c85d1ea43735ade9e36
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2023-12-03 10:46:46 +0100
Commit message:

 docs: add missing entry for lysarginase
 
Package: biocthis
Commit: 2f8bc84c7c00761bb06950a6b97f262dd55d01c2
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2023-12-02 12:55:46 -0600
Commit message:

 Add a contributing guide
 
Package: seventyGeneData
Commit: 14e5ced50900fa8964095e072498f6192c0f806e
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-02 13:55:36 -0500
Commit message:

 docs: replace sweave vignette to rmarkdown html format
 
Package: seventyGeneData
Commit: 763fd4c4f88d87bb24fb60d8a1942db58542b8ea
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-12-02 11:54:42 -0500
Commit message:

 chore: prepare insfrastructure for rmd vignette
 
Package: seventyGeneData
Commit: b33f0b7525c85b3a3de836db947e7d9e551af2b5
Author: luciorq <luciorqueiroz@gmail.com>
Date: 2023-11-30 17:01:12 -0500
Commit message:

 chore: include new contributors and update vignette rendering
 
Package: ggkegg
Commit: fa0a7bd5df62ece49302b9d2a374b1be2746e369
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-12-02 18:50:20 +0900
Commit message:

 dev version bump 1.1.8
 
Package: ggkegg
Commit: dcb3623546a7c3f58f2c5dc085ba21acec257544
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-12-02 16:53:50 +0900
Commit message:

 a change in process_reaction (all columns preserved)
 
Package: alabaster.base
Commit: 6f0e6b774193dc261616af6fa98755b3e2b07ca6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-12-01 23:33:54 -0800
Commit message:

 Updated vendored libaries to coax the Windows build.
 
Package: ggkegg
Commit: e907d336d9a7fb6d47e314a36ae934fd998e6e86
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-12-02 13:28:23 +0900
Commit message:

 bump dev version (1.1.7)
 
Package: ggkegg
Commit: 063f484fd9cda046bd768bb149b15db3cc9a55ad
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-12-02 13:23:46 +0900
Commit message:

 change the parsing pattern in process_reaction
 
Package: ggkegg
Commit: c4e565cc0fe8f0de3f63bcaa46d0f54d285f0072
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-12-02 12:36:36 +0900
Commit message:

 dev version bump (1.1.6)
 
Package: ggkegg
Commit: 0d13b054ae7f4e427be010fb7c584418903b1059
Author: noriakis <nori@hgc.jp>
Date: 2023-12-02 10:27:25 +0900
Commit message:

 return_graph argument in highlight_entities
 
Package: ggkegg
Commit: 67666db1e0c20e6bc35e935d63bec4b8f0eb50ea
Author: noriakis <nori@hgc.jp>
Date: 2023-12-02 10:10:10 +0900
Commit message:

 highlight_entities accept named numeric vector
 
Package: ggkegg
Commit: 12587f486db195a2ca5056081744bddb34922b31
Author: noriakis <nori@hgc.jp>
Date: 2023-12-01 13:04:35 +0900
Commit message:

 Show the message if none of the nodes (or all the nodes) is highlighted
 
Package: timeOmics
Commit: 94b540bf09bc2ab1ebfeb40912f37251b711cab9
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2023-12-01 17:02:14 -0500
Commit message:

 add diff threshold to UpDown Cluster and summary.getCluster()
 
Package: GenomicScores
Commit: 5d531b1ede01586c413b2b6f73296aab7038f590
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2023-12-01 21:01:03 +0100
Commit message:

 Version bump
 
Package: GenomicScores
Commit: c971d06b674b2a8e02527dbb3e9b086fc41bcbad
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2023-12-01 20:59:49 +0100
Commit message:

 Updated vignette
 
Package: infercnv
Commit: cca1b6f9fba95075c8e83677eb88fea005234cf1
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 13:33:50 -0500
Commit message:

 Version bump to 1.19.1
 
Package: infercnv
Commit: dc018d4c2d0b5ca790be6e6a08102b7797ee7c39
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 13:09:42 -0500
Commit message:

 Fix version number in latest NEWS
 
Package: infercnv
Commit: 72ad8cb2baef17493e32f48295f19a92c758b703
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 13:03:57 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: infercnv
Commit: 23e33ad40408c7c2aa8dc7b7992953a290ac2a54
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 13:03:48 -0500
Commit message:

 Revert "Version bump to 1.17.1"

This reverts commit 45b1233255145fe891ff6d9e4c7bc4affab50694.
 
Package: infercnv
Commit: 45b1233255145fe891ff6d9e4c7bc4affab50694
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 12:58:33 -0500
Commit message:

 Version bump to 1.17.1
 
Package: infercnv
Commit: edc7d7938df7026c16ae56c7134d8933d82f229e
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 12:58:08 -0500
Commit message:

 Update NEWS file
 
Package: infercnv
Commit: 9cf9bd3c6625777d5d0eb75543c9c2a4f2693fcf
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-12-01 12:57:28 -0500
Commit message:

 Update doc
 
Package: infercnv
Commit: d019c2091a55352788960db5422777680d562b13
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-11-28 21:11:22 -0500
Commit message:

 Transfer cluster_by_groups option to HMM when running in samples mode to allow running the HMM on "all_observations".
 
Package: infercnv
Commit: dc9a3c8a3b0c46db60c4355c634e8f1010504b98
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-11-28 21:05:55 -0500
Commit message:

 Add useRaster option to plot_per_group method and transfer it plot_cnv calls.
 
Package: infercnv
Commit: 97d55a21b4a8e57437b7268cbf6c31fb85190cd0
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-11-28 21:05:05 -0500
Commit message:

 Fix for plotting with dynamic_resolution enabled when the png size limit of cairo is hit to not have parts of the plot that try to be plotted outside the limit.
 
Package: infercnv
Commit: 8a46eaf8ed15c06fb8f35f52d4fb6b07ceb10463
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-11-28 21:03:58 -0500
Commit message:

 New default setting for leiden_resolution now set to "auto" which will very roughly set a resolution value that scales with the number of cells to avoid over splitting subclusters when the number of cells increases.
 
Package: infercnv
Commit: 7b8affc2166b18729054776ee9a550f07c68bc79
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-11-28 13:49:22 -0500
Commit message:

 Update to work with Seurat v5 object changes.
 
Package: infercnv
Commit: f1077335300ae2f6f90cc63f4b74d2579f3a5d29
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-05-29 15:41:40 -0400
Commit message:

 Allow i3 HMM to run without references, results will be based on all observations, so results will be relative to proportion of healthy to tumor cells.
 
Package: infercnv
Commit: 270f045206dd563bb54cdb95da392f77520ca0d5
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-05-24 13:36:23 -0400
Commit message:

 Fix typo in CLI script for one of the arguments.
 
Package: infercnv
Commit: 8c74854ffa97f313f2f69b5a3c508c53fa93522a
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-05-24 12:33:11 -0400
Commit message:

 Change how the available number of cores is checked for random trees subclustering so that it checks against the max number of cores rather than what is defined by BIOCPARALLEL_WORKER_NUMBER which is set to 4 in the base BioConductor image.
 
Package: infercnv
Commit: 4fd085ac760de0f1c20f25b042c5ad4f8f70de89
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-05-23 16:00:33 -0400
Commit message:

 Add a "no_" at the start of CLI script options that flip a boolean from a default TRUE to FALSE so that it is clearer that it disables the option.
 
Package: infercnv
Commit: 956030955d25c8699bb8a14815e672062392350b
Author: GeorgescuC <GeorgescuC@users.noreply.github.com>
Date: 2023-05-23 15:58:03 -0400
Commit message:

 Update CLI script to have all options, new and older that just never got added to it.
 
Package: simona
Commit: 199f7382aecc8d6b5761afcacc27fc44679f2614
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-12-01 18:27:17 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: simona
Commit: 3ddb0629945831e30cef704440a221be2aa48635
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-12-01 18:27:10 +0100
Commit message:

 version bump
 
Package: simona
Commit: a95e38810006defc5db99711cc895ee34cab9ce6
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-12-01 18:19:29 +0100
Commit message:

 add a new vignette
 
Package: simona
Commit: 4a0e3d6ac889212c21e59fee5a9f0460b4eca86e
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-29 21:23:53 +0100
Commit message:

 modified show method
 
Package: simona
Commit: ff53691f4c972113000e8d0dd3cc46ad4166ae49
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-28 13:30:02 +0100
Commit message:

 version bump
 
Package: simona
Commit: 1bf31a743e48126277d8cc74a3d959221915270f
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-28 13:29:04 +0100
Commit message:

 version bump
 
Package: VplotR
Commit: 6abac9439399b328ad9ed1a417a78188b4a1d068
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-29 20:30:46 +0100
Commit message:

 Merge branch 'RELEASE_3_18'
 
Package: VplotR
Commit: cf5097df635217b1fc46c3b584cd35ad0a0ae823
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-29 17:38:54 +0100
Commit message:

 fix: rm magrittr general import to avoid conflict with GenomicRanges::substract
 
Package: VplotR
Commit: 7ee0be06c38f52dfcea72f4b45f160c4fc6b6f9c
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-29 17:16:00 +0100
Commit message:

 ci: update workflows
 
Package: betaHMM
Commit: 2d33fb78e623b10606e17bb7988db40fb1de7394
Author: koyelucd <koyel.majumdar@ucdconnect.ie>
Date: 2023-12-01 16:02:29 +0530
Commit message:

 Unit tests added after 2nd BioConductor review
 
Package: scMitoMut
Commit: cc019a914aa1d43c01444cb24a2a619a4d261776
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-12-01 11:25:48 +0100
Commit message:

 Bump version
 
Package: scMitoMut
Commit: e9bbaa6005d2fcc1400158a5bb64da9a1118fd3e
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-12-01 11:22:51 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/scMitoMut into devel
 
Package: scMitoMut
Commit: 422cee5e6aac6a6b769aa4e50e359af8387c0c34
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-12-01 10:39:43 +0100
Commit message:

 Merge pull request #4 from wenjie1991/devel

Devel 
Package: scMitoMut
Commit: 95e408827d61449ca4a6240aa0bf6d9e9c39818a
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-12-01 10:38:18 +0100
Commit message:

 Merge branch 'main' into devel
 
Package: scMitoMut
Commit: cee04b09d67c6db987f14ae1e32db1e108b8eb10
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-12-01 10:35:35 +0100
Commit message:

 Announce R/Biocondutor package & contribution
 
Package: scMitoMut
Commit: 6ec141025da09166131b00b294970db176c145fe
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-09 13:38:28 +0100
Commit message:

 Update r.yml 
Package: DExMA
Commit: 20a72552f028cfb7cfc71d717e6f0e86befafcff
Author: Juananvg <juanantoniovillatorogarcia@gmail.com>
Date: 2023-12-01 09:51:10 +0100
Commit message:

 Fix some bugs
 
Package: cleaver
Commit: 266d9759b772ccf5d170e2f96677b5a95ef9dada
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2023-11-30 21:44:15 +0100
Commit message:

 chore: bump version number
 
Package: cleaver
Commit: 1ac5b30ad28b781fd1df6868b7ce04ff82ecacd2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2023-11-30 21:43:48 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel'
 
Package: cleaver
Commit: 7f071c535a6fb18d80cbb5a1883b47afd1f9b8c4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2023-11-30 21:42:38 +0100
Commit message:

 feat: add LysargiNase
 
Package: alabaster.se
Commit: 76d979cfd0cc81a74cfb0ac5d044c76e237e0aa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-30 16:47:59 -0800
Commit message:

 Delete commented test as we never save empty rowRanges.
 
Package: alabaster.matrix
Commit: e6e9fc550b70de4375800352f0ce639eccfe75c3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-30 16:46:14 -0800
Commit message:

 No need to defend against truncated string attributes from rhdf5.
 
Package: alabaster.base
Commit: 733424528df5fd2287933f82863b9a6759414807
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-30 16:39:20 -0800
Commit message:

 No need to extend StrType size by 1 for HDF5 attributes.
 
Package: scMitoMut
Commit: 59fbac3988a8c506be7b420193d1b9a462725d67
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2023-12-01 00:05:36 +0100
Commit message:

 Bump version
 
Package: scMitoMut
Commit: 09a0f9f92a31b265ff8300298a15eabdda6c031a
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-30 17:48:52 +0100
Commit message:

 Merge pull request #3 from wenjie1991/main

Update BugReports and URL of package 
Package: scMitoMut
Commit: 719615c40c3ef7f7888caa225fd03675be7a035b
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-30 17:45:35 +0100
Commit message:

 Update BugReports and URL of package
 
Package: scMitoMut
Commit: 797a2a6a2b29eb52f608284800cb4e4cf8acb958
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-29 17:20:25 +0100
Commit message:

 Merge pull request #2 from wenjie1991/main

Merge branch 'wenjie1991-master' 
Package: scMitoMut
Commit: 4959ae406ee8a20ef6ce1ef91905fb3fc341ec53
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-29 16:57:35 +0100
Commit message:

 Merge branch 'wenjie1991-master'
 
Package: scMitoMut
Commit: b5b4dd3fddb4b4ae5e0cb54bf1942bb0d5887617
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-11-09 13:37:47 +0100
Commit message:

 Update r.yml 
Package: scMitoMut
Commit: 196ff7d7382ff2885735dbefd580d9a950ceecf1
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2023-11-01 00:19:37 +0100
Commit message:

 Update author info
 
Package: scMitoMut
Commit: 80c1ac0aac097fca9c4925a3a49e26dabebdf8bb
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2023-10-31 17:00:01 +0100
Commit message:

 Merge pull request #1 from wenjie1991/devel

Update workflow R version 
Package: DeepTarget
Commit: 2a9d4d0970c0b599bb89db961aacb8daa4af1f56
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 16:16:45 -0500
Commit message:

 bump version
 
Package: DeepTarget
Commit: d4251e04f37fffd645292ea68db951bd8c5a83f0
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 16:13:42 -0500
Commit message:

 remove hidden files
 
Package: DeepTarget
Commit: f8c540c3537e03a70eae0cc4eeaa166d4cbe67c3
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 15:48:35 -0500
Commit message:

 updating version from 0.99.11 to 0.99.12
 
Package: DeepTarget
Commit: 8dff0e95801c86cdb96d0e87696e955a51d5a96a
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 14:57:44 -0500
Commit message:

 updating recommendations and requirements from reviewer
 
Package: DeepTarget
Commit: 0da39ce5ffb0e74d572a82c17d4f211d05cbcc0e
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 14:44:48 -0500
Commit message:

 update README.md
 
Package: DeepTarget
Commit: 6f767c71e96eaa0db82b91cd4c401e8ee77ff172
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2023-11-30 14:18:31 -0500
Commit message:

 adding NEWS.md
 
Package: DeepTarget
Commit: 3ff5046d70555a82cda7336980df73321e118cd0
Author: Trinh Nguyen <lovsmalgir@yahoo.com>
Date: 2023-11-30 12:22:47 -0500
Commit message:

 Delete DeepTarget directory

Accidentally push the whole project as sub. 
Package: DeepTarget
Commit: dd842fb3b5f6b6e700fa316d745f464c5f38a017
Author: Trinh Nguyen <50640811+TrinhNguyenP@users.noreply.github.com>
Date: 2023-11-30 11:15:50 -0500
Commit message:

 revised and fixed following reviewer's requirement and recomendation
 
Package: rhdf5
Commit: 4e62f4610599fd24006307dde9d57a2500e847c2
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-30 15:49:54 +0100
Commit message:

 Add correct signature for _h5fileLock to header.
 
Package: enrichplot
Commit: 9598579d15309d2a75b5d4f03d453159406b2330
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-30 22:53:51 +0800
Commit message:

 ridgeplot supports passing a vector of selected pathways, #193
 
Package: enrichplot
Commit: 0295c3435f3199762f60f08172c0a4e7426146d0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-31 09:13:31 +0800
Commit message:

 update docs
 
Package: enrichplot
Commit: 74b6b4c210dcdb41a0272d6df146a7fa999c7f03
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-31 09:12:02 +0800
Commit message:

 Merge pull request #260 from huerqiang/treeplot

Fix treeplot() 
Package: enrichplot
Commit: 6fbcce45278b25346a76f7d7b2ed8315627f6b22
Author: huerqiang <13766876214@163.com>
Date: 2023-10-28 22:21:37 +0800
Commit message:

 fix treeplot()
 
Package: enrichplot
Commit: b86b0a1770e954f2ea82aac4f6a93bee9544d1a1
Author: Erqiang Hu <13766876214@163.com>
Date: 2023-10-28 14:32:02 +0800
Commit message:

 Merge pull request #47 from YuLab-SMU/devel

merge 
Package: enrichplot
Commit: 7836fbac55f782e78b42e9e85a38b7fc85601fc1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-25 17:12:46 +0800
Commit message:

 update bioc version
 
Package: enrichplot
Commit: ba9da6f29360f7f1924596a61ea2b3aece6fdc6d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-25 17:12:46 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
 
Package: enrichplot
Commit: 0d0e32afa5be40c4df8f80e853091c69df292c62
Author: Erqiang Hu <13766876214@163.com>
Date: 2023-09-16 06:41:23 +0800
Commit message:

 Merge pull request #46 from YuLab-SMU/devel

merge 
Package: enrichplot
Commit: 8c0a693e5136ab547444e83fa1e6abec42e3efb6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-09-16 00:30:31 +0800
Commit message:

 update
 
Package: Ribostan
Commit: 733b3ca474e398b4a96328ada0c1ca3b0e9fd913
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-11-30 15:33:45 +0100
Commit message:

 Bump version
 
Package: Ribostan
Commit: 4bb6d9f91eca57ffec1b651729533b7bea0ac272
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-11-30 15:33:12 +0100
Commit message:

 Fix missing comma
 
Package: Ribostan
Commit: 51d201aee3552b9459e553f036a4e2d791f98638
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-11-30 15:27:34 +0100
Commit message:

 Bump version
 
Package: Ribostan
Commit: bb7b4afddfbfe00075bc897ddcb436b1a31afb29
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-11-30 15:17:45 +0100
Commit message:

 Cope with Ns in start codons
 
Package: Ribostan
Commit: 109c7574953920487458b74f5031f2b7f7d86e88
Author: ggvillamil <32459419+ggvillamil@users.noreply.github.com>
Date: 2023-11-08 14:27:19 +0100
Commit message:

 Merge pull request #3 from ggvillamil/main

Fix minor issues and update namespace tags 
Package: Ribostan
Commit: 0b2e512c9d023e54cbdbc205de5c2bfa759c6205
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-11-02 20:16:50 +0100
Commit message:

 Fix another instance of str_detect()
 
Package: Ribostan
Commit: 614a9c0c68a697627d531cda3b71df3c0e0d646f
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-10-31 20:50:01 +0100
Commit message:

 Convert to vector before passing to str_detect()
 
Package: Ribostan
Commit: c130071b4c2a316c22ddfacfe65354594c1053b1
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-10-30 15:01:52 +0100
Commit message:

 Add export tag to the function make_ext_fasta()
 
Package: Ribostan
Commit: 07e8881270ef1edf15962643096fd601d8f5e57b
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-10-30 14:57:49 +0100
Commit message:

 Add pintersect to imports and update with roxygen
 
Package: Ribostan
Commit: 27855fe315ea4b745bd6af3fddb4a8228055b848
Author: Gabriel <gabriel.villamil@mdc-berlin.de>
Date: 2023-10-26 18:44:44 +0200
Commit message:

 fix typo in data frame column name
 
Package: Ribostan
Commit: bdab1aee88c09fd547452596ad8c6c0be32070f4
Author: Dermot Harnett <zslastman@gmail.com>
Date: 2022-02-28 12:17:01 -0500
Commit message:

 dplyr removal
 
Package: Ribostan
Commit: 91ac40431a45ecb69dcc365882616a5d854f5b0c
Author: Dermot Harnett <zslastman@gmail.com>
Date: 2022-02-24 16:51:06 -0500
Commit message:

 dplyr NSE removed
 
Package: Ribostan
Commit: bf1de26eac972ac51ee506213c01b068769f41d1
Author: Dermot Harnett <zslastman@gmail.com>
Date: 2022-02-23 12:07:01 -0500
Commit message:

 function match fixes
 
Package: MGnifyR
Commit: 0a349662146c786cda1cf5e39bdf8499cc49419c
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-30 14:21:58 +0200
Commit message:

 Trigger bioc build
 
Package: MGnifyR
Commit: c4e8a07fea87ec67d99839f6072b5e0b1ec91d55
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-30 13:47:41 +0200
Commit message:

 Increase waiting time
 
Package: rawrr
Commit: 1a02a8a60c7c9cbb7e43ff15d961adc331c815d2
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2023-11-30 12:44:42 +0100
Commit message:

 use textconnection for readTrailer and readIndex
 
Package: MGnifyR
Commit: d3b090f77923c7d6202438ccc87d4c306a6d2061
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-30 13:32:44 +0200
Commit message:

 up
 
Package: Spectra
Commit: 64bd08c54ae77a9d27d0b9928c231d5e7cc55754
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-30 11:48:17 +0100
Commit message:

 refactor: address Sebastian's comment

- Bump version of Spectra object.
- Update bundled Spectra object.
- Disable parallel processing in vignette.
 
Package: Spectra
Commit: 9ac911b15fdca8603f17a8d923222bc963926322
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2023-11-30 10:06:55 +0100
Commit message:

 Merge pull request #306 from rformassspectrometry/processingChunkSize

Enable chunk-wise processing for all peaks data functions 
Package: Spectra
Commit: 3ba908bcae019718307493b3430f3a319045bcd9
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-30 09:55:41 +0100
Commit message:

 docs: fix comment from Andrea
 
Package: Spectra
Commit: 0e555dc720421d93ee6fda97830054c2817cff0b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-24 16:08:30 +0100
Commit message:

 refactor: add parameter f to more functions
 
Package: Spectra
Commit: 194f10439737d2aee85927d4d323e889d7dcf02a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-24 15:05:40 +0100
Commit message:

 refactor: address Phili's comments
 
Package: Spectra
Commit: e6a50c813ed4a949aa013e3cd84fc61225a6ccb2
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-24 08:48:44 +0100
Commit message:

 refactor: update function to all use the new chunk settings

- Use `processingChunkFactor` instead of `dataStorage` in functions to define
  splitting and processing.
- Remove unnecessary functions.
- Add a vignette on parallel/chunk-wise processing.
 
Package: Spectra
Commit: 72c65ea89a154a1763d3f3ba0b408a67689d7564
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-22 09:33:27 +0100
Commit message:

 docs: fix version
 
Package: Spectra
Commit: 67c88e387e7d86a6af35fb56b1e4bc623e9cbfaf
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-22 09:32:18 +0100
Commit message:

 Merge branch 'main' into processingChunkSize
 
Package: Spectra
Commit: 17e733f075d7d8103a444cc209dbc61871c5d44f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-22 09:27:01 +0100
Commit message:

 feat: enable chunk-wise processing for peaks data operations

- Add and modify functions to enable default chunk-wise processing of peaks
  data (issue #304).
- Split the documentation for chunk-wise (parallel) processing into a separate
  documentation entry.
 
Package: Spectra
Commit: 2e7366e75433107eb2f2502ad037454241d86487
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-21 06:56:38 +0100
Commit message:

 docs: start refactoring the parallel processing documentation
 
Package: Spectra
Commit: 432efc26c6605388f3e2d48fe784f80834db32eb
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-20 17:11:35 +0100
Commit message:

 refactor: move function
 
Package: Spectra
Commit: 37b8c99d897991ff0d409d08792b8e9011167619
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-11-20 14:57:25 +0100
Commit message:

 feat: add functionality enabling chunk processing by default

- Refactor the code to decide how to split `Spectra` for parallel processing:
  it's no longer done automatically by `dataStorage`.
- Add a slot to `Spectra` allowing to set a processing chunk size. Issue #304
- With chunk-wise processing only the data of one chunk is realized to memory in
  each iteration. This also enables to process data in parallel.
 
Package: MGnifyR
Commit: 85c46ce46d184960175a5da85bacb032bebd182d
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-30 12:58:15 +0200
Commit message:

 Do not run all examples
 
Package: rawrr
Commit: e45b9c0eace3ea5fb0dfb0d74bdc39c52c27fe88
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2023-11-30 09:49:46 +0100
Commit message:

 add LockMassCorrection plot method
 
Package: csaw
Commit: b6fe9349368cd4b1fb998a8f80fc884ebeb986b0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 23:21:57 -0800
Commit message:

 Relaxed numeric precision in tests to pass CHECK on Arm Macs.
 
Package: BiocNeighbors
Commit: 95c21b828c64bf7ec0fe19ec49160c820dc6473a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 23:19:29 -0800
Commit message:

 Relaxed numeric precision in tests to pass CHECK on Arm Macs.
 
Package: CelliD
Commit: c5cced2dcb730cfd6a98d1b234405383ae2d78a6
Author: Cortalak <acortal@ip-10-0-138-31.ap-southeast-1.compute.internal>
Date: 2023-11-30 06:48:22 +0000
Commit message:

 version bump in devel
 
Package: CelliD
Commit: d06413d7654debc43dd89fd5f92636fa540c3813
Author: Cortalak <acortal@ip-10-0-138-31.ap-southeast-1.compute.internal>
Date: 2023-11-30 06:46:32 +0000
Commit message:

 bug fix: seurat v5 bug fix
 
Package: ggsc
Commit: 7c02be5c303faa84681aeaad54e79a72f523988f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-30 11:21:03 +0800
Commit message:

 update
 
Package: ggsc
Commit: ede2fcfdfad31f167bedc1b0a01c37ad71e91f33
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-29 16:13:15 +0800
Commit message:

 update desc
 
Package: ggsc
Commit: 4314f136c38b65e9b912572dec2d3f7e4b728814
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-29 16:07:49 +0800
Commit message:

 update installation
 
Package: ggsc
Commit: 1ea91d715f89d9bfec8170f645202cdf9547adb3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-29 15:46:23 +0800
Commit message:

 update docs
 
Package: ggsc
Commit: b5a3ac1461d25c818b5f1c2c81ee7518e28990ab
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-29 14:36:05 +0800
Commit message:

 Merge pull request #15 from noriakis/sc_dot

Implementation of `sc_dot` method 
Package: ggsc
Commit: c2572e2a1ff4633ad4b39bc24e929cd2740e10b5
Author: noriakis <nori@hgc.jp>
Date: 2023-11-29 08:46:44 +0900
Commit message:

 revising the codes
 
Package: ggsc
Commit: 9a84deac9403da0729572b83f024df80e705dea0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-27 11:01:11 +0800
Commit message:

 update news
 
Package: ggsc
Commit: cf80706293712c7fc9aef2ca2e96f7ee4386e232
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-11-27 10:57:13 +0800
Commit message:

 Merge pull request #14 from lch14forever/devel

retrieve embedding without FetchData 
Package: ggsc
Commit: 0afcf76be758f9ffeb9dc008ce8196581b91da7d
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-11-25 21:26:24 +0900
Commit message:

 cluster.idents and feature.groups
 
Package: ggsc
Commit: ea6d9efa46e7237772b761d995983ab1d6866901
Author: noriakis <nori@hgc.jp>
Date: 2023-11-24 12:13:12 +0900
Commit message:

 Resolving rcmdcheck
 
Package: ggsc
Commit: d1e602dc48af002f49d5f20a29cc721e2b5f0cff
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-11-23 22:47:09 +0900
Commit message:

 update sc-dot.R param description
 
Package: ggsc
Commit: 5e89476f6bd6bcec76b46b77349d2ce5e69845b0
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2023-11-23 21:45:46 +0900
Commit message:

 roxygenise sc-dot
 
Package: ggsc
Commit: 22dd11fb21f19677ccc0673b6f82cf49200cf717
Author: noriakis <nori@hgc.jp>
Date: 2023-11-21 12:10:34 +0900
Commit message:

 set default group.by
 
Package: ggsc
Commit: 99af227abcac1d36017de1c690bdd35e96afe777
Author: noriakis <nori@hgc.jp>
Date: 2023-11-21 08:45:02 +0900
Commit message:

 example and documentation improvement
 
Package: ggsc
Commit: 4e2eb0fd023f1f7ce011deb2bc8783650a83a78d
Author: noriakis <nori@hgc.jp>
Date: 2023-11-21 08:38:34 +0900
Commit message:

 implementation for Seurat object
 
Package: ggsc
Commit: 5f130b465aee63b34cf285d2237beaeb87bf8ce5
Author: noriakis <nori@hgc.jp>
Date: 2023-11-20 21:38:45 +0900
Commit message:

 Compatible with the original function (for SCE)
 
Package: ggsc
Commit: 52a2567afa739b9e756a46acc0c8722d9ac27be2
Author: noriakis <nori@hgc.jp>
Date: 2023-11-20 18:19:18 +0900
Commit message:

 split.by in SCE
 
Package: ggsc
Commit: 8da8959be14b5e00de95208a4195dc19051df10e
Author: noriakis <nori@hgc.jp>
Date: 2023-11-20 17:42:48 +0900
Commit message:

 basic sc_dot in SCE object
 
Package: ggsc
Commit: b0544bd1250b497eac7d171e47ee00e4d0795c77
Author: Chenhao Li <lichenhao.sg@gmail.com>
Date: 2023-11-06 17:10:00 +0000
Commit message:

 retrieve embedding without FetchData
 
Package: ggsc
Commit: af951af4148315ca3edcdaaf7ea82a9e663eb99a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-31 23:59:54 +0800
Commit message:

 update docs
 
Package: ggsc
Commit: f3c97788a393c391c9d3a68e1f6208463008bc4a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-31 23:46:43 +0800
Commit message:

 Merge pull request #13 from xiangpin/master

fix the issue for Seurat object 
Package: ggsc
Commit: e1b137f3cc4d3ea3018ddde3200e6976d640e04a
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 20:55:28 +0800
Commit message:

 Merge branch 'master' of https://github.com/xiangpin/ggsc
 
Package: ggsc
Commit: 8c9fa08d9c27e621ff88293a5b152c07c4e3cdfa
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 20:01:36 +0800
Commit message:

 adjust the legend name when density = TRUE
 
Package: ggsc
Commit: 95f3037ac726cf0745b87df1bcd0c1d7d4a6a256
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 17:27:27 +0800
Commit message:

 fix the sc_spatial bug for Seurat
 
Package: ggsc
Commit: b77b445dbb17c7cac03abf57881b876992f81c48
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 16:11:56 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
 
Package: ggsc
Commit: 2f0ef04b2a030c004fb91615abe371b04fee5fbc
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 16:09:05 +0800
Commit message:

 fix the api of sc_violin
 
Package: ggsc
Commit: 041e3c2ca125f9c29a1f8d7cfcad41b36ccb935a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-31 15:30:27 +0800
Commit message:

 ignore document source branch
 
Package: ggsc
Commit: 540be745c951c289ca4b770d6c340c2eb26dcb49
Author: xiangpin <xshuangbin@163.com>
Date: 2023-10-31 09:59:25 +0800
Commit message:

 fixed the violin plot data api for seurat object
 
Package: alabaster.sce
Commit: 83d0c10263cf08cfdd5f9f09bd4fb11e5de0c0d2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 13:39:29 -0800
Commit message:

 Bumped version and date for BioC-devel.
 
Package: alabaster.sce
Commit: 15c5f3fadd4270f9af26b2399418bdb5f3bf77a8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 13:29:52 -0800
Commit message:

 Migrate SCE saver/loader to the new, simplified world.

This relies on the new takane C++ validators to enforce file contents.
 
Package: alabaster.se
Commit: 66df0381b5968a7396f0a7a02499456002c17af8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 13:02:43 -0800
Commit message:

 Save the representation's version for RSE's saveObject.
 
Package: alabaster.se
Commit: 5afcb909cc54f6231bb60ba2bd29cc4027a71c70
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 10:46:49 -0800
Commit message:

 Automatically omit row_ranges if the rowRanges are detected as being empty.
 
Package: alabaster.se
Commit: 8b67947be3b71aa57fbd6157320544316a98c65e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 10:27:48 -0800
Commit message:

 Allow saving/reading of SummarizedExperiments with no 'assays' subdirectory.
 
Package: alabaster.se
Commit: 1e11a6d249b4bdb2fbd9c51adc791f2e57c29055
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 07:36:42 -0800
Commit message:

 Bumped version and date.
 
Package: alabaster.se
Commit: 3f1bc1da7d45e3cdd975c8d588893328ed41c88d
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 23:50:43 -0800
Commit message:

 Transition (R)SE savers and loaders to the new simplified world. (#2)

This aligns with the new takane validators in alabaster.base. 
Package: alabaster.base
Commit: e7502326e47a5145b374aa8618ee3cc0d5a94d24
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-29 07:33:52 -0800
Commit message:

 Further updates to the takane libs.
 
Package: alabaster.base
Commit: 79967e02acbb22dd9c1a54d9283da4fd43cb9738
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 17:14:19 -0800
Commit message:

 Skip loading of mcols/metadata if the corresponding paths are NULL.
 
Package: alabaster.base
Commit: bb2ca6a814a1f70aa7b599d96b2c0c2eb57dfb27
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 15:35:46 -0800
Commit message:

 Updated the vendored takane libraries.
 
Package: alabaster.base
Commit: b1f6dbe2e601e32abd5561416e374e76311756df
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:26:51 -0800
Commit message:

 Bumped version and date for BioC-devel.
 
Package: alabaster.base
Commit: 3bd3d67e02d49dd0339812df9ae6d00a447c9613
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 07:50:36 -0800
Commit message:

 Moved the base list format global switch into saveBaseList.R.

This also centralizes the documentation for the switch with the saving
method that it affects for easier discovery.
 
Package: alabaster.base
Commit: 4d6adf519f4eb544c56e31fede75986be53a71e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 23:09:21 -0800
Commit message:

 Avoid expansion of nested objects as DF columns.
 
Package: alabaster.base
Commit: af591a0c1e963fdfeaed3f5bab3c9db4667b61a7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 12:56:15 -0800
Commit message:

 Exposed more HDF5 utilities for use by downstream packages.

This allows for iterative writing of large vectors, e.g., for sparse matrices.
 
Package: alabaster.base
Commit: 8e900d5c955d597201439c29391a1a021949bc91
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 10:33:28 -0800
Commit message:

 Updated takane with the latest array validators.
 
Package: alabaster.base
Commit: 4c720cae27afdee8dd87787ea0d9e836e4974671
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 08:08:20 -0800
Commit message:

 Exported utilities to find actual NAs in numeric data.
 
Package: alabaster.base
Commit: c23c6bffb7a437d8fe81a57e295f40251c82c6a7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 19:02:35 -0800
Commit message:

 Bugfix to drop dimensions when reading atomic vectors.
 
Package: alabaster.base
Commit: 36a0b39c90ba9dbaff727e4566d55678b090256d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 18:51:33 -0800
Commit message:

 Further updates to the takane validators.
 
Package: alabaster.base
Commit: 1ba09b6244d45b7dfc25a1258550f5ee48382d98
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 18:27:51 -0800
Commit message:

 Exported the missing placeholder name variable.

Also split up HDF5-related transformation/placeholder utilities.
 
Package: alabaster.base
Commit: 986531fda1a76ab8ae2d6c411af4c2a2ea0a99c7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 18:02:18 -0800
Commit message:

 Bugfix to correctly handle NA factors inside lists.
 
Package: alabaster.base
Commit: 2ea43698eefd5772bb8271e35dc110d7d49cbfc5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 17:52:53 -0800
Commit message:

 Remove extraneous internals for the base list HDF5 saver.
 
Package: alabaster.base
Commit: 42f36afeedfc3ba8150a770c679fb0df78038a24
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 17:34:45 -0800
Commit message:

 Do not rely on rhdf5's high-level functions. (#22)

In general, we get more control by just assembling the low-level 
functions ourselves. Some more specific reasons are listed below:

- Avoid excessive rhdf5-specific attributes for logical, NA handling.
- Easier saving of scalar datasets, which needs the handles anyway.
  This allows us to remove the C++ code and reduce the binary size.
- Easier specification of custom HDF5 datatypes without having to
  constantly reopen dataset handles that were just created. 
Package: alabaster.base
Commit: 281186aeb36a22db3dcb8f37be4f64a9ab34c3b1
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-23 23:54:04 -0800
Commit message:

 Updated takane  validators and accompanying R bindings.

This adds validation support for various genomic ranges classes, such as the
genomic_ranges itself, sequence_information and various compressed lists.

We also transition to saving factor codes as unsigned integers. This is, on
the whole, more sensible, as downstream consumers don't have to check whether
the codes are negative (which would make no sense outside of missing
placeholders, and we don't need half the integer space for that).
 
Package: alabaster.base
Commit: 48d7a42e11f6d002240bd4fec809586d80094ae6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-19 19:04:56 -0800
Commit message:

 Forbid registration of readers for existing types.
 
Package: alabaster.base
Commit: d9f16f1645ee20b26dbb66d853687af684cbc22d
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-19 18:03:43 -0800
Commit message:

 Validate all on-disk representation immediately after saving. (#20)

This uses the latest takane C++ validators to check the contents of the
directories created by saveObject. This enforces consistency in the
representations across all frameworks that use the same validators.
Extension developers are now expected to register their own validation
functions, either directly in R or by adding an appropriate C++ validator. 
Package: alabaster.base
Commit: 396f307445237d058836801ceab0cfb39c4da7d5
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-16 23:54:44 -0800
Commit message:

 Switch to a simplified layout for the readers and savers. (#19)

This eliminates the involvement of schemas, allowing each reader and saver to
handle its own affairs without coordination with a separate metadata schema.
The only mandate now is an OBJECT file that controls loader dispatch; all other
files are left to the discretion of the reader/saver specification.

This enables major simplification on several fronts. There is no need to save
metadata and pass it between methods; we don't need to consider a staging
directory and we can save each object directly to its own directory; and thus
there is no need for many of the special directory-manipulating functions. The
instructions for application/extension developers is also greatly simplified.

The old functions are still kept around for back-compatibility, but we stripped
out the documentation to make it clearer for new developers. 
Package: alabaster.base
Commit: 2aac6389680951167c3e352e775f669a84513b4f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-12 16:56:19 -0800
Commit message:

 Remove unnecessary rownames from the mcols when staging.

These will get overridden by the names on the Vector object itself
anyway, so there's no need to waste a column storing them again.
 
Package: alabaster.matrix
Commit: 294a42e76fe033de103ac766fa77f12a522c55ee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:30:25 -0800
Commit message:

 Bumped version and date for BioC-devel.
 
Package: alabaster.matrix
Commit: d60fce684d90513eb73ba0abb2d1d0a9ecf8a4f3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:30:11 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: alabaster.matrix
Commit: 7905e7125a9c6b65eb687bfbc29a6dafa3abe0b4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:23:49 -0800
Commit message:

 Fixes to pass CHECK.
 
Package: alabaster.matrix
Commit: 50b11b6ec7b4c9d22fd642524a95a666dbb1f4ee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:04:11 -0800
Commit message:

 Updated the user's guide.
 
Package: alabaster.matrix
Commit: 03e18a5c39742666104b632c5f66d0990e21dfa2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 08:28:53 -0800
Commit message:

 Introduced the ReloadedArray class to track reloaded arrays.

This allows the saveObject method to optimize roundtrips by just
skipping the entire process and copying existing files.

All read* functions now emit a ReloadedArray class, with an option
to create an appropriate in-memory representation if so desired.
 
Package: alabaster.matrix
Commit: 88f85577ea53f8bb78f850ece964b1cd7b0b45bc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 23:10:38 -0800
Commit message:

 Bugfix for correct dimnames reading in dense arrays.

Also extended tests for arrays inside DFs to the new world.
 
Package: alabaster.matrix
Commit: afc5c55ad2c509243f7b537a698f84eadc7c105a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 22:59:29 -0800
Commit message:

 Separated array tests for old and new worlds into separate files.

Also added some missing tests for the sparse matrices, namely around dimnames,
pristine diversions, and non-default placeholders.
 
Package: alabaster.matrix
Commit: 013b5b1c585afe2a15ae210a0455d17f0c19d270
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 22:54:22 -0800
Commit message:

 Added simplified saving methods for DelayedArrays.

Currently these just divert to the dense/sparse savers; support for
preservation of delayed operations via chihaya will be added later.

Also unlocked the sparse tests so that they check the block processing.
This also involved some bugfixes.
 
Package: alabaster.matrix
Commit: d9e324c94e7da5ad738e4223ecc34413cb4d3690
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 21:37:01 -0800
Commit message:

 Minor patches for HDF5Array bugs in sparse matrix tests.
 
Package: alabaster.matrix
Commit: b72494feaa0fafe9442e0994b33117ba19581a63
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 16:58:28 -0800
Commit message:

 Might as well depends on alabaster.base.
 
Package: alabaster.matrix
Commit: b4a44ab2644db80c7f9e221284f7fd321635158f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 16:57:56 -0800
Commit message:

 Use readObject in tests to check for correct dispatch.
 
Package: alabaster.matrix
Commit: 05c072f68e0227509114d7d579c1b16ce7d2cda3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 16:49:01 -0800
Commit message:

 Migrated the saving/loading of sparse matrices to the simple approach.
 
Package: alabaster.matrix
Commit: e2dba083e16891f7b28632b4eda85b8b55ab9def
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 12:30:18 -0800
Commit message:

 Extend the optimizer so that it works for sparse arrays.

This includes the usual sparse Matrix classes, SVT_SparseMatrix objects,
and sparse block processing of everything else.
 
Package: alabaster.matrix
Commit: d52ab0b2426ca94cf58c63a7a561f406a326226e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 10:56:16 -0800
Commit message:

 Use optimized types when saving a dense array.

Also switch to direct writes of blocks via low-level rhdf5 functions
instead of relying on writeHDF5Array; this is because we need to
substitute NAs for placeholders on the fly to save memory.
 
Package: alabaster.matrix
Commit: 366ef6e2bdbc35081f6633629d91ce843c54a616
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-27 10:41:03 -0800
Commit message:

 Added internal utility to optimize HDF5 storage type based on array contents. (#6)

This also finds a suitable missing value placeholder if NAs are present in the array. 
Package: alabaster.matrix
Commit: f74651ff360c1756185ff2c6f840d84b91e654d5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-26 23:17:01 -0800
Commit message:

 Tighted DelayedMask behavior to align with missing value policies.

The major change is that, if 'is.na()' is TRUE for a placeholder, we will mask
all values for which 'is.na()' is TRUE; this includes NaNs that were previously
not masked. This aligns with the takane policy of not trusting NaN payloads.

Another change is that, if we see an integer dataset with a NA and the
placeholder is not NA, we throw an error because the dataset's NA was likely an
attempt at -2^31, which we just can't represent as a regular integer in R.
 
Package: alabaster.matrix
Commit: 5ca5c176815511349c982b99ba13fc04e6875e11
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-26 23:16:11 -0800
Commit message:

 Switched the array savers/loaders to the simplified approach. (#5)

This eliminates the dependence on schemas and aligns with the C++
validators implemented in takane (and compiled in alabaster.base). 
Package: spatialLIBD
Commit: ef76198a98c73b713de4b6a8795604b6b7d593ed
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2023-11-29 14:51:34 -0600
Commit message:

 Fix spacing
 
Package: spatialLIBD
Commit: 94048657dd0cf134b8e2347933e4302f75cec415
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2023-11-29 14:50:17 -0600
Commit message:

 v1.15.1 -- Add DropletUtils to Suggests as recommended by Jennifer Wokaty
 
Package: MGnifyR
Commit: dd3bfce6f8a58ce0daab7aa605669c255ddac37d
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-29 20:28:33 +0200
Commit message:

 Make tests shorter
 
Package: rhdf5
Commit: 3c508774f1ad2c9bc7a3ef6723111140c787391e
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 16:46:57 +0100
Commit message:

 Typo
 
Package: rhdf5
Commit: 12839c49241acaa24a26b4564fe2cb33dafd7d59
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 15:16:52 +0100
Commit message:

 Merge pull request #135 from grimbough/issues-from-LTLA

Fixing issues from LTLA 
Package: rhdf5
Commit: a8be09b2ef4ef4e5bf8ed88ca49cc1de067e0263
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 14:29:56 +0100
Commit message:

 Skip S3 tests on CI and BBS
 
Package: rhdf5
Commit: 1fd6af33e41f85aa5e9533820cd01e65d54a1013
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 13:48:28 +0100
Commit message:

 Fix leaking reference to dataspace
 
Package: rhdf5
Commit: 00744fc79e62f4cc68fa68a998d9f88079775abc
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 12:24:33 +0100
Commit message:

 Version bump
 
Package: rhdf5
Commit: cdd83f0a8a7d4fb9c20d13c23ee971d680a341c8
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 12:24:13 +0100
Commit message:

 Update NEWS
 
Package: rhdf5
Commit: 997ede98d111420ceb8f9b05293f2679b036f572
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 12:21:02 +0100
Commit message:

 Additional unit tests for zero length vectors
 
Package: rhdf5
Commit: aa4993df43f15bca5a2c048b341d03eabe210c6c
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 12:20:45 +0100
Commit message:

 When reading zero elements from integer and float datasets immediately return an appropriatly shaped R array and skip trying to actually read anything.  We alread do this for strings. Fixes #134
 
Package: rhdf5
Commit: 7573f25da5c25c9af6e5661486cef8085386dc9a
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 10:06:56 +0100
Commit message:

 Merge bioc upstream changes

Merge branch 'master' of git.bioconductor.org:packages/rhdf5 into issues-from-LTLA

# Conflicts:
#	DESCRIPTION
 
Package: rhdf5
Commit: f1e8b069801d92daa697321c4ed0c51ecddeb248
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 10:02:44 +0100
Commit message:

 Unit test for reading fixed then string attributes
 
Package: rhdf5
Commit: 5cc0f3253011352947c28b8d3930245b7d1d27e5
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-11-29 10:02:28 +0100
Commit message:

 Refactor string datatype reading so H5Dread and H5Aread use the same code.  This also fixes #132
 
Package: rhdf5
Commit: cb102ba93d22a703de118e4e8e65ae73c4aaff0c
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-10-20 16:23:24 +0200
Commit message:

 Be explicit about BiocSyle functions in vignettes
 
Package: rhdf5
Commit: a1053f20bbe193a65d5fa9efa79de4d6eaa8e713
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-10-19 14:11:43 +0200
Commit message:

 Be explicit about BiocSyle functions in vignettes
 
Package: rhdf5
Commit: e2e4ef7899f23579a815764b0a39406b893ab561
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-09-19 13:00:32 +0200
Commit message:

 Update version

Merge branch 'scverse-hackathon' into devel

# Conflicts:
#	DESCRIPTION
 
Package: rhdf5
Commit: 4d430edf2a95cc9a2e4dfbf857ff6ff41cdef61d
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-07-12 11:09:12 +0200
Commit message:

 Install rhdf5filters separately
 
Package: rhdf5
Commit: 5b6d4e85a98c449bcaafbad0f326e1919682dcd7
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-07-12 10:32:47 +0200
Commit message:

 Remove unused import
 
Package: rhdf5
Commit: f37bf0190869d918780a601b369f4414aa885b58
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-07-12 10:14:41 +0200
Commit message:

 Update workflow runners
 
Package: rhdf5
Commit: 093de937105c4e126fe584ce786d3b444ee4d1b0
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-07-10 11:23:30 +0200
Commit message:

 Comment out class for now
 
Package: rhdf5
Commit: e59a50ae1fb287755a1ad71a74524cbbdc022f58
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-05-11 12:29:43 +0200
Commit message:

 Remove exprimental class.  Addresses #125
 
Package: rhdf5
Commit: eaf8d2447175a5b54de4298071ff6eba5b554c64
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-25 14:30:33 +0200
Commit message:

 Add TODO
 
Package: rhdf5
Commit: 8f70f64a8c974efa8c094c18fd44e52689ccdeda
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-24 14:47:20 +0200
Commit message:

 Version bump
 
Package: rhdf5
Commit: 1028b5ebff11ddac518b985ea1ae3ff5ca949ca2
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-24 14:46:17 +0200
Commit message:

 Add option to read anndata nullable arrays
 
Package: rhdf5
Commit: ecc313980baf83978669a270ac6e4f16842583db
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-24 14:45:38 +0200
Commit message:

 Add nullable example file
 
Package: rhdf5
Commit: 2d68158fc7bdfa85b7757a0df28f9dc23c590ed2
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-21 11:38:36 +0200
Commit message:

 Add function to get the values from an enum datatype
 
Package: rhdf5
Commit: 59de63cc449dde8f3fa4e50732480b644faa6d07
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-20 14:08:23 +0200
Commit message:

 Missed some
 
Package: rhdf5
Commit: a88566298089851cea358273360de0649950227e
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-20 13:59:44 +0200
Commit message:

 More updates for handling enum datatypes
 
Package: rhdf5
Commit: eb8144b65610dc8ac9a9a7f1d50c9b1af0bf91fb
Author: Mike Smith <grimbough@gmail.com>
Date: 2023-04-19 16:01:38 +0200
Commit message:

 Testing ENUM attributes for #125
 
Package: SingleRBook
Commit: 5463c405368a23d64243bf1d5b7d15488939b890
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 22:55:00 -0800
Commit message:

 Bumped version and date.
 
Package: SingleRBook
Commit: 11889a5021043f7ef937dae325e812f765a41093
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 22:54:33 -0800
Commit message:

 Cut out the failing ontology chapter and all references to it.
 
Package: CRISPRball
Commit: bfd09589a6029a7f07eee96c1dfbccdd939d3080
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-28 17:21:17 -0600
Commit message:

 version bump
 
Package: ReactomeGSA
Commit: 8fd9e471c63d9e23821927e4a7a8bb32cbba7218
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2023-11-28 22:33:40 +0100
Commit message:

 Added support for public data retrieval
 
Package: CRISPRball
Commit: 8316cd0fc65c3f7d067421d23a1b2d826277d69b
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-28 14:58:11 -0600
Commit message:

 test fix, version bump
 
Package: alabaster.ranges
Commit: c6e63acb1ab588490de08094bc107ceb0cc79491
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:29:31 -0800
Commit message:

 Bumped version and date for BioC-devel.
 
Package: alabaster.ranges
Commit: c4091043b34b7ad76cf3eeb5591c807b748a5b76
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-28 09:29:19 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: alabaster.ranges
Commit: bdb0afc30b0de54889038e1b2cd6baf18bb80522
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-24 18:54:09 -0800
Commit message:

 Updated code to align with the latest takane validators.

Also switched to low-level rhdf5 functions, consistent with alabaster.base.
 
Package: alabaster.ranges
Commit: 210234538f35e811964e45470c0cb7befbdca60b
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2023-11-20 10:44:58 -0800
Commit message:

 Transition to the simplified on-disk layout that doesn't use schemas. (#1)

This eliminates the involvement of schemas, allowing each reader and saver to
handle its own affairs without coordination with a separate metadata schema. 
Package: decoupleR
Commit: 2a57d2a93709001ca54f0a5701f413ce6b4fe3bb
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-11-28 17:03:29 +0100
Commit message:

 Bump version: 2.9.0 → 2.9.1
 
Package: decoupleR
Commit: 28f0b3d1093dbbdfe8122983f941af75f39dba53
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-11-28 17:03:21 +0100
Commit message:

 Matched bump2 verison to 2.9
 
Package: decoupleR
Commit: e94bc51eb14ba0ec9328f94ff5c638ba6dc17b09
Author: deeenes <turei.denes@gmail.com>
Date: 2023-11-21 18:22:26 +0100
Commit message:

 merge from bioc
 
Package: decoupleR
Commit: c30d980fc8ac0c31aa6539961bf9f6c56093a036
Author: Pau Badia i Mompel <44896790+PauBadiaM@users.noreply.github.com>
Date: 2023-11-14 09:59:17 +0100
Commit message:

 Merge pull request #101 from adugourd/master

Update README.md 
Package: decoupleR
Commit: 51fda83f996a979b5a9016cafd3594fd7234ebd9
Author: Aurelien Dugourd <aurelien.dugourd@bioquant.uni-heidelberg.de>
Date: 2023-11-14 09:57:30 +0100
Commit message:

 Update README.md 
Package: decoupleR
Commit: dd9d47ea884570977fc88f8d10a579d40921b9a5
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-10-06 09:11:57 +0200
Commit message:

 Updated tf bulk vignette
 
Package: decoupleR
Commit: d3b53dc89e847a5837893a81e1e9dad04c57259c
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-09-27 15:08:44 +0200
Commit message:

 Fixed label mistake in TF vignette
 
Package: decoupleR
Commit: bc7a1576deb2ae8a7d57441f6324441e18b6e474
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-19 00:15:51 +0200
Commit message:

 added `bump2version` config
 
Package: decoupleR
Commit: 2dec3fc4b35a3857b70d0136117d96b76fcfc0d9
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-19 00:14:46 +0200
Commit message:

 Bump version: 2.7.0 → 2.7.1
 
Package: decoupleR
Commit: f586e370fcb6b4201433f4f486487e964f12cbdc
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-19 00:13:57 +0200
Commit message:

 `utils-omnipath`: added static table fallback
 
Package: decoupleR
Commit: 75a57d997a73d4dcebe487cc9c2b8d20c975d464
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-18 17:45:08 +0200
Commit message:

 `check_organism`: maintain minimal functionality also offline
 
Package: decoupleR
Commit: 5f40db462e8c5c6282cce6077ee3d0200e7bb056
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-18 16:03:40 +0200
Commit message:

 fixed old OmnipathR warning message + merged duplicte code
 
Package: decoupleR
Commit: eed1093d07904e4e1d1dfd9b6c0e69ed9eaf06a4
Author: deeenes <turei.denes@gmail.com>
Date: 2023-09-18 11:47:37 +0200
Commit message:

 merge
 
Package: decoupleR
Commit: cf86464e854fef7c7bb63963e397fe66649d4772
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-08-18 10:45:10 +0200
Commit message:

 Changed versioning of glmnet
 
Package: decoupleR
Commit: 500f73413938909d82eacb601107f44551feacc3
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-06-20 13:33:49 +0200
Commit message:

 Updated docs
 
Package: decoupleR
Commit: 42cd036dcb784019968c2408551390d659a59468
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-06-15 17:51:47 +0200
Commit message:

 Made ulm faster
 
Package: decoupleR
Commit: f21143f3da16b4385f5cad9d55e25f62da4ace21
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-10 15:52:31 +0200
Commit message:

 typo
 
Package: decoupleR
Commit: 14e0524080f73ba143488dc7fc90f229e1d2cb31
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-10 15:23:18 +0200
Commit message:

 `inst/doc` into `.Rbuildignore`
 
Package: decoupleR
Commit: 9f61705bd76a32f35c8316b0899c0967f83635b4
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-10 15:22:35 +0200
Commit message:

 do not build vignettes in check-r-package
 
Package: decoupleR
Commit: 324ea73a9287b61de87a85f1dcb5df5bc972dd25
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-10 01:08:29 +0200
Commit message:

 typo
 
Package: decoupleR
Commit: d9b3f4c6884d8114206a067812021e5518bd73f6
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 22:54:22 +0200
Commit message:

 github action: unquoted string parameter
 
Package: decoupleR
Commit: 86b66dcbea0147c6ea73c17f39d4a1af9fcf656e
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 22:24:29 +0200
Commit message:

 github action: install qpdf and do not fail on R CMD check warnings
 
Package: decoupleR
Commit: cdf0d17deac8d3b78b50cae2a8a9f95f309d47bb
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 22:18:51 +0200
Commit message:

 missing NSE variable names
 
Package: decoupleR
Commit: a76fca971a3d47e6ee45b65c878b59d0b89fe96e
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 22:10:30 +0200
Commit message:

 Rbuildignore: removed end of string anchors from directory names
 
Package: decoupleR
Commit: 9c3ba0eca74031358697fc9294b0a377604715ae
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 18:44:03 +0200
Commit message:

 added `parallelly` to dependencies
 
Package: decoupleR
Commit: 37c7d8da02b5eb7d41b73f44c7087c1966d9971c
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 18:12:31 +0200
Commit message:

 `nproc` based on available cores
 
Package: decoupleR
Commit: f7fc2e6dd5e0d0dd5d77b9713ce6d658e27e59f4
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 18:11:40 +0200
Commit message:

 trying to get rid of `doc` in github builds
 
Package: decoupleR
Commit: cc0eab2daee8e9fc7980be589bf86297c9f2722a
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 17:09:59 +0200
Commit message:

 minor updates on github action
 
Package: decoupleR
Commit: c2bd89ccc723460ff3648916026359e01dc98ae6
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 17:03:50 +0200
Commit message:

 github action: use r-lib actions for caching installed packages and R CMD check
 
Package: decoupleR
Commit: fcf3511ff0d2e64c54386ba3b490e8388c94e66c
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 14:53:47 +0200
Commit message:

 `docs` into `.Rbuildignore`
 
Package: decoupleR
Commit: ab887b459c75adbdb255ec6b765eb73ba57c0b59
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 13:22:25 +0200
Commit message:

 import only necessary functions from `rlang`
 
Package: decoupleR
Commit: 120907d1a01d4636f9929a3781929d5daf78782c
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 13:14:49 +0200
Commit message:

 docs rebuild
 
Package: decoupleR
Commit: c3ad69dc130412d7256d0c71fff1c43d0b0afd61
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 13:14:37 +0200
Commit message:

 replaced deprecated `lift_dl`
 
Package: decoupleR
Commit: b67ef8e99fe0eb354084c8abd24cd8dc1b972634
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 12:03:21 +0200
Commit message:

 removed `.data` usage
 
Package: decoupleR
Commit: 497c43c9b81ba5cafe357c831044c395e2e342eb
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-09 11:48:41 +0200
Commit message:

 remove `.data` in `utils-omnipath`
 
Package: decoupleR
Commit: 33101805c41718f90372eef9ebac772c2bfcd317
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-08 22:50:09 +0200
Commit message:

 cleaned up some R CMD check warnings
 
Package: decoupleR
Commit: 6c0c447fcd4d1b73477be520f1876a335cdd197d
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-08 22:49:46 +0200
Commit message:

 github CI: BioC 3.16 → 3.17
 
Package: decoupleR
Commit: 9ae78faa496ba7e053ca5f64a48bd6beea22d8de
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-06-05 12:52:54 +0200
Commit message:

 Fixed typo
 
Package: decoupleR
Commit: 0aaa89164a648fdbb7f19ad08b67dd8826c79fef
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-06-02 16:50:15 +0200
Commit message:

 Added magick
 
Package: decoupleR
Commit: 02739d9af63abeb634e740b43592ddd5680ab868
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2023-06-02 16:03:20 +0200
Commit message:

 Fixed omnipath issues for collectri
 
Package: decoupleR
Commit: cc649c9a775e3c9c46b4b6682d9e06b7319950c7
Author: deeenes <turei.denes@gmail.com>
Date: 2023-06-01 20:12:12 +0200
Commit message:

 improved organism handling
 
Package: decoupleR
Commit: b4671e883ffee83de512cb51e2c077ef80256fcf
Author: Pau Badia i Mompel <44896790+PauBadiaM@users.noreply.github.com>
Date: 2023-05-03 15:42:00 +0200
Commit message:

 Merge pull request #82 from smuellerd/master

Fixed translation to mouse 
Package: decoupleR
Commit: ad3b93bb6c526c6477c36879d834ea17a59d7254
Author: Sophia Müller-Dott <78087387+smuellerd@users.noreply.github.com>
Date: 2023-05-03 14:49:21 +0200
Commit message:

 Fixed translation to mouse 
Package: PIPETS
Commit: ab3f531a9b0f92a9511dff24e73e1883c19fb71e
Author: qfurumo <furumq@gmail.com>
Date: 2023-11-28 09:30:39 -0500
Commit message:

 Version Bump to repush to Bioconductor
 
Package: PIPETS
Commit: 50d3aba7959b954340fb53299cec5e7407c26245
Author: qfurumo <furumq@gmail.com>
Date: 2023-11-22 14:28:05 -0500
Commit message:

 Added GRanges functionality and changed downstream functions to match.
 
Package: PIPETS
Commit: aee2d710dbb72467b5104e5c500a91af74c5cad3
Author: qfurumo <furumq@gmail.com>
Date: 2023-11-15 14:11:04 -0500
Commit message:

 Version Bump
 
Package: PIPETS
Commit: 160cc3b37d4e4fac312fc5c31963d5aecc46e089
Author: qfurumo <furumo@bc.edu>
Date: 2023-11-10 11:52:06 -0500
Commit message:

 Made changes to align with Bioconductor reviewer comments.
 
Package: PIPETS
Commit: ab3f531a9b0f92a9511dff24e73e1883c19fb71e
Author: qfurumo <furumq@gmail.com>
Date: 2023-11-28 09:30:39 -0500
Commit message:

 Version Bump to repush to Bioconductor
 
Package: simona
Commit: c6e8b80b96c05c4b23977ae46e1a1ec126330306
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-28 13:28:29 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: simona
Commit: b0de913fb51ffd1165de1f74d206d6a486e24a32
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-28 13:28:15 +0100
Commit message:

 version bump
 
Package: simona
Commit: b0ef8519b463e4d7a68dbef3a7af59ed611c79b0
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-27 09:23:58 +0100
Commit message:

 update
 
Package: simona
Commit: 7f850c6f0c61b530d3e8da20f0b97f12bc67b94a
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-27 07:36:54 +0100
Commit message:

 add dag_permutate_children()
 
Package: MGnifyR
Commit: 3a6f40c1acafbe4a65d8eae1e3f3dd4fd7ab1118
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-28 12:04:15 +0200
Commit message:

 Version bump
 
Package: MGnifyR
Commit: 52dc040c0192fd6edd3c6f107e5f7cfb1f42a4d7
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2023-11-28 11:44:30 +0200
Commit message:

 Fix vignette (#24)

 
Package: distinct
Commit: 6cd50ca748dd541206ed0a340df056fa1030f2f2
Author: SimoneTiberi <simone.tiberi@uzh.ch>
Date: 2023-11-28 10:52:55 +0100
Commit message:

 C++17 Updated
 
Package: distinct
Commit: f633b52352a536c530287d597b237bc8eb2f58ad
Author: SimoneTiberi <simone.tiberi@uzh.ch>
Date: 2023-11-28 10:51:05 +0100
Commit message:

 C++17 Updated
 
Package: distinct
Commit: 11a17f8d76c66f815852ca52f5c67755961c24fb
Author: Simone Tiberi <simone.tiberi@unibo.it>
Date: 2023-11-22 13:18:48 +0100
Commit message:

 Update README.md 
Package: OHCA
Commit: 7cbd04df359ec9cba86b83f282761c5cdabb41f7
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-28 08:14:26 +0100
Commit message:

 bump to 0.99.1
 
Package: OHCA
Commit: d0b4151290402ac3a4a5ca373da2bb728fec6e33
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-28 08:12:39 +0100
Commit message:

 bump to 0.99.1
 
Package: OHCA
Commit: 3eba547b43b20f621e326bc58a6f5f4e424b6b5b
Author: js2264 <jacquesserizay@gmail.com>
Date: 2023-11-28 08:12:24 +0100
Commit message:

 feat: rm pdf rendering for now
 
Package: BERT
Commit: a86e2411e9b10b91e6ba009c26ab5a3f334e0644
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-28 07:37:33 +0100
Commit message:

 Set vignette seed for reproducibility
 
Package: SpatialFeatureExperiment
Commit: 6e76c283d5141a0ad0e8f7cb9996b3f3dbc2d0a8
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-11-27 19:49:35 -0800
Commit message:

 Attributes are so annoying
 
Package: SpatialFeatureExperiment
Commit: 4cec47aeb886c6ad308e5afc5810e99ffa0c33c6
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-11-27 19:15:18 -0800
Commit message:

 Merge branch 'main' into devel
 
Package: SpatialFeatureExperiment
Commit: 42e1b593f4dbad9994a89d2d6bedba4c69407a7f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-11-27 19:15:04 -0800
Commit message:

 Exclude all attributes in graph tests; attributes I want are tested separately. Closing #17
 
Package: SpatialFeatureExperiment
Commit: e4948c8c8e7c5caa0710aeceecac9997d9d2c060
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-25 12:27:14 -0700
Commit message:

 GitHub Actions test with devel Bioc
 
Package: SpatialFeatureExperiment
Commit: 8841d758d11b06aa9cf59ec95b5f010a942357f7
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-25 12:21:12 -0700
Commit message:

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 
Package: SpatialFeatureExperiment
Commit: 901fbf1b9dd6f69daea830fdcb03fa76a3cd9986
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-25 12:21:05 -0700
Commit message:

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	R/read.R
 
Package: SpatialFeatureExperiment
Commit: a296a7d067e93c19305b5822da46c05e556e78cc
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-25 12:19:22 -0700
Commit message:

 Import DropletUtils

Merge branch 'RELEASE_3_18' of git.bioconductor.org:packages/SpatialFeatureExperiment

# Conflicts:
#	DESCRIPTION
 
Package: SpatialFeatureExperiment
Commit: 10b58e02e8cb6861d8b4e6b9e99d55a286bd6a9c
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-25 12:12:39 -0700
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/SpatialFeatureExperiment into devel
 
Package: SpatialFeatureExperiment
Commit: 1773010d55575511e479daec30c4e01b9d755e61
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-05 15:42:20 -0700
Commit message:

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 
Package: SpatialFeatureExperiment
Commit: fbb963b3c9d8a643c062ebb7d0753385260fdaf4
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-05 15:42:18 -0700
Commit message:

 Include row names in the detected_transcripts.csv toy dataset to be more realistic
 
Package: SpatialFeatureExperiment
Commit: f480ac05ec45d25ee9b918d832085fb95f847d59
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-10-03 21:28:01 -0700
Commit message:

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 
Package: SpatialFeatureExperiment
Commit: 03cb8644324c1ae2012e6fab1e6c6c27afd3a5b2
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-27 17:22:02 -0700
Commit message:

 Added transcript spots test data
 
Package: SpatialFeatureExperiment
Commit: 3ea7625716dbc2f5a9b710292aa840ed08585826
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-22 19:59:21 -0700
Commit message:

 Updated NEWS and minor changes
 
Package: SpatialFeatureExperiment
Commit: c2000d088d13e52a53bf945b0f1ec5daf0b88de4
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-22 18:34:53 -0700
Commit message:

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 
Package: SpatialFeatureExperiment
Commit: cf23476b90c744aa3eba9545ebdec73c69bd1b38
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-22 18:33:52 -0700
Commit message:

 Pass existing unit tests, except for mysterious arrow segfault
 
Package: SpatialFeatureExperiment
Commit: 29d7d329b779816d7bb72bfb0ce47440f796aef0
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-22 16:17:37 -0700
Commit message:

 Forgot to remove missing methods for localResults and annotGeometries
 
Package: SpatialFeatureExperiment
Commit: 2c7b1b7939596dd5cf22c1f0d9aeafaaa9849713
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-22 15:52:10 -0700
Commit message:

 Removed the missing methods that clutter documentation pages. The default arguments should preserve behavior from users' point of view
 
Package: SpatialFeatureExperiment
Commit: 582ef85a82b159d9eb30f91cee58a2f078d92cd0
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-09-21 18:39:51 -0700
Commit message:

 Fixed problem cropping with geometry when sample_id = NULL and there's one sample
 
Package: SpatialFeatureExperiment
Commit: 3dde57b372f1a3d5093ce07821b69f36342a5c37
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-24 21:41:19 -0700
Commit message:

 Need to update _pkgdown.yml to manually create the sections. Truly addressing #7
 
Package: SpatialFeatureExperiment
Commit: 16bd428b93981a53c8b7b24c26ec5dd1c9b00501
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-23 22:00:38 -0700
Commit message:

 Added concept in documentation, closing #7
 
Package: SpatialFeatureExperiment
Commit: d68d3723de506d9ce1a54116ee4920f8f9b34020
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-23 21:41:24 -0700
Commit message:

 Allow predicates in crop, closing #6
 
Package: SpatialFeatureExperiment
Commit: bf421daebb46e5b5534b07195450cb50ca5e37ac
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-18 18:43:44 -0700
Commit message:

 Import median
 
Package: SpatialFeatureExperiment
Commit: 49864abb83c26b441fc0bdbd2a9a3616f20378b6
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-18 18:15:34 -0700
Commit message:

 Merge branch 'saveterrards'
 
Package: SpatialFeatureExperiment
Commit: 1185d2f9a3518400707c58418cadae48cf07c027
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 19:29:37 -0700
Commit message:

 Unwrap SpatRaster images in imgRaster
 
Package: SpatialFeatureExperiment
Commit: 3856c3adc9fe69fa704c7c373188fa87123e3851
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 22:28:26 -0700
Commit message:

 imgData is DF with 0 cols and 0 rows rather than NULL
 
Package: SpatialFeatureExperiment
Commit: 4eb6c8af93549f401525a127750e5c0e8dd27353
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-18 18:11:40 -0700
Commit message:

 Version bump and updated NEWS
 
Package: SpatialFeatureExperiment
Commit: 21d970a74e384858c2025ac933b1f3a95fcc915f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-18 17:59:24 -0700
Commit message:

 For the release version, to foreshadow what's to come in devel
 
Package: SpatialFeatureExperiment
Commit: 07c2ce3c6003f40693721b29aeeeeb5f581a75f5
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-18 17:58:16 -0700
Commit message:

 Allow bbox as matrix for different samples, closing #5
 
Package: SpatialFeatureExperiment
Commit: ac7e57b3a03393b50d118ef2c272488f1574294f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 22:28:26 -0700
Commit message:

 imgData is DF with 0 cols and 0 rows rather than NULL
 
Package: SpatialFeatureExperiment
Commit: a7280c6c8a833e52ab00c71ae452674dedae2d26
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 19:29:37 -0700
Commit message:

 Unwrap SpatRaster images in imgRaster
 
Package: SpatialFeatureExperiment
Commit: 22a0c24fbb9f2b4a52b0527c11c47ad14176252e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 18:52:36 -0700
Commit message:

 Merge branch 'saveterrards' into devel
 
Package: SpatialFeatureExperiment
Commit: be42b5f85cd17fa2c5c987f04f5fade910af1a28
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-16 18:51:00 -0700
Commit message:

 Added saveRDS method for SFE, addressing #2
 
Package: SpatialFeatureExperiment
Commit: 17eff19ee19fc24c8793084f687160040fe489da
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-12 00:13:17 -0700
Commit message:

 Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureExperiment into devel
 
Package: SpatialFeatureExperiment
Commit: 09145e1bcfecf6fced681916e27c3406e821a4a4
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-12 00:11:22 -0700
Commit message:

 devel version number
 
Package: SpatialFeatureExperiment
Commit: 47da1c45457e656884b14fc5bf17c651f823da10
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-12 00:08:36 -0700
Commit message:

 Two additional bugs I discovered when writing tests for #1: Visium graph not added in read10xVisiumSFE when there's 1 sample, and function to determine spot spacing doesn't work when there're singletons outside tissue.
 
Package: SpatialFeatureExperiment
Commit: 8b20a46bb59b92118d71051c6ee0abd8bd5a3761
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-11 22:08:20 -0700
Commit message:

 Wrong images and wrong bboxes
 
Package: SpatialFeatureExperiment
Commit: b30a2397fbfcc49a4bfdfbe19e249ee1177d6722
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-11 18:25:12 -0700
Commit message:

 Use devel version
 
Package: SpatialFeatureExperiment
Commit: 56b48677e78a10a6c5a85254f2df635a0d8eda07
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-08-11 17:40:05 -0700
Commit message:

 Added citation
 
Package: SpatialFeatureExperiment
Commit: c12c25d5ca084a81ced650a27d086bc84d8ccd57
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-07-29 21:24:02 -0700
Commit message:

 Added citation
 
Package: SpatialFeatureExperiment
Commit: 3f176dee8470fc51053b06a58a5c1a3d30483197
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-07-21 16:17:33 -0700
Commit message:

 Merge branch 'main' of https://github.com/pachterlab/SpatialFeatureExperiment
 
Package: SpatialFeatureExperiment
Commit: d3ae235b623fa098e22c07b89a48be67d94ec294
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-07-21 16:17:22 -0700
Commit message:

 Fixed embarrasing documentation error
 
Package: SpatialFeatureExperiment
Commit: 723632e0fa46537c104a100b1445939a99cd11a3
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-07-06 11:23:47 -0700
Commit message:

 Crop images for all samples
 
Package: SpatialFeatureExperiment
Commit: 8ae81aceb85ec00b501a4582b7e74a87c6ec9235
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-06-05 16:58:46 -0700
Commit message:

 Haven't updated README for ages
 
Package: SpatialFeatureExperiment
Commit: bf34cd927c9173c43cd880a9bddd718bd0243121
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2023-05-15 18:01:52 -0700
Commit message:

 Don't use devel version number
 
Package: CDI
Commit: 72f1e436dd63e57ccac1061d179b83819d52eb03
Author: jfanglovestats <jfanglovestats@gmail.com>
Date: 2023-11-28 10:06:38 +0800
Commit message:

 Delete inst/.DS_Store 
Package: CDI
Commit: 53c524a2696054a3e9fc6bdc99c95af232746a76
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2023-11-28 09:58:03 +0800
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/CDI
 
Package: CDI
Commit: 5ac333cff4538749f9a4dba77f428046d4861cd5
Author: Jiyuan Fang <jf243@duke.edu>
Date: 2023-11-28 09:49:13 +0800
Commit message:

 unitest bug
 
Package: tidySpatialExperiment
Commit: 95557549a996919d00059505c49c04b3e7a1842c
Author: William Hutchison <william.8191@fastmail.com>
Date: 2023-11-28 10:17:24 +1100
Commit message:

 Version up
 
Package: Statial
Commit: 777633d56f768c06703c4eb7fc7a067315baefd0
Author: Nick <nickrrrr@gmail.com>
Date: 2023-11-28 10:12:16 +1100
Commit message:

 delete html
 
Package: Statial
Commit: 70bf4cac9625f946584280a6865af35aa4ce2b3b
Author: alexq <alexq@maths.usyd.edu.au>
Date: 2023-11-24 13:41:57 +1100
Commit message:

 bugfixes for abundance
 
Package: Statial
Commit: 201884b48c2fdd26812b8052dd094e74f6d54688
Author: fame2827 <fame2827@uni.sydney.edu.au>
Date: 2023-11-15 12:56:32 +1100
Commit message:

 updated vignette
 
Package: ISLET
Commit: 83416881d90f8b95b7713e6fe29f8a135d27dc69
Author: Hao Harry Feng <fenghaoea@gmail.com>
Date: 2023-11-27 16:14:39 -0500
Commit message:

 personalized deconvolution methods
 
Package: SummarizedExperiment
Commit: 59caa627c5fdab4fe0b747ce9051c06227dae282
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-11-27 12:14:56 -0800
Commit message:

 Update comment in realize() method for SummarizedExperiment objects
 
Package: HDF5Array
Commit: ad98c559c5e8d4ebf5083eb80a3bf39e2fe9a212
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-11-27 12:06:01 -0800
Commit message:

 update doc
 
Package: Macarron
Commit: 4b50e01196a64a6cad89f1fe068d5ec2e4f9ffb8
Author: sagun <sagun_90@hotmail.com>
Date: 2023-11-27 14:50:03 -0500
Commit message:

 Reverted version
 
Package: Macarron
Commit: 5fd5489da87a7f2892d8a7c5ada240436f627be8
Author: sagun <sagun_90@hotmail.com>
Date: 2023-11-27 14:48:00 -0500
Commit message:

 Fixed version number
 
Package: Macarron
Commit: ac0967c094002ced1254e31403668d4d6b1d0ee0
Author: Amrisha Bhosle <abhosle@broadinstitute.org>
Date: 2023-11-27 12:02:55 -0500
Commit message:

 Updated NEWS and version after file renaming
 
Package: Macarron
Commit: 628b3715888af6d7c8b089a11587b85a9faa8bc8
Author: Amrisha Bhosle <abhosle@broadinstitute.org>
Date: 2023-11-27 11:36:00 -0500
Commit message:

 Fixed filenames
 
Package: Macarron
Commit: 414c0ad30c270545a2cb1acfd042f4d5e8a6e14c
Author: Amrisha Bhosle <abhosle@broadinstitute.org>
Date: 2023-11-27 10:55:03 -0500
Commit message:

 Deleted output
 
Package: HDF5Array
Commit: 3a0d43470a71f01ec2bcdc8b96cc538c1cac3298
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-11-27 11:31:32 -0800
Commit message:

 Change 'with.dimnames' default to TRUE (was FALSE) in writeHDF5Array()
 
Package: S4Arrays
Commit: 613391f67cab4923acb17f748d3dc2744b4edc4c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2023-11-27 10:25:21 -0800
Commit message:

 Pass result of realize() thru DelayedArray() constructor

This is to make sure to always produce a DelayedArray object or derivative,
even after the following planned change for the default realize() method.

Planned change for the default realize() method: The plan is to change
what 'realize( , BACKEND=NULL)' does. Instead of returning an ordinary array
wrapped in a DelayedArray object like it does at the moment, it will return
a **naked** ordinary array. This change is planned for DelayedArray 0.29.1.
 
Package: TCGAbiolinks
Commit: 3598148c8ee6c04df0500848685ba58987fc1cb3
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2023-11-27 15:06:46 -0300
Commit message:

 Update
 
Package: TCGAbiolinks
Commit: c4457d9c1f3f13907f70b8be05c77d98fc3cc981
Author: Tiago Silva <tiagosilva@Tiagos-MacBook-Pro-2.local>
Date: 2023-11-27 15:05:44 -0300
Commit message:

 Fixing MAF for BEATAML #573
 
Package: RolDE
Commit: f6c4ac1fab07cfd70d897f7ca8abe1ccafc3ee70
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2023-11-27 18:44:28 +0200
Commit message:

 Change author email
 
Package: MetaScope
Commit: 745e4c3b7f15b24de652a7674f256c797da25836
Author: Aubrey Odom <aodom@bu.edu>
Date: 2023-11-27 10:22:48 -0500
Commit message:

 Fix bowtie parameters
 
Package: BERT
Commit: 904d68328c7a1e79518f16f7bbc0a883b1f74a9b
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:31:55 +0100
Commit message:

 Revert "Revert "Experienced error when pushing""

This reverts commit 1444fa52f8eda909b7278a8f0687bab6ee49c8e3.
 
Package: BERT
Commit: 8dc1c80e31ebc6b2332189bb4be3dca3b8a9b45b
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:31:50 +0100
Commit message:

 Revert "Revert "Renamed BPPARAM""

This reverts commit 41a46e6cedb6c97bd967556a5fa24454c4d6b293.
 
Package: BERT
Commit: 41a46e6cedb6c97bd967556a5fa24454c4d6b293
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:29:58 +0100
Commit message:

 Revert "Renamed BPPARAM"

This reverts commit 382a493e4782ccd93372a97d461d804b6badf989.
 
Package: BERT
Commit: 1444fa52f8eda909b7278a8f0687bab6ee49c8e3
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:29:47 +0100
Commit message:

 Revert "Experienced error when pushing"

This reverts commit 5ea1fecce433e658780ba868a6f8050e6a1d221a.
 
Package: BERT
Commit: 5ea1fecce433e658780ba868a6f8050e6a1d221a
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:29:44 +0100
Commit message:

 Experienced error when pushing
 
Package: BERT
Commit: 382a493e4782ccd93372a97d461d804b6badf989
Author: deryannis <yannis.schumann@hsu-hh.de>
Date: 2023-11-27 14:26:51 +0100
Commit message:

 Renamed BPPARAM
 
Package: gDR
Commit: df1103d38077a5c088824673a61f988153bd5004
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 08:45:39 +0100
Commit message:

 Merge pull request #43 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDR
Commit: b4e5322b25dbf92bcf4a204c63fd6c599981279f
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:15:04 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDR
Commit: 35a700c328be19b76d51b1fdd27fb8d43cb70898
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 15:48:03 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRcore
Commit: 6a54e8902ecb50813e94edf0937361943f65e8d1
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2023-11-27 13:05:54 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: gDRcore
Commit: 93f81aa7d2467e6e7940ac7fe876897c46bf5f58
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 09:39:05 +0100
Commit message:

 Merge pull request #125 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDRcore
Commit: 288de9c4848a5fc99104e944df8ae64ffb396028
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:11:19 +0100
Commit message:

 chore: sync master with devel branch
 
Package: gDRcore
Commit: f96ce0911cf55d02d098936ffdb04fd190edc626
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 16:05:44 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRcore
Commit: c01f729bf728c3ee713fb0c06eda3dd99bd34f24
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2023-11-07 15:39:51 +0100
Commit message:

 Merge pull request #123 from gdrplatform/GDR-2226

Gdr 2226 
Package: gDRcore
Commit: 8dea068faaf5212a72895a282097a3ccc82bd6fb
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-11-07 13:42:13 +0100
Commit message:

 ci: sync with master
 
Package: gDRcore
Commit: 607ad56f8e242784d009684ff6ce4fc6eb900f32
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-10-25 15:47:09 +0200
Commit message:

 Merge pull request #124 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 
Package: gDRcore
Commit: b078c66fc4f4d48b47b031bba1f1d06e9e2971de
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-10-24 16:42:46 +0200
Commit message:

 feat: add Treatment as template identifier
 
Package: gDRcore
Commit: f3ebd2563a07f51706ce73bdc2cc8e55120d34ae
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-23 15:56:30 +0200
Commit message:

 fix: asserts
 
Package: gDRcore
Commit: 24d5f274e8246ab25a1c3e40be2d4c238294c434
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-23 13:51:22 +0200
Commit message:

 test: add unit tests
 
Package: gDRcore
Commit: 68dabe75579e3641f9005ffd84cc3f5703c928c3
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-23 13:51:12 +0200
Commit message:

 doc: update documentation
 
Package: gDRcore
Commit: ce41f1bbb040ee2f1c817d7e1356cb39e85c8549
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-20 13:51:02 +0200
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRcore
Commit: 50676f176b847a33efcdfe215d37eda60f417668
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-20 13:47:06 +0200
Commit message:

 feat: add support for unifying duplicates in combo matrix data
 
Package: gDRtestData
Commit: 4b28a8a02ef982f072f8ace90cc0ba85928e2521
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 08:45:18 +0100
Commit message:

 Merge pull request #53 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDRtestData
Commit: 74672f6f73d4a07480de37e536d50d9f609f31ab
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:08:57 +0100
Commit message:

 chore: sync master with devel branch
 
Package: gDRtestData
Commit: 5ba759e2c90c610398a6e5cba549f75280e68a23
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 17:05:13 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRimport
Commit: 6e18db2ac6c3265726b809a6cacd7628fb390fe2
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 09:39:19 +0100
Commit message:

 Merge pull request #72 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDRimport
Commit: e4ceef84f020d104b288682a00909798cfaee9a2
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:12:38 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRimport
Commit: cbdd1bb57ddd58ba923d8e722779434ef9480868
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 16:39:57 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRimport
Commit: 641d1db3fa653438d39e5c75b982fe498048b622
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 16:33:31 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRimport
Commit: c23d083af9a55fb75ac79b87a50e2705a415a299
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-10-25 15:46:43 +0200
Commit message:

 Merge pull request #71 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 
Package: gDRimport
Commit: 1201e7981ddbb4fa86c553ce972692ae1c130358
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-10-24 16:11:48 +0200
Commit message:

 feat: add Treatment as template identifier
 
Package: gDRutils
Commit: 701d4907269cfb883af9de06b9e9bfa5cd7dcf29
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 09:38:53 +0100
Commit message:

 Merge pull request #99 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDRutils
Commit: ce9df36f7b61fbc51c86d8f115ab6e9f90261656
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:10:06 +0100
Commit message:

 chore: sync master with devel branch
 
Package: gDRutils
Commit: f80e948cd015abfdbc7b7361d0639ae7c4a527e9
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 16:46:31 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRutils
Commit: fbbe001049b518624b46fcdfc1f06216ec4c7c9f
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 16:45:10 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRutils
Commit: 93c617930fc9e2533e89d3ab6e945fb50ebca99a
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2023-11-13 11:18:33 +0100
Commit message:

 Merge pull request #97 from gdrplatform/GDR-2278

Gdr 2278 
Package: gDRutils
Commit: f122ecb6c0697be8ea8712000db8cc88c4c8c298
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-11-13 10:42:08 +0100
Commit message:

 ci: trigger build
 
Package: gDRutils
Commit: 8c59c7a6e6f7c58e08588c4bd8b5a8da635716cd
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-11-10 13:47:24 +0100
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRutils
Commit: bd6f13c39d1b65fdf4208b0435476e138f61af39
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-11-10 13:47:17 +0100
Commit message:

 feat: extend the support of NA in ref division time
 
Package: gDRutils
Commit: bb42c0674dfea6dc1695e5b9aab75a8293e8e7b9
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 10:54:51 +0100
Commit message:

 Merge pull request #96 from gdrplatform/GDR-2222

Gdr 2222 
Package: gDRutils
Commit: 340ed4cc94e6202b121d0fde31e06899fd0e70a3
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-07 09:32:52 +0100
Commit message:

 added example
 
Package: gDRutils
Commit: 8ee4b01dca6ba5a9196dd4e5014a675ced28f4d1
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-07 08:38:46 +0100
Commit message:

 CI
 
Package: gDRutils
Commit: 244cc72b3f34e108042eac25ff3eddcea197965e
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-06 15:44:44 +0100
Commit message:

 CI
 
Package: gDRutils
Commit: cf71f19d74aad35a6198e194b3f3f35892fbb54d
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-06 09:57:33 +0100
Commit message:

 Merge branch 'master' into GDR-2222 
Package: gDRutils
Commit: cdf47100331ea7e9988ec7ba0960517e5facca8f
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-06 09:44:08 +0100
Commit message:

 bump version
 
Package: gDRutils
Commit: 3b3bed34406c5a3a5fa2b28c6c4d2bfd450d8a08
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-06 09:41:52 +0100
Commit message:

 fixed linter
 
Package: gDRutils
Commit: 2c28c52c1b82e2565d58c568c9ec7b365a4c3239
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-03 08:09:40 +0100
Commit message:

 Merge pull request #94 from gdrplatform/GDR-2222

Gdr 2222 
Package: gDRutils
Commit: be8b28cf8c5c64f5755ce777f53aa6b8f514c0d5
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-02 13:39:30 +0100
Commit message:

 Merge branch 'GDR-2222' of github.com:gdrplatform/gDRutils into GDR-2222
 
Package: gDRutils
Commit: 3669d3dcb424f6973ed820708d3376097d54e558
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-02 13:39:13 +0100
Commit message:

 updated headers tests
 
Package: gDRutils
Commit: 32a21b659721f539a9718ed8541c78cdb6e00d41
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-11-02 13:38:53 +0100
Commit message:

 added asserts and tests for gemoetric_mean
 
Package: gDRutils
Commit: 180cc2a9d61ad36004322843f08690c050c48e6c
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-02 10:18:02 +0100
Commit message:

 Merge branch 'master' into GDR-2222 
Package: gDRutils
Commit: e73e2cb16a52dcef475508404e2be896df700609
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2023-10-31 09:32:53 +0100
Commit message:

 Merge pull request #95 from gdrplatform/GDR-2250_2

Gdr 2250 2 
Package: gDRutils
Commit: f4b096fcf9d543dca1fae376f0cae242404f5e7f
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-30 17:12:38 +0100
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRutils
Commit: 022e12b70a8c8c77fbd3ac84e9d1972adbae9cdb
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2023-10-30 17:12:30 +0100
Commit message:

 refactor: switch into numeric types in predict_efficacy_from_conc
 
Package: gDRutils
Commit: a7b0aaf3684ca761154bf526436f9593606affd9
Author: darsoo <daro.scig@gmail.com>
Date: 2023-10-30 16:32:20 +0100
Commit message:

 Update utils.R 
Package: gDRutils
Commit: b93c8adb3183454b214c5d0e93f65758e776843e
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-10-26 10:57:33 +0200
Commit message:

 rebased
 
Package: gDRutils
Commit: 42de29eb374f8253fb85709b1a4c33b9a931757f
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-10-26 10:54:47 +0200
Commit message:

 bump version
 
Package: gDRutils
Commit: 27cc3f0aed5aa846daf5e54bdb48173f337c5df9
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-10-26 10:53:46 +0200
Commit message:

 updated documentation
 
Package: gDRutils
Commit: b9a3256468add6fa77316ae0dbe2f574a5a30077
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2023-10-26 10:53:15 +0200
Commit message:

 moved function from gDRserach2
 
Package: gDRutils
Commit: b675d71d70b08babbf83e9cc4e13226bd7af5547
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-10-25 15:46:50 +0200
Commit message:

 Merge pull request #93 from gdrplatform/GDR-2227

[GDR-2227] Treatment instead of template 
Package: gDRutils
Commit: fb5e14393ab445612868271c65021b61a306efce
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-10-24 16:00:25 +0200
Commit message:

 feat: add Treatment as template identifier
 
Package: UCell
Commit: 5f12a9d426576facded703a60c67fd2df4dd949d
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2023-11-27 12:07:25 +0100
Commit message:

 Work with Seurat objects with split layers
 
Package: gDRstyle
Commit: 26d22c0ee70d8150ac5bfb387f33678f06c83bd9
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2023-11-23 09:21:59 +0100
Commit message:

 Merge pull request #63 from gdrplatform/GDR-2261

[GDR-2261] Update versioning of open-sourced packages 
Package: gDRstyle
Commit: 3c688b2fca5ca71965b936432bb624f54b2b1408
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-23 08:16:10 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRstyle
Commit: 9bfa0ad5ffb52e86f88845fb0bf5719ffbef6b5b
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2023-11-22 15:20:03 +0100
Commit message:

 chore: sync main with devel branch
 
Package: gDRstyle
Commit: e97fd2f9b4f1d6966e33b1160508b7f10ed2afd9
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 10:54:45 +0100
Commit message:

 Merge pull request #62 from gdrplatform/GDR-2222

Gdr 2222 
Package: gDRstyle
Commit: b957e2a43f8b843ee15d2cc013dc0570291e9859
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 10:17:59 +0100
Commit message:

 CI 
Package: gDRstyle
Commit: 37b3076cee63965a0bd00c78f2ee47b5813db769
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 08:33:35 +0100
Commit message:

 Update NEWS.md 
Package: gDRstyle
Commit: e8128046d8f5a2676773a93465203f10d136b65f
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 08:29:16 +0100
Commit message:

 Update DESCRIPTION 
Package: gDRstyle
Commit: faca9eb35a4f6b05f08bc02dd8119b08fcc579d5
Author: darsoo <daro.scig@gmail.com>
Date: 2023-11-07 08:28:40 +0100
Commit message:

 Update check.R 
Package: DExMA
Commit: 64113b37c147e90016aba92f9d96662bdb0e212f
Author: Juananvg <juanantoniovillatorogarcia@gmail.com>
Date: 2023-11-27 11:04:41 +0100
Commit message:

 Fix some bugs
 
Package: MGnifyR
Commit: 9f218c8d7f09733662ad0b7816ccf603a5a7b9e8
Author: TuomasBorman <tvborm@utu.fi>
Date: 2023-11-27 09:48:34 +0200
Commit message:

 Minor fix
 
Package: biomvRCNS
Commit: ee30c51457e1720d9c27758cb75c86d28c107c07
Author: yd23 <idananan@gmail.com>
Date: 2023-11-27 08:33:45 +0800
Commit message:

 resave variosm.rda as version 2 to reduce R version dependance
 
Package: simona
Commit: 0403be1d6906838cff2cc2cd581c4b8e929fcb9a
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-26 22:29:20 +0100
Commit message:

 merge with master
 
Package: simona
Commit: 75308ee423715eeed1b9218a9e742ea6cfdd647b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-26 22:20:48 +0100
Commit message:

 updated website
 
Package: simona
Commit: 7b6099027bbe8655316d322493671ef0a1d1d9a6
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-26 22:16:21 +0100
Commit message:

 add dag_random
 
Package: simona
Commit: 22c29a0c33ee61dfb57b5376288e08207109648d
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-15 15:59:20 +0100
Commit message:

 improved partition_by_size()
 
Package: simona
Commit: 97c61576b8e865f6ee9dd532021a7f0eea8bd0f7
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-14 13:29:08 +0100
Commit message:

 update website
 
Package: simona
Commit: cd9ce837a3beef38a1bd83c8dd4cc9081b2a3785
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-11-14 13:22:50 +0100
Commit message:

 revised plot.R
 
Package: simona
Commit: 13ea6a34105461cdee5ec4add9a7ece0a6874d73
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-10-22 21:29:17 +0200
Commit message:

 update
 
Package: simona
Commit: 8d64e5e95978dd840c4bfe314d2bd251182ac2ab
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-10-21 12:39:59 +0200
Commit message:

 Revert "merge"

This reverts commit c5edd66c896b7187381a782f9b5d9678dd78060a.
 
Package: simona
Commit: c5edd66c896b7187381a782f9b5d9678dd78060a
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-10-21 12:39:49 +0200
Commit message:

 merge
 
Package: simona
Commit: 5d5194e76a8be058d2cbfd7ae9f17c7749d13a99
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-10-20 10:09:20 +0200
Commit message:

 update
 
Package: chimeraviz
Commit: 925f9928e074cd62dedbf0642c4fa087ea5af788
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2023-11-25 17:53:49 +0100
Commit message:

 Fix citation list
 
Package: tximeta
Commit: daf779d0d6522afdbdb679cf3532762203193d34
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2023-11-24 16:41:00 -0500
Commit message:

 version bump
 
Package: tximeta
Commit: f8cd55b8ecff395885b3482a06e58b5e202d6d6f
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2023-11-24 16:40:09 -0500
Commit message:

 addresses bug introduced in 1.20, fixes #80
 
Package: CRISPRball
Commit: 2a4d9e7ef1f34f99e4d9cba8d08d080654f62895
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-24 12:16:22 -0600
Commit message:

 version bump
 
Package: CRISPRball
Commit: 079d0e03a55a86b31552d9c4a553379e3a9c6ae2
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-24 12:15:46 -0600
Commit message:

 Update get_depmap_plot_data.Rd
 
Package: CRISPRball
Commit: 015713ac24a2ebdab5881b4ebfc70a31710f5a09
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-24 12:14:07 -0600
Commit message:

 Update plotting_depmap.R
 
Package: DeProViR
Commit: 203d9a6e15ca9c5ef785697c1e86b33003c044c3
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-11-24 11:55:22 -0600
Commit message:

 version bump0
 
Package: CRISPRball
Commit: 5327b228c2c68e5fe14192a05b6826a9d1570666
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-24 11:52:23 -0600
Commit message:

 version bump
 
Package: DeProViR
Commit: 7c38bf5a80e07ad4feaf24e665808ee211d74f1c
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-11-24 11:46:29 -0600
Commit message:

 edit man file
 
Package: CRISPRball
Commit: f78a9a29bb78ddcbcda126cb954dd5f83b4cb32c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2023-11-24 11:39:06 -0600
Commit message:

 dontrun for longrunning example
 
Package: DeProViR
Commit: a85526a7433d90f164a1db42cd05bbe4787b6f44
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-11-24 10:42:46 -0600
Commit message:

 version bump
 
Package: DeProViR
Commit: 1a754b62ff2f55cc324fbdc1ba73018eaaee2741
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-11-24 10:32:25 -0600
Commit message:

 changing runtime
 
Package: DeProViR
Commit: d43c91d51404ac72b9912c4cb479601fc1fced5a
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-11-24 09:15:57 -0600
Commit message:

 version bump & some editing
 
Package: ropls
Commit: e33ade0ff623323d401c2bb757d0d9207e873cbc
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2023-11-24 15:50:59 +0100
Commit message:

 v1.35.2: gg_scoreplot: update to handle OPLS models
 
Package: IsoBayes
Commit: 74ae9f5cdfca73847153be2741bc6f974b48bc40
Author: SimoneTiberi <simone.tiberi@uzh.ch>
Date: 2023-11-24 15:30:19 +0100
Commit message:

 Updated to C++ 17
 

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