Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.
This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.
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version UP from Bioconductor dev Merge branch 'master' of git.bioconductor.org:packages/tidybulk Conflicts: DESCRIPTION
update dependencies
Merge pull request #242 from stemangiola/dev Dev
Merge pull request #241 from stemangiola/deprecate_log_transform_for_function deprecation untested
Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
fix CHECKs
deprecation untested
drop tsne test
Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
fix CHECKs
deprecation untested
make tests more detailed
use |> for tests
add news and version UP
Merge pull request #244 from stemangiola/parallel-cibersort implementation parallel cibersort
Update check-bioc.yml
Update check-bioc.yml
Merge pull request #235 from stemangiola/polish_aggregation_tibble Polish aggregation tibble
fix CHECKs
add docs
fix CHECK
Merge branch 'deprecate_log_transform_for_function' of github.com:stemangiola/tidybulk into deprecate_log_transform_for_function
deprecation untested
deprecation untested
Merge pull request #236 from stemangiola/robustify_deconvolution_SE allow other feature column for SE
Merge pull request #238 from stemangiola/allow-mapping-to-other-genomes avoid human annotation
Merge pull request #239 from stemangiola/deprecate_dot_contrasts deprecate .contrasts and update tests
Merge branch 'dev' into deprecate_dot_contrasts
fix aggregation
merge dev Merge branch 'dev' into polish_aggregation_tibble Conflicts: R/methods_SE.R R/utilities.R tests/testthat/test-bulk_methods_SummarizedExperiment.R
Merge pull request #237 from stemangiola/SE_to_tidybulk_new_vocabulary implement new vocabulary
fix back deconvolution
fix tests
fix tests
fix examples
fix dependencies
fix tests
get as_tibble from tidySE for tidybulk()
temporary save to work on other branch
deprecate .contrasts and update tests
fixed pivot_
update docs
avoid human annotation
fix tidybulk()
fix typo
allow other feature column for SE
Merge branch 'dev' of github.com:stemangiola/tidybulk into dev
replace if_else once
Merge branch 'master' of github.com:stemangiola/tidybulk
implement new vocabulary
simplified aggregate for se and add test
fix bug
fix bug
polish and make more robust also for SE
make non standard columns not a problem
replace if_else once
implementation parallel cibersort
Merge pull request #234 from stemangiola/update-action-3.15 Update github action to Bioc 3.15
Edit to action
Update github action to Bioc 3.15
fix bug imputation
merge
update
bump x.y.z version to odd y following creation of RELEASE_3_11 branch
bump x.y.z version to even y prior to creation of RELEASE_3_11 branch
merge
update email
Merge branch 'devel'
Support empty dims (#235) * add rmarkdown to Suggests * fix bioc error * Support empty dims * fix_bug
Merge branch 'master' of github.com:RGLab/openCyto
Minor improvements to openCyto (#229) * Add data.table method to gatingTemplate(). * Add informative error message when dims are empty.
update email
update email
R/faust_gating_plot.R
bump
Update DESCRIPTION
Merge pull request #74 from RGLab/add-license-1 Create LICENSE file
Create LICENSE
dispatch cytoframe method to flowFrame
fix test
manually dispatch cs method to fs
Create build.yml
Added RuleSet3 sequence
Updating basilisk
bump
update email
bump x.y.z version to odd y following creation of RELEASE_3_15 branch
bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
Adding rs3 data
Merge pull request #197 from databio/dev v1.5.2
set up different colors for plotFeatureDist with GRList input
remove redundant argument
update calc chrom plot function for GRlist input
Update DESCRIPTION
big fix with new update loading reference data from GDData changed
partitionList - fix issue if 5' or 3' UTR are NULL
remove "reduce" - works without and was triggering error
Add master branch to GitHub Action workflows
Fix CHECK warning
Fix CHECK warning
Fix CHECK warning
new version 2.7.1
Fix check errors
Fix README
Added more unit tests
Merge remote-tracking branch 'bioc/master' into devel
roxygen
Update documentation, together with minor bug fixes
Update documentation of workflow related to new HVG and scaling scheme
Fix CHECK and BiocCheck
upgrade R 4.2.0
Refine changes previously made, and minor bug fixes
Update UI according to the last commit
Efficiency and user experience improvement & BUG fixes for TSCAN workflow
Reformat the use of withConsoleMastRedirect; A few UI bug fixes
Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
Minor UI fixes
Merge pull request #600 from npervaiz/devel Import data UI modified
minor tweak fixed
Merge branch 'devel' of https://github.com/npervaiz/singleCellTK into devel
Import data UI modified
Merge pull request #599 from mvfki/devel IMPORTANT BUG FIXES & Finished A La Carte Workflow Tutorial
Finished a la carte workflow UI+console tutorial
IMPORTANT BUG FIXES
Merge upstream and fix conflict
Update A La Carte Workflow tutorial UI part
Merge pull request #598 from irzamsarfraz/devel Refactor due to seurat scaling
doc fixes
Re-indent and re-format code
Minor fixes
Updates to seurat scaling
Merge remote-tracking branch 'upstream/devel' into devel
Some fixes due to new seurat scaling mechanism
Update feature selection related functions
Fixed seurat scale data
Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
Updating A La Carte Workflow Tutorial
Merge pull request #597 from npervaiz/devel TSCAN example case bug fixed
TSCAN example case bug fixed
Fixed conflicts Merge remote-tracking branch 'upstream/devel' into devel # Conflicts: # inst/shiny/server.R # inst/shiny/ui_05_1_diffex.R # inst/shiny/ui_05_2_findMarker.R
Some updates
Merge pull request #596 from mvfki/devel A BUNCH of UPDATES
Fix check error
Add params of dimreduce to metadata & minor updates for clustering funcs
Update HVG PCA UMAP cluster UI
re-enabled seurat tab lock
Run scaling on the go for seurat tab
Merge upstream and fix conflicts
Add UI tutorial screenshots
Draft UI tutorial
Function updates for HVG, PCA, UMAP and TSNE
Updates
Merge pull request #594 from npervaiz/devel notification spinner added to UI
edits in notification spinner
notification spinner in UI with minor changes
notification spinner added to UI
Fix R CMD check error
Update doc accordingly
Update volcano plot func to support featureDisplay setting; update this feature for all other DEG UI
apply global displayFeature setting to DEG heatmap
Update clustering documentation accordingly
Update clustering UI accordingly
Merge branch 'devel' of https://github.com/compbiomed/singleCellTK into devel
Add Leiden option for runScranSNN; related bug fixes
Merge pull request #593 from npervaiz/devel new example dataset added
New example dataset added
Merge upstream Merge remote-tracking branch 'upstream/devel' into devel # Conflicts: # inst/rmarkdown/seurat/reportSeuratResults.Rmd
import new example data
Minor update
Updates to module filter
Added module filter to diffex
Updates to module filter and added it to find markers tab
Merge pull request #591 from npervaiz/devel documentation edits
edits in TSCAN function name
documentation edits
Merge branch 'devel' into devel
documentation of TSCAN added
Merge branch 'master' into devel
new version 2.6.0
Merge pull request #589 from salzcamino/master Fix Seurat Report knit
Merge pull request #35 from compbiomed/devel Devel
fix seurat report knit error
Merge pull request #34 from compbiomed/master upstream
Updates to seurat report
Merge pull request #588 from irzamsarfraz/devel Fixed showSession issue with seurat reports
Minor updates to seurat reports
small vignette tweaks
remove library call for scran
rm DS_Store:
DES
DES
equal last
fix docs, thanks igordot
equal
minor
equal sign again
fix a typo.
add support for motif logo for lollipop plot.
bumper
rm equal signs
- Fixing an incompatibility issue with cBioportalData package
rm equal signs
rm equal sign
description rev
rm ds
Merge branch 'master' of https://github.com/jichunxie/CDI
Merge pull request #5 from jichunxie/main merge
add DES
Merge branch 'main' of https://github.com/jichunxie/CDI
resolve
Merge pull request #4 from jichunxie/master Merge pull request #3 from jichunxie/main
Merge pull request #3 from jichunxie/main Merge pull request #2 from jichunxie/master
Merge pull request #2 from jichunxie/master Master
Merge branch 'main' into master
09903
Delete .DS_Store
Delete .DS_Store
Delete .DS_Store
Delete .DS_Store
Update README.md
Merge branch 'main' into main
version number
Merge pull request #1 from jichunxie/master Master
Create README.md
Delete README.md
Update README.md
update vignette re scaling
bump
tmp
tmp
3.99.3: failing a test in Mac OS
#added cds2codonaln
"delete files"</div>
0.99.9</div>
"Bump version to 0.99.9"</div>
forgot to add moreboxplot help file
add deprecation notes from 1.4.1
fix deprecation notes
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'
improved special boxplot and added it to export
Merge remote-tracking branch 'upstream/master'
make boxplots transparent if violin plots are added; better description of plotDnf
some boxplot bugfxining
v3.5.5 - version bump
wrong first argument in `count_references`; fixes #43
Updated vignette
Bumping version up
Readu to merge
Adding DeepSpCas9
fix git issue of safe directory (#107)
udpdate badges based on biocthis (#106)
Updated manual
Switched off AHub dl for BioCheck
improve the speed for searchTFBP
fix the issue for sample size is bigger than shuffled sequences.
add ushuffle
Add reverseComplement search for conservedMotifs.
use bioc-devel docker image for github action (#105) * use bioc-devel docker image * fix name of docker repo
added a filtering step in data import to prevent NA entries
3.99.2
3.99.2
version bump in devel
Removed the constraint to only use 50% of the cores max for parallel tasks
version bump in devel
bug fix: Documentation related fixes to eliminate warnings during build
Updated frozen AH resource list
sce, parallel
version bump 1.9.0 -> 1.9.1
Merge remote-tracking branch 'bioc/master'
add checks for NSR to overlap a split read (#41) * Add check for non spliced reads * Bugfix for the merging where some non spliced reads kept within the dataset without a corresponding junction. Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de>
use inclusive cutoffs for aberrant event detection (#37) Co-authored-by: Christian Mertes <mertes@in.tum.de>
readme
sce,parallel,unittest
increment version
namespace and example fixes
added comment in vignette about windows comptability
Correcting a variable name
- Fixing documantation for oneOfEach
- adding oneOfEach functionality.
version bump in devel
bug fix: Various small important bugfixes
correct for seqAlleleCount returning NA when no samples selected seqAlleleCount is called separately for males and females for sex chromosomes. Previously it would return 0 when no samples were selected, but as of SeqArray 1.37.1 it returns NA in that case. Thus the SeqVarData allele count functions were returning NA in cases where all samples were male or female. Correct for that by setting count=NA to 0 when selecting samples by sex.
Merge pull request #23 from adefelicibus/fix-doc fix modules doc
bumped
layout improvement
fix modules doc
Merge pull request #61 from jwokaty/add-back-b9-doi Add back 'B9' in DOI to match older Bioconductor packages
Add back 'B9' in DOI to match older Bioconductor packages
version bump 1.15.1
Merge pull request #62 from seandavi/repositoryStats Add repositoryStats function from AnVIL, credit to @mtmorgan
whitespace updates
update to use RMarkdown in docs
update documentation
add repositoryStats function
Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
Fix broken DESCRIPTION file
Update package description
Add pkgdown logo
Merge branch 'master' of git.bioconductor.org:packages/rhdf5filters
Update NEWS.md
version bump in devel
bug fix: Various small importnt bugfixes
Merge branch 'main'
added 3 new datasets
merge
fix Latin encoded keyword in GvHD (#232) * update email * rm \x encoded str from GvHD * bump x.y.z version to even y prior to creation of RELEASE_3_15 branch * bump x.y.z version to odd y following creation of RELEASE_3_15 branch Co-authored-by: mikejiang <mike@ozette.ai>
update yaml
fix the issue if more than 2 Enhancers for conservedMotifs.
add html output for conservedMotifs
Add support for HTML output for the alignment.
Add support for multiple alignments for alignment function.
added Bayes Factor helper
updated workflow to use magick@7
Bumped version number
Added getExpected plot helper
error more explicitly when mc.cores is not coercible to scalar integer - minor related code clean-up
merge
Merge pull request #53 from RGLab/fixed-logical-gate-compute Fixed logical gate compute
fix build
bump
bump x.y.z version to odd y following creation of RELEASE_3_15 branch
bump x.y.z version to even y prior to creation of RELEASE_3_15 branch
fix logical gate recompute issue
Merge branch 'master' of git.bioconductor.org:packages/densvis
Merge pull request #6 from Aurelius333/make-Y-init-work Make the `Y_init` parameter work
Make the Y_init parameter work Before this change, it seems like the Y_init parameter isn't actually used. This commit does the following: 1. Pass the Y_init parameter to densne_cpp. 2. Tell the DENSNE::run function to skip_random_init when init is true.
Updated and working GHA
Genentech bioc action
Merge branch 'master' of git.bioconductor.org:packages/densvis
use bioc action
Merge branch 'master' of git.bioconductor.org:packages/densvis
v1.1.11; bugfix when passing data to Rtsne normalise fn
change sleep to sys.sleep
make a test that takes a long time
add copy of apeglm function to avoid import
updating vignette
working on tests
working on ashr lfc threshold
cleaning up for ashr LFC threshold
Version 1.11.1
Version 1.9.2
update
Merge branch 'master' of https://github.com/RaikOtto/Uniquorn
update
"Bump the version to 0.99.9"</div>
merge with bioc devel
version bump
roxygenize documentation
altmetric badge
github pages
add pkgdown documentation
move project site from Sourceforge to Github
bump version
added form definition
update vignette for omikli, DBS and MBS
version bump
replaced BiocParallel::MulticoreParam(workers = 1) with BiocParallel::SerialParam() in tests
fix typos
Merge branch 'master' of git.bioconductor.org:packages/ASICS # Conflicts: # DESCRIPTION
change depreceated parameter from ropls package
Bumped version and date.
Migrated the classic marker C++ code to singlepp. Updated the singlepp library. This required updates to the C++ code, to account for renamed Classifier class and to use the umbrella header.
Minor fixes to the docs.
Parallelize getClassicMarkers for many labels, closes #227. This involved switching to a C++ implementation with, which makes the whole thing a lot faster than intended. </pre> </div> Package: Rsubread
Commit: a88381cd2a73c8eb96b3bc780bbfb4fd1c44bdeb
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-06-27 04:16:42 +1000
Commit message:
Split the "voting table" data structure into twoPackage: BioNetStat
Commit: 411fa49db10886cda5137d45ff3fa483e385069a
Author: jardimViniciusC <viniciusjc@gmail.com>
Date: 2022-06-26 13:48:26 -0300
Commit message:
size loading filesPackage: MultiAssayExperiment
Commit: 734e96a6d40c12be21d70ce96f4a1e592b9e896a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:47:05 -0400
Commit message:
update indentation for roxygenPackage: MultiAssayExperiment
Commit: cd8c7b12b52231a729d45d4e06309cae30d6dbf4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:42:19 -0400
Commit message:
version bump, 1.23.2Package: MultiAssayExperiment
Commit: f5e98401df5999d9918bb3daefc2cf0488d48b90
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:42:06 -0400
Commit message:
update to changes in roxygen 7.2Package: MultiAssayExperiment
Commit: c1aa7d5b9ddb6d5bd9815814d7adca5f7e6b4310
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:41:19 -0400
Commit message:
update NEWSPackage: MultiAssayExperiment
Commit: a240679c1097ab4d5dd3b01aef365946ba065d8a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-25 16:39:49 -0400
Commit message:
update wideFormat documentation, closes #312Package: MultiAssayExperiment
Commit: 2b834b5f15eaad658aa9ccc6bf3593c3b5f41246
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-05-18 12:50:34 -0400
Commit message:
update GHAPackage: OncoSimulR
Commit: 79ffadf37e6924c8fc19d52253d8926b612b931a
Author: ramon diaz-uriarte (at Phelsuma) <rdiaz02@gmail.com>
Date: 2022-06-25 16:24:13 +0200
Commit message:
3.99.1: interventions, death with fdf, user variablesPackage: basilisk
Commit: 27244b5ff0d640df0727d20acabba43520889dea
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-25 00:24:24 -0700
Commit message:
Pin the scipy version to avoid GLIBCXX errors.Package: basilisk
Commit: 18c56ff2aeb6309cb1a3470d354492e5b90c6346
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-23 22:12:35 -0700
Commit message:
Commented onexpectations around basilisk.R.Package: basilisk
Commit: 6a25e1d864ccd825b375812376f77f8b3e4088ab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-23 20:41:43 -0700
Commit message:
Exported utility to get the path to a BasiliskEnvironment.Package: basilisk.utils
Commit: 2044ccf86f172c55c9ea647b0aca49829d4d020a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-06-25 00:23:49 -0700
Commit message:
Try harder to find a good port when activating the environment. (#5)Package: crisprDesign
Commit: df73c83eb0a506cecc50ee2e94145e9f7a5a1487
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:37:48 -0700
Commit message:
Fixed bug in opsPackage: crisprDesign
Commit: c43f940d6d947082170ce5fb47ced32f4db063c3
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:28:02 -0700
Commit message:
Fixed ops codePackage: crisprDesign
Commit: 6489b51a1cff7092f7ff6059e5a9037f800a6873
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 09:01:09 -0700
Commit message:
Done with creating add functions for PairedGuideSetPackage: crisprDesign
Commit: 658a433141855d4703cd5f91748f08a1cef493cc
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 08:12:56 -0700
Commit message:
Added generic for addOffTargetScoresPackage: crisprDesign
Commit: 71f770d5dcc01d9a1205159e7d30a99040436f52
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-16 08:06:51 -0700
Commit message:
addgene and addtss have now dispatch methodsPackage: crisprDesign
Commit: f9a5bd6270505bcd80a0753a37f58378eb2ac064
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:58:17 -0700
Commit message:
Ready to merge with masterPackage: crisprDesign
Commit: f564487935db1f839b1711f6243fc2b850a0dd15
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:56:03 -0700
Commit message:
Done for todayPackage: crisprDesign
Commit: 5c32c869915dd2a23d91fbfc457f02c4ffd2f68e
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 16:50:22 -0700
Commit message:
Added addRepeatsPackage: crisprDesign
Commit: 410289524478c638f5277db53697646d019a05d7
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 15:58:45 -0700
Commit message:
Creating more generics for handling PairedGuideSetPackage: crisprDesign
Commit: 7634d6bc35823369cf7004f933705036ec7ec320
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 15:44:53 -0700
Commit message:
Documented PairedGuideSetPackage: crisprDesign
Commit: 2f118e7724151d7845e898c33021ef1d325e313b
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-15 14:26:30 -0700
Commit message:
Merge branch 'master' into pairedPackage: crisprDesign
Commit: 002b9d7e3681f6d6e8439a678908a2c188383ec7
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-14 21:27:43 -0700
Commit message:
Added generic for on-targetPackage: crisprDesign
Commit: b767ffe2f212e950f341c32c4e975e0a7ed07471
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-14 21:12:10 -0700
Commit message:
Merge branch 'paired' of github.com:Jfortin1/crisprDesign into pairedPackage: crisprDesign
Commit: 3f38e23908dcfcb65680ded1cdd7ef305f4424de
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 17:48:21 -0700
Commit message:
Done for todayPackage: crisprDesign
Commit: 300d592f219d2a37dbc613903a2a350ff01d390d
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:18:01 -0700
Commit message:
Added imports for first<- and second<-Package: crisprDesign
Commit: 1d258ea12038f229635380a2907dad4633c0b63a
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:17:12 -0700
Commit message:
Formatted filePackage: crisprDesign
Commit: a512d049bacc68e7b5702424afdfab035c3c8bfc
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:15:50 -0700
Commit message:
Started adding internal functions to add annotations to PairedGuideSetPackage: crisprDesign
Commit: 32e4b6758d5714b2e3321c1ed751fa5cef4fd254
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 17:48:21 -0700
Commit message:
Done for todayPackage: crisprDesign
Commit: 1249f127227890ee3cbaae2166f9ced17095eb35
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:18:01 -0700
Commit message:
Added imports for first<- and second<-Package: crisprDesign
Commit: b6a2438cf7f00b73ebaa044e03bdaaa16967a78f
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:17:12 -0700
Commit message:
Formatted filePackage: crisprDesign
Commit: 2565ad3ab70217eac2e6b2aa40c91ead5c097604
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-10 15:15:50 -0700
Commit message:
Started adding internal functions to add annotations to PairedGuideSetPackage: crisprScore
Commit: 6f2475d61a0623b7dd82df77d6bfbbf88c5c6daf
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-24 12:08:17 -0700
Commit message:
Updated doc, and added crisprRaterPackage: crisprScore
Commit: a1fef447884bd1dde5e7824998aa4d21258809be
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-23 07:20:41 -0700
Commit message:
Merge branch 'crisprater' of github.com:Jfortin1/crisprScore into crispraterPackage: crisprScore
Commit: 9b7c8a0002d3a54f27aaf731cd6ab35522322790
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-22 14:34:48 -0700
Commit message:
Started integrating crisprRaterPackage: crisprScore
Commit: 65fcd2909fb08964b13249e3d164180dee417fe8
Author: fortinj2 <fortin.jeanphilippe@gene.com>
Date: 2022-06-22 14:34:48 -0700
Commit message:
Started integrating crisprRaterPackage: RiboDiPA
Commit: 6cb8b3fe468a76717799f9ce6826c58f97edad3d
Author: Dr. Ji-Ping Wang <jzwang@northwestern.edu>
Date: 2022-06-24 12:54:23 -0500
Commit message:
bug fix for parsing gtfPackage: RiboDiPA
Commit: 6ff6cbe6a4e08d5135851c76e8242d023259e1ff
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2022-04-26 16:12:25 +0000
Commit message:
bug fix for parsing gtfPackage: msa
Commit: d6f4b25eda7b0599135cd6a38754f96a0b1fb570
Author: UBod <ulrich@bodenhofer.com>
Date: 2022-06-24 19:41:17 +0200
Commit message:
fix in texshade.sty as suggested on TeXshade homepage at CTAN; version number bumped to 1.29.2Package: signeR
Commit: d44a81f1a3f48c28fa45ad51e2a34f4de62adcd4
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2022-06-24 14:31:38 -0300
Commit message:
signerflowPackage: katdetectr
Commit: 6af9c8a88199b352f276aa07d465b757dcad1b2a
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:50:03 +0200
Commit message:
replaced @ symbol with corresponding getter functions in testsPackage: katdetectr
Commit: aab65207a09839102af692b3d0f62eaa86037761
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:49:38 +0200
Commit message:
removed github installation procedure from vingette and add toc:TRUEPackage: katdetectr
Commit: 7719a49c0f5abd992e6f53a0693fa30cc4da0715
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:49:02 +0200
Commit message:
replaced BiocParallel::MulticoreParam(workers = 1) with BiocParallel::SerialParam()Package: katdetectr
Commit: 4d5d362add87ca9e4ce54a562da94ae1933a7a34
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:48:42 +0200
Commit message:
removed installation from github explantation and browsevingette() suggestionPackage: katdetectr
Commit: dd3145ca6add8c473567a3f3e9b8818b79c12aa4
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-24 18:48:12 +0200
Commit message:
add correct link to issues page and version bumpPackage: ANCOMBC
Commit: ceb5ad5f595e91630055eb030fcd44caea58c41d
Author: Huang Lin <huanglinfrederick@gmail.com>
Date: 2022-06-24 11:17:48 -0400
Commit message:
Author list change and bug fixPackage: MetNet
Commit: efc1ef44e8838a305157005ac0ccbd3e10890682
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-06-24 11:31:55 +0200
Commit message:
implement corpcor package, bump to version 1.15.3Package: Rbowtie2
Commit: c96aa6e06b37827c4ca7397221c352819ebc62de
Author: wzthu <wzweizheng@qq.com>
Date: 2022-06-24 15:55:46 +0800
Commit message:
version bumpPackage: Rbowtie2
Commit: deccc7c2e63f26998d2e3693f29c991b7f7a3c2c
Author: wzthu <wzweizheng@qq.com>
Date: 2022-06-24 15:54:12 +0800
Commit message:
Merge branch 'master' of git.bioconductor.org:packages/Rbowtie2Package: Rbowtie2
Commit: 6cee528c8a06fe1ff8e2b90474246708e2509b9f
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2022-06-24 15:50:57 +0800
Commit message:
Merge pull request #5 from jsun/master escape file path to bt2index.Package: Rbowtie2
Commit: 0af53695553899281686238231f03b5abcd204fd
Author: jsun <sun@aabbdd.jp>
Date: 2022-06-24 11:17:17 +0900
Commit message:
escape file path to bt2index.Package: omada
Commit: c1ad01731d9d66a843fdab0132bdc8dd9093859f
Author: Sokratis Kariotis <sokratiskariotis@gmail.com>
Date: 2022-06-24 09:23:31 +0300
Commit message:
bumping version for new buildPackage: MatrixGenerics
Commit: ab97ac048888e497731883715f48bdb2bdb9dfd8
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:25:30 +1000
Commit message:
Update NEWSPackage: MatrixGenerics
Commit: ace5cf69d4888c938d8ac62247ce3391e602cc89
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:08:15 +1000
Commit message:
Version bumpPackage: MatrixGenerics
Commit: f7dca54132adfd4e2c503e0d559876719c895327
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:08:03 +1000
Commit message:
Make R CMD check happy by adding Matrix to SuggestsPackage: MatrixGenerics
Commit: ca52284150533933bf1ed98e449c7df05af9e425
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2022-06-24 11:03:06 +1000
Commit message:
Update roxygen versionPackage: MatrixGenerics
Commit: 53aa2271782f3569aaa6deeedea92b4bf9fa0813
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-11 15:14:58 +0200
Commit message:
Add test to check that dynamic loading worksPackage: MatrixGenerics
Commit: a7bcbc077a43721c2892c817352574c24ffad4a9
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-11 15:06:25 +0200
Commit message:
Override the [row|col]AvgsPerColSet ANY generics to match the arg namesPackage: MatrixGenerics
Commit: dce305f97a84af9f34b8b28b7f6ffa4b28dd30e9
Author: const-ae <artjom31415@googlemail.com>
Date: 2022-06-03 19:34:39 +0200
Commit message:
Fix #28 Unlike most other functions rowLogSumExps first argument is called `lx` instead of `x`. This caused `make_default_method_def("rowLogSumExps")` to generate erroneous code. To fix the issue I inline the correct code manually.Package: katdetectr
Commit: 06b1334b6b04cfcf5f6f31785d737cd442e95c24
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 22:24:12 +0200
Commit message:
Fix warning due to reference in documentationPackage: katdetectr
Commit: 399c4659b896978b2e9b416054dd87ee823514a9
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:28:29 +0200
Commit message:
version bumpPackage: katdetectr
Commit: 7a495f92d96f8cc5c59647797c46c7c1dbb598da
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:08:15 +0200
Commit message:
build documentPackage: katdetectr
Commit: 337b35e80960d83450d4cbd3992c186b17fdd32c
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-23 19:07:13 +0200
Commit message:
added manually calculating mutation rate for chromosomes with less than 5 variantsPackage: katdetectr
Commit: 4ea46ce04dc41270d6a22d13452b9f3a0fff3574
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-21 16:48:06 +0200
Commit message:
implementing comments from bioconductor reviewerPackage: katdetectr
Commit: 8e5239c68f7f66240ec1cbb047a284a5e43bbcd7
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:54:45 +0200
Commit message:
comment out General overview for testingPackage: katdetectr
Commit: 24749da4eaf99d2ce4d87fb62d4056039f47cd4a
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:48:50 +0200
Commit message:
update gitignorePackage: katdetectr
Commit: 0bea3ca722b7981a99dbf4f03edd06a868bcc262
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-06-20 18:48:37 +0200
Commit message:
update documentation rainfallPlot()Package: PharmacoGx
Commit: f6800889523eb97aac35a46b3405cf19e6ef9a82
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 12:32:14 -0400
Commit message:
Fix mismatched quotation in CreatingPharmacoSet vignettePackage: BiocCheck
Commit: 620c128fc4c1a81e6b79c38a5c6d900fd9d17292
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:16:15 -0400
Commit message:
version bump, 1.33.10, closes #161Package: BiocCheck
Commit: 4711b2f0061504b5a0a1f5b1f46c0a105d51cafc
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:15:50 -0400
Commit message:
update NEWSPackage: BiocCheck
Commit: 715b68f50cf6c907830f06ff24b2b7f25806c083
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-06-23 12:12:03 -0400
Commit message:
add single char lookback to remove list$F matches in T/F use WarningPackage: BgeeDB
Commit: f52f54e153216eb2131ebbe101b72689bc312134
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 16:34:36 +0200
Commit message:
bump versionPackage: BgeeDB
Commit: 3d6d9dd11d58419a54eabdd22e41a407b2b48f26
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 16:33:55 +0200
Commit message:
update how data are uncompressedPackage: spbtest3
Commit: 8c0f1ef496fada235b98528c106ba3d27b1a946f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-06-23 09:55:52 -0400
Commit message:
Bump version in description to trigger buildPackage: sSNAPPY
Commit: b5a52b7b69c7e488b52ec83fba07b06f583d8d65
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 22:32:17 +0930
Commit message:
fixed typo in descriptionPackage: sSNAPPY
Commit: d44f0cb1831bf77e148e58188fb1be67d7149fab
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 22:29:43 +0930
Commit message:
fixed typo in descriptionPackage: sSNAPPY
Commit: 1b119d523ad802fe28efba5940d0db3ee91246dc
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 17:39:14 +0930
Commit message:
fixed conflictPackage: sSNAPPY
Commit: 8c694f714583ef5f548e226d109f166f5d54dff0
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 16:54:55 +0930
Commit message:
fixed typo in descripPackage: rexposome
Commit: c9bb6d47fffe04be9388b6e90ed3f7dfabfbe6fa
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:45:45 +0200
Commit message:
solve merge conflictsPackage: rexposome
Commit: 8ad0a2ebf8b16164c5b9eef3282825040adda36a
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:52 +0200
Commit message:
bumped versionPackage: rexposome
Commit: 20bc7bec7c118e337855be5c747f88c46b731dff
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:31 +0200
Commit message:
fixed standardize bugPackage: rexposome
Commit: ce3fe79d3399cd2a41a1a05763fe6c9963bd1f70
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:41:07 +0200
Commit message:
fixed exwas bugPackage: rexposome
Commit: 6e6f0285b2c677799b1be3352cb47a142d296be5
Author: Xavier <xavier.escriba.montagut@gmail.com>
Date: 2022-06-23 12:28:26 +0200
Commit message:
Merge remote-tracking branch 'upstream/master'Package: rexposome
Commit: 49e1dbde53c66247b981317cd76d8c09d1ad3fef
Author: Xavier EscribĂ Montagut <xavier.escriba.montagut@gmail.com>
Date: 2021-12-17 18:21:49 +0100
Commit message:
put 0 in numeric test dataPackage: fastreeR
Commit: e574c5b2c8b6a0f5d3edab2b857e5e92f930e882
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2022-06-23 12:33:39 +0200
Commit message:
Update vignette minor bug.Package: BgeeDB
Commit: 31b91658febccdfb6f9c1c1ca9a3bdcce41c8129
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:27:30 +0200
Commit message:
Merge branch 'RELEASE_3_15' into BIOC_masterPackage: BgeeDB
Commit: 04c89fd9d42003fc852acc1121fe999742c97edb
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:11:18 +0200
Commit message:
bump versionPackage: BgeeDB
Commit: 2594ccafe82690a76d1100d9e42f12e046fc32f3
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-23 12:10:51 +0200
Commit message:
update documentationPackage: BgeeDB
Commit: 6ca006d8b317257d23ffe59795c8fdd82bc72784
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-16 14:22:59 +0200
Commit message:
bump package versionPackage: BgeeDB
Commit: 5eb6602da2b01adc8558082e855e1b2b11891bcb
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-06-16 11:49:20 +0200
Commit message:
allows user to define its own download timeout when using webservice for topAnatPackage: BgeeDB
Commit: 23e9a901dfa37bad22e7fbb89f96997a9cba04be
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-05-06 16:22:52 +0200
Commit message:
update citationPackage: BgeeDB
Commit: 0af86025f90c8b3724bd9d1cdd76d3805a799c78
Author: Julien <julien.wollbrett@gmail.com>
Date: 2022-05-06 16:19:19 +0200
Commit message:
update example and timeout value to avoid timeoutPackage: imcdatasets
Commit: 42cb2dc918b0fa87099467a8be7948a4dda1a7d3
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2022-06-23 09:30:03 +0000
Commit message:
Merge remote-tracking branch 'upstream/master'Package: imcdatasets
Commit: f28e240b3a9329a881608bc809cae799774f26f1
Author: ndamond <nicolas.damond@gmail.com>
Date: 2022-03-22 16:44:34 +0000
Commit message:
Merge branch 'master' of ssh://github.com/BodenmillerGroup/imcdatasetsPackage: imcdatasets
Commit: 0062fdee24ef6bc699866f8df54de638fccb2f8c
Author: Nicolas Damond <nicolas.damond@gmail.com>
Date: 2021-10-27 10:40:23 +0200
Commit message:
Merge pull request #12 from BodenmillerGroup/RELEASE_3_14 bump x.y.z version to even y prior to creation of RELEASE_3_14 branchPackage: zellkonverter
Commit: 280620b25e5b99b4d7572c5e52253def86671995
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-06-23 10:15:48 +0200
Commit message:
Merge branch 'RELEASE_3_15' * RELEASE_3_15: Move verbose from zellkonverterAnnDataEnv()Package: zellkonverter
Commit: 437ff0219ea4e2e59c7c0d291db4f42aab14cc98
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2022-06-23 10:13:26 +0200
Commit message:
Move verbose from zellkonverterAnnDataEnv() Needs to be able be directly sourced by {basilisk}Package: sSNAPPY
Commit: 2df5dc6f01ceb9b8c60bea3f498758a1b89edeef
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 17:35:31 +0930
Commit message:
fixed a typoPackage: sSNAPPY
Commit: 9195e45e68e03bdf28d1233f9c37f4cf6a0c7471
Author: Wenjun-Liu <a1680844@student.adelaide.edu.au>
Date: 2022-06-23 16:54:55 +0930
Commit message:
fixed typo in descrip "rebasing"#Package: rGREAT
Commit: 8c09b897ba41521cc48119e6ae83d1685a1fb368
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 09:45:12 +0200
Commit message:
fix a problem of par()Package: rGREAT
Commit: 11bc42393f3c7f7cc224a3db126c2efdbc98b522
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 08:06:19 +0200
Commit message:
version bumpPackage: rGREAT
Commit: 9e9155ad2678027ae4cf5b41cf204896f391c5b6
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2022-06-23 08:01:03 +0200
Commit message:
use gzfile()Package: PharmacoGx
Commit: 056b3444c2919dedaa1b6f3db167fed2b059c06e
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 01:01:55 -0400
Commit message:
Version bump for Bioc pushPackage: PharmacoGx
Commit: 7a0010fc1a3764b24fe14e8b75670081d5cac6d6
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-06-23 00:54:50 -0400
Commit message:
Merge pull request #119 from bhklab/development Basic synergy metricsPackage: PharmacoGx
Commit: 68b885e5791dbd124a9aad70f1f5eb4708717e41
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-23 00:33:40 -0400
Commit message:
Debug BiocCheck to false positive T/F usage in geneDrug*.R files * There is already an issue open https://github.com/Bioconductor/BiocCheck/issues/161Package: PharmacoGx
Commit: b17985ea91a72a37794fa6b9dfe5ca45d5a93a4a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 23:55:06 -0400
Commit message:
Renamed some files; added more examples to appease BiocCheckPackage: PharmacoGx
Commit: 27623c243a95f0e75991eb6b2a3c90184883b2e8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:53:23 -0400
Commit message:
Added BiocStyle to SUGGESTS to allow vignettes to buildPackage: PharmacoGx
Commit: 58bcaecb6df8182b4821c65d48b55c14f5211580
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:03:57 -0400
Commit message:
Resolve conflicts with masterPackage: PharmacoGx
Commit: a51668e3b281fc167a19b6054c79c9cd04e420e3
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 22:02:37 -0400
Commit message:
Fix some minor NAMESPACE issues; add Fei as authorPackage: PharmacoGx
Commit: c9f8f03e418a716cd618c9987d52c4b628673a07
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 21:41:57 -0400
Commit message:
Convert vignettes to HTML so I (hopefully) never have to debug a LaTeX error againPackage: PharmacoGx
Commit: e6b095b294a27563acc66fcf0157d60b3c73e29d
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2022-06-21 17:53:25 -0400
Commit message:
Merge pull request #118 from bhklab/fix_sProfiles fixed bugs related to using sProfiles in drugSensSigPackage: PharmacoGx
Commit: 0d23aca75c0576f7e2fadf6912d1d3fd50b99e2e
Author: Petr Smirnov <psmirnov2000@gmail.com>
Date: 2022-06-21 17:51:35 -0400
Commit message:
fixed bugs related to using sProfiles in drugSensSigPackage: PharmacoGx
Commit: 9e6fb691b4a63e2ad91195f24d5e45ecab8e7bbc
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:37:14 -0400
Commit message:
Fix PharmacoGx build to allow bioc2022Workshop to buildPackage: PharmacoGx
Commit: 3d3e7e60240806040bdd21e7be2742236b2b8175
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-21 14:34:14 -0400
Commit message:
Loewe methods addedPackage: PharmacoGx
Commit: 76e1aa6c5c5168074ceed6f36e6ee95bec931099
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 13:51:19 -0400
Commit message:
Fix wrong argument name in .PharmacoSet for PharmacoSet2 constructorPackage: PharmacoGx
Commit: 9d525702809927cb1af9335415b0d6585b970efa
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 12:41:31 -0400
Commit message:
Update sensitivitySlot to treatmentResponse method to match new package nomenclature * Aliased treatmentResponse to sensitivitySlot in CoreGx for backwards compatibilityPackage: sesame
Commit: caa961ec756edb4560d067d339086adea8821b47
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-06-22 22:03:46 -0400
Commit message:
bump to 1.15.3Package: sesame
Commit: 0a094f87c3848d3f26af7e0d883c1fb82372626a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-06-13 11:20:00 -0400
Commit message:
update to summaryExtractTestPackage: sesame
Commit: 0275992120346b70ec5a479dc9d838fdcbaee89c
Author: Zhou <zhouw3@c7d363v6qq.chop.edu>
Date: 2022-06-08 13:09:25 -0400
Commit message:
fix singularity case in DMRPackage: CoreGx
Commit: 6c7e434d35b7beab564cda8b24da69502aeae4f7
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 20:43:48 -0400
Commit message:
Version bump for Bioc push; add Fei as contributor (thanks for unit tests)Package: CoreGx
Commit: 2642c2f330f585c1a4abc4a74880e58eb0ee0b5d
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-06-22 20:36:53 -0400
Commit message:
Merge pull request #150 from bhklab/development Finally passing the checks. R NAMESPACE errors are the worst.Package: CoreGx
Commit: 9126239d0314cf4a305e3625c358255bc5e31564
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 20:22:44 -0400
Commit message:
Passing rcmdcheck with only notes finallyPackage: CoreGx
Commit: 3b494e11b5dc18a49f978c0dc74fa0419b37ec1a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 19:38:23 -0400
Commit message:
Debugging NAMESPACE related warnings in rcmdcheckPackage: CoreGx
Commit: 5a8b70216624533aa932c0241a29b6cba155c2af
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 19:15:52 -0400
Commit message:
Fix sensitivityRaw assignmentPackage: CoreGx
Commit: d0a0faa8308509aa0f1a47b59b7a5c5991a65839
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 18:28:25 -0400
Commit message:
Fixed tests after modifying assay,LongTable-method for summary assaysPackage: CoreGx
Commit: 7fbcf571837f8d54e77029763a7461735b1c113c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-22 16:24:34 -0400
Commit message:
Added summarize argument to assay which only returns columns mapping 1:1 with the assayKey when TRUEPackage: CoreGx
Commit: 42e83ba2aec42ab00d64fbf6f2359189562eac64
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:37:44 -0400
Commit message:
Update CoreGx to allow bioc2022Workshop to buildPackage: CoreGx
Commit: 5e6921ae6b4e32ab880c03a06e4986e930a3b022
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 15:34:38 -0400
Commit message:
Debugging endoaggregate methodPackage: CoreGx
Commit: e4b26409a157a9879e0c4e3daafe4b0b3f21d06c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 14:09:57 -0400
Commit message:
Fix #155 by adding by=.EACHI to cartesian join to prevent allocating the entire table as once, but this has slowed down assignment significantlyPackage: CoreGx
Commit: e66ffb6a7a10a98b212b6d2627b063c76b301393
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 12:07:06 -0400
Commit message:
Fix #154, was being caused by failure to import bpprogressbar<- and bpworkers<- in aggregate file * Resulted in hasMethod for these two generics to always return FALSE, since they weren't available in the local environmentPackage: CoreGx
Commit: 53d332c5667373e1147bc305762192a2e44eded9
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-21 11:27:56 -0400
Commit message:
New endoaggregate method working for assigning new assays; testing for updating existing assaysPackage: CoreGx
Commit: 5813df334fd63f027b2b76d3a094de5f5a5936d8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-20 20:04:45 -0400
Commit message:
Fix molecularProfiles bug caused by name clash between function argument and assay function callPackage: CoreGx
Commit: 3e85b8dbb296ee1c5002f3444c0da5085939e6a6
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-20 00:48:16 -0400
Commit message:
Merge branch 'development' of github.com:bhklab/CoreGx into developmentPackage: CoreGx
Commit: 2d0a1f3388701d0e71c3dc8caa8c7811a48262ee
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-19 19:05:57 -0400
Commit message:
Update .Rbuildignore and NAMESPACEPackage: CoreGx
Commit: ca41d7da827c3691bdf9fac29b1b821511e95f39
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 19:51:32 -0400
Commit message:
Add summarized of synergy metrics via meanPackage: CoreGx
Commit: 21a419de5c7b2541388610862521fd7e32acfc89
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 12:39:42 -0400
Commit message:
Update man and NAMESPACE to fix sensitivitySlot method issuesPackage: CoreGx
Commit: 50bce1aea1905b02a9f5bc103bf7d4cade7bc9ef
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-18 01:31:12 -0400
Commit message:
Merge branch 'development' of https://github.com/bhklab/CoreGx into development Merge pull w/ localPackage: CoreGx
Commit: 3f2a6839fd87113ef25213c31b038c028e990d40
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-18 01:22:21 -0400
Commit message:
Added testing code for calculating Loewe CI in aggregate-method.RPackage: CoreGx
Commit: 5321c36be6fe719749d6433807b594ca06fe8c63
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-18 00:38:11 -0400
Commit message:
Fix bug in .rebuildProfiles by summarizing values in sensitivityProfiles if they map to dosePackage: CoreGx
Commit: ec1a88c6e4b07df396b777ee11dc37f0e68c2b5b
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-06-15 13:40:26 -0400
Commit message:
Method for grouping monotherapy and drug-combination responses within an assay table added to utilities.RPackage: CoreGx
Commit: 30ac4abd5ec26953067fb53da9cba692a174513a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-15 15:44:21 -0400
Commit message:
Add testing code for drug combination modelling in aggregate-method.R filePackage: CoreGx
Commit: 41bf8d4b29b9d374a46861bfbb413a66a498d18b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-13 18:04:32 -0400
Commit message:
Fix #151 by swapping all.equal for .table_is_subset inside assay<-,LongTable,character-methodPackage: CoreGx
Commit: 5aefb199eeb63d9351d3369558c68c5415032fac
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 18:41:33 -0400
Commit message:
aggregate2 and aggregate,TreatmentResponseExperiment-method now work with enlist=FALSE argument, which evaluates closer to raw data.table group byPackage: CoreGx
Commit: 9ec789baa3429d1c7fed4fd5d57ed1c90bca8e27
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-07 12:42:07 -0400
Commit message:
Renamed method sensitivitySlot to treatmentResponse, aliased back to sensitivitySlot for backward compatabilityPackage: CoreGx
Commit: 4b76feee0cf1eb00bcc4525d84a3c2fcc8550898
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 18:01:31 -0400
Commit message:
Fix aggregate2 method so it only tries to set bpworkers for BPPARAM classes which define that methodPackage: CoreGx
Commit: bbf7dce64133790932691a246a6043b54cb60196
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 17:44:38 -0400
Commit message:
Merge branch 'main' into developmentPackage: CoreGx
Commit: 3a2d42906431051ad14ca1a2c421f2367706f883
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 17:42:13 -0400
Commit message:
All unit tests passingPackage: CoreGx
Commit: b4564b0760d82ecec4210dff6f5e3f5fe1574ced
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 16:37:45 -0400
Commit message:
Updated comments for .subsetByIndexPackage: CoreGx
Commit: 29f8f9326f8a98269ffdd65e71b374ba483dd406
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-06 16:00:30 -0400
Commit message:
Update .subsetByIndex to apply unique to each assay data.table before assigning back to the TRE object; this fixes #149Package: CoreGx
Commit: 3afb956a4099978737e5ea74f12f3906f7dbd960
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 18:19:51 -0400
Commit message:
Debugging issue with assignment of summary assaysPackage: CoreGx
Commit: 318aeb59ae33dbfda5b94c9c2934c5ac3fe037d1
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 17:31:02 -0400
Commit message:
Add tests to ensure assignment of summarized assays works correctly; fix #147; add test case for #147Package: CoreGx
Commit: 092f09849a901748fa24070521c01bc77cef5f8b
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 17:08:52 -0400
Commit message:
Add test to ensure that automatic column name generation works in aggregate2 and aggreagate,LongTable-methodsPackage: CoreGx
Commit: d26babf0642a484639a96dc09d3f87e4ff185bc6
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:53:10 -0400
Commit message:
Add test to ensure aggregate,LongTable-method is equivalent to data.table aggregation of the associated assayPackage: CoreGx
Commit: 9197a4a666abbc5a7dbc17c0e6ab6a9aabe027e2
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:41:06 -0400
Commit message:
Add tests to ensure aggregate2 results are identical to data.table aggregationPackage: CoreGx
Commit: dcfbeb2332fed6715697dbd018ea2c2f9df12b29
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 15:09:14 -0400
Commit message:
Fix bug in aggregate2 causing default name parsing to fail when no aggregation calls have namesPackage: CoreGx
Commit: a98a408fb52979248c5a9bb4d9af453b0388efbb
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 14:38:38 -0400
Commit message:
Forgot to git add some stuf f in last pushPackage: CoreGx
Commit: be619223d787f26a5a6a61c97e0c5ed90e94567d
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 14:38:02 -0400
Commit message:
All unit tests now passing with modified subset,LongTable-method algorithmPackage: CoreGx
Commit: 7ac7ca0784a2112d9f5f8a0681009b1d7ab845c5
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 13:15:05 -0400
Commit message:
Update unit tests to account for change in how subsetting a LongTable worksPackage: CoreGx
Commit: 070cecc0e274ca23a59b9ce8c736436a96a25186
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 12:39:25 -0400
Commit message:
Fix unit tests for subset,LongTable-method to account for the fact that additional row or colKeys may get dropped when there are no observations remaining in the tablePackage: CoreGx
Commit: 33f9dc4ba761340a42caf4aedd50b77a7f1442d7
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2022-06-03 12:33:26 -0400
Commit message:
Add .table_is_subset utility for use in unit testPackage: CoreGx
Commit: 9341ac135e31d479f0696a47e5a55b37fd297128
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-03 09:24:10 -0400
Commit message:
Debugging LongTable/TRE unit testsPackage: CoreGx
Commit: 9fbfa79ee0d58bb5a87ee2e61de6063c4fe1e3b2
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:48:02 -0400
Commit message:
Merge branch 'development' of github.com:bhklab/CoreGx into developmentPackage: CoreGx
Commit: fe497df9f92e090a63a3510a24f801c575cce173
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:46:35 -0400
Commit message:
fix #148 by feeding back rowKeya nd/colKey from assays to index after subsetPackage: CoreGx
Commit: 783617bc70efd25a75deeaf118116605dfe270e2
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 18:46:35 -0400
Commit message:
Fix #148 by feeding back rowKeya nd/colKey from assays to index after subsetPackage: CoreGx
Commit: 496ba7fa2299ec1b22254b73d17a590ecd1607e5
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 17:29:42 -0400
Commit message:
Refactored row and colData<-,LongTable-method to use a shared helper methodPackage: CoreGx
Commit: 9e33136f691caadd0fafb4503c8b279438bca50c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 13:06:47 -0400
Commit message:
Basic aggregation of TreatmentResponseExperiment now workingPackage: CoreGx
Commit: 26a37b9cc0ecd8bf388025d17ea9a36427a3568b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 12:36:33 -0400
Commit message:
Revert "Revert "Revert "Update issue templates"" to fix accidental push to main :sunglasses:" This reverts commit 69fbee5002276a080190bb21f7a6c8f996c3e8e8.Package: CoreGx
Commit: 59a85888a1e012e447d048caa9ff3ddac722a322
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-02 12:35:44 -0400
Commit message:
RE fixing #146, merge with main reverted it apparentlyPackage: CoreGx
Commit: 69fbee5002276a080190bb21f7a6c8f996c3e8e8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:52:07 -0400
Commit message:
Revert "Revert "Update issue templates"" to fix accidental push to main :sunglasses: This reverts commit 5532ca4ecd2abdee0dcfb558d1e36ddd0549ca52.Package: CoreGx
Commit: 164a94ddf6ff86e5cc5012fefe8753bbbeafb3c0
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:51:39 -0400
Commit message:
Merge branch 'main' into developmentPackage: CoreGx
Commit: 460f3da9f1a8f9c838de0679b57a16eb79223fd3
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 17:51:24 -0400
Commit message:
Still accidentally commiting to main instead of development :cry:Package: CoreGx
Commit: 2be9809f03513a670a8df1a4a867fb2737e85ce8
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 16:07:41 -0400
Commit message:
Added some benchmarking code to test aggregate2 performance across different parallelization backendsPackage: CoreGx
Commit: 5532ca4ecd2abdee0dcfb558d1e36ddd0549ca52
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:20:40 -0400
Commit message:
Revert "Update issue templates" This reverts commit 23ba0a3ed9d6091141cd296eaeca277634efdd2d.Package: CoreGx
Commit: 299b38abbcfcf964cb274c83fb750352ca625228
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:14:44 -0400
Commit message:
Merge branch 'development' of github.com:bhklab/CoreGx into developmentPackage: CoreGx
Commit: 267dbd3f6aade6674b0d34c7d622144fb3c2d965
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:13:56 -0400
Commit message:
Merge accidental push to main into development :joy:Package: CoreGx
Commit: 8f780b95d0bb2c42c7b1cce973768b8797c8c99c
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 14:12:36 -0400
Commit message:
Added benchmarks to aggregation with computeAUC; accidentally pushing to main :sadface:Package: CoreGx
Commit: 917e753cb71ea935cab622d020c4243279f41cbc
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-06-01 13:56:18 -0400
Commit message:
Parallelization working in aggregate2 data.table methodPackage: CoreGx
Commit: b5120758e69579e6bfcc4676342f12cf8e7fffa1
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-31 19:13:08 -0400
Commit message:
Add basic function documentation for aggregate2 functionPackage: CoreGx
Commit: 1782513e00e2a6dd5ad0d1d1dddfd900f64b9659
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-31 19:00:50 -0400
Commit message:
Add draft of aggregate method for data.table, to be used in TRE aggregate methodPackage: CoreGx
Commit: 97abebb4c2665455da70ef0e2be65e75752b30d3
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 17:01:04 -0400
Commit message:
Split unit tests by .R files.Package: CoreGx
Commit: 52b0cde46600f4c2a5047fb81d71f38c067b9be9
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 16:17:52 -0400
Commit message:
resolved merge conflictsPackage: CoreGx
Commit: d1937eebecaad8d9c6c6ed26ff85b47039b6fd9e
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-30 16:08:27 -0400
Commit message:
New subset() tests added. Compressed test dataset. Added missing colData param check for LongTable consturctor.Package: CoreGx
Commit: 23ba0a3ed9d6091141cd296eaeca277634efdd2d
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2022-05-30 12:11:13 -0400
Commit message:
Update issue templatesPackage: CoreGx
Commit: 51f850883594d7a799d5ea0d6df8ad0e9625777a
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-30 11:33:38 -0400
Commit message:
Add GHA CI/CD for release branchPackage: CoreGx
Commit: d394583fa5a4593a3b8d8e4b5ec94124d8f3afb5
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-30 11:20:03 -0400
Commit message:
Fix duplicated detection in rowData methodPackage: CoreGx
Commit: 644c8cee299a88cf5cfb4365586d199c2ee10b16
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-26 20:44:41 -0400
Commit message:
Added NCI-ALMANAC TRE subset to the package.Package: CoreGx
Commit: 3de48780f9cbfc45edbacab7aa76bf57f929d356
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-26 19:57:52 -0400
Commit message:
New test cases for subset method and TRE class addedPackage: CoreGx
Commit: 3793f60e8be91ffbc4e11afc2ab8f650b6c28d55
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-26 12:34:17 -0400
Commit message:
Add warning for duplciated idColumns in rowData assignment method; stil need to propogate change to colDataPackage: CoreGx
Commit: a1aabd6112ef05ad4faaf4252305c73abbf8726b
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-26 11:19:14 -0400
Commit message:
Renamed all instances of lt to tre in tests to represent updated package nomenclaturePackage: CoreGx
Commit: 957fe2c2e89662f6800d7d783cccf8a6c95a6253
Author: Christopher Eeles <christopher.eeles@outlook.com>
Date: 2022-05-25 14:53:51 -0400
Commit message:
Fix #146: join on wrong index in reindex,LongTable-method was failing to update the assayIndex row and colKeysPackage: CoreGx
Commit: b8aaad5f1d0ff15f31bde01a714ed6c916b80dc6
Author: ff98li <li.feifei.official@gmail.com>
Date: 2022-05-20 18:50:47 -0400
Commit message:
Minor fix: subset i rowname length check works now
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