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This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.
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adding app sketch; shinyapps.io not taking R 3.6
updating README.md resources
Added a getAttributes() method
1.27.2 resolve upstream conflict
1.27.2 bugfix mt() example. Update README
fixed small bug in overLapper
finishing vignette
Merge pull request #58 from stianlagstad/improve-test-coverage Improve test coverage
Ignore these
Fix too long lines
Add tests for parameter-validations
Test .is_ylim_valid
v1.11.22 minor internal corrections
minor changes
new material for extending an ontology, updated vignette
Bump version
Update README
Add bioc badge
Bump version
Add Zenodo link
fixed author syntax
test
Update citation file
Bump version number in devel
Merge branch 'issue-20' Bug fix for missing columns of output with more than 3 factor groups. Thanks to @jrhawley for pointing this out and proposing the change.
Test patch to issue #20 Thanks to @jrhawley for pointing out the issue and proposing the change.
bump version with rXdN addition
bump version with rXdN addition
add rA:dN rC:dN rG:dN and rT:dN in CFDscore calculation
v bump 1.3.4
v bump 1.3.4 improved fragLen_calcStranded() performance to avoid timeout in package CHECK.
v bump 1.3.3 docs pass CHECK
bugfix: fetchGRanges * target_strand always missed
added parallel processing to ssvFetch* functions.
updated tests for new export environment.
ssvFetchGRanges, improved functionality to match ssvFetch* (target_strand, return_data.table, win_method, anchor).
v bump to 1.3.1
Merge remote-tracking branch 'upstream/master' to continue work on bioc devel.
added ssvFetchGRanges. added x_precision to centerAtMax.
Merge branch 'master' of https://github.com/jrboyd/seqsetvis Conflicts: R/functions_fetch_bam.R
bug fix: don't try to add sample names to empty result
bug fix: don't try to add sample names to empty result
bug fix: allow splice strategy "splice_count" in fetchBam
qgr$name now used clean up exports
docfix : fetchBam() splice_count added
Merge branch 'master' of https://github.com/jrboyd/seqsetvis
bigfix: missing id in output when qgr$id set but not names(qgr) Fixes #1
bigfix: missing id in output when qgr$id set but not names(qgr)
update
fix bug
fix bug of unexpected )
fix bug for non-hunman-and-mouse genome reference lacked of blacklist and DHS file
Add env for password. As the rstudio docker image requires this now.
bump
More "condition has length > 1" fixes
add one-step visualization for browseTracks
Update citation
bug fix
* fix prototype mismatch issue * fix plot error: non-finite ylim when pvalue=0
Merge remote-tracking branch 'upstream/master'
elmer bug fixes
bug fix in elmer section
bug fixes in GDC api
Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI
Changing from minfi to sesame
Removing masking from matrix DNA methylation to SE
Adding IDAT prepare to vignette
Removing note
fixing appveyor
bug fix
Fix Description
updating aapveyor and namespace
Version bump
Update internal function for idat function
Adding IDAT pprepare using sesame
Update README.md
Add loop for GTF conversion on the fly - ensembl started blocking consecutive hits on gtf directories which would cause the generation to fail. A trycatch loop was added that if the access is denied (errors) it will wait 10 seconds and try again and completely fail after 3 attempts.
More clean up
tryCatch in 2bit for cleanup
man page mismatch
v1.4.1
v1.5.1
test
patching
Add citation
Small fixes to vignettes and citation
move TEMPLATE_DIR to .onLoad()
add a new vignette
update readme
update readme
test
Version Bump
News
Remove CompPASSplus Hide GetPPN
Change to BiocStyle
Discard CompPASSplus
15 Feb 2019: limma 3.39.12 - arrayWeights() now checks for and skips over any genes with zero residual variances.
fix an edge case related to previous commit
bump
Merge branch 'master' into trunk
fix aggregation and labeling when selecting markers for the heatmap
modify test case to work with cytolib2
remove trailing whitespace in deps list
Update .travis.yml
Update .travis.yml
Update .travis.yml
Merge pull request #12 from UW-GAC/admixMap Allow SeqArray GDS files in admixMap
version bump
remove obsolete code
update man page with SeqVarIterator option for admixMap
unit test compares output from two types of GDS files
don't include alleles in admixMap output
fix dimensions of frequency, set indentation
use new internal function to check for identical list elements
Merge branch 'master' into admixMap
bug fix: allow >2 matrices in fitNullModel Previous fix for checking list elements identical only worked for 2 elements in list.
allow SeqVarData objects in admixMap (WIP)
move some internal code for GenotypeData objects into methods
add coverage with covr
use bioc-devel for travis
set up travis CI
Merge branch 'devel'
updated configure.sh src/Makevars modified instead of DESCRIPTION
disabling wrappers for Windows
Update README.md
Update paper.md
v1.11.2Ã0 minor internal modification
Add 'gzindex' argument to FaFile() constructor (points to bgzip index) Also added 'gzindex' field to FaFile objects and gzindex() getter/setter.
v1.9.2 -- add the async argument to snaptron_query() to resolve https://github.com/ChristopherWilks/snaptron/issues/11
add support for mapToTranscripts() to map ranges that span introns
Edited DESC: removed maintainer (already in Authors@R)</div>
Vignette update
updated author information
14 Feb 2019: limma 3.39.11 - contrasts.fit() now removes any test statistics or p-values found in the fit object. This avoids a mis-match between coefficients and test statistics if eBayes() has been run on the object previously.
14 Feb 2019: limma 3.39.10 - arrayWeights() now chooses between the REML and original gene-by-gene algorithm automatically by default. REML is chosen when there are no prior weights or missing values and gene-by-gene is used otherwise.
optimize
mv vignette to book
fixed R check and introduce asis in [ method
Merge pull request #10 from fmicompbio/rhisat2 Rhisat2
Travis debug
Debug travis
Remove empty Details section
Add R version dependency
Don't try to extract NH tag from unaligned reads.
Consistent argument names in qProjectUpdate
Only read gene annotation if splice site file should be recreated.
v1.23.14 - ported filter_hisat2.c from samtools to htslib API
use htslib header
Merge branch 'master' into rhisat2
Merge pull request #9 from hpages/master Migrate QuasR to Rhtslib and Rsamtools 1.99.1
Migrate QuasR to Rhtslib and Rsamtools 1.99.1
Try to install remotes again
Cache packages travis
Use Rhisat2 from Bioconductor
Fix test
Merge master into Rhisat2
Cosmetic changes
Simplify align_Rhisat2
Simplification (same call to Rhisat2 for spliced and unspliced alignment)
Clean up
Add documentation for qProjectUpdate
Add unit tests, export qProjectUpdate
Merge pull request #7 from fmicompbio/rhisat2_maxhit filter Rhisat2 alignments to conform with maxHits argument
Fix print method for qProject class
Change representation to slots in qProject class definition
Set lib.loc to NULL if missing
Fix unit tests for Rhisat2 alignments (with the filtering).
Add maxHits argument to align_Rhisat2, call filtering function.
Merge align_Rhisat2 and align_Rhisat2Spliced functions. Set -k to maxHits+1
symbol lookup fix
added unit test for filterHisat2
fix flag for unmapped reads
v1.23.9 : added filterHisat2()
Merge branch 'master' into rhisat2
Fix merge conflicts
Typos
Merge branch 'master' into rhisat2
Make sure that the splice site file is used if provided
Add unit tests for Rhisat2 alignments
Fix test failing when bam files are provided
Merge master into rhisat2
Add AnnotationDbi
Add some documentation
Check whether splicesite file needs to be regenerated.
Only redo alignments if necessary
Add geneAnnotation to alnInfo
Create md5sum file for geneAnnotation
Don't check for compatible geneAnnotation if aligner is Rbowtie
Move parsing of spliced alignment parameter
Move definition of alignment parameters to after aligner definition
Fix addition of geneAnnotation to qProject object
Check for presence of spliceSites file
Update show
Small fixes
Provided geneAnnotation now path to either gtf or sqlite file
Default txdbFile NA
default txdbFile is 'none'
Merge branch 'master' into rhisat2
Add update function
Spacing
Renaming
Process the provided annotation
Add spliceSiteFile slot to qProject class
Install Rhisat2
Merge master
hisat2-specific checks for alignment success
Too early specification of proj@aligner
Set hisat2 alignment parameters
Add Rhisat2 as a supported aligner.
Rhisat2 not supported for qMeth
Add space
Move Rhisat2 to Imports
Add alignment functions for Rhisat2
Add index building capabilities for Rhisat2
Add Rhisat2 to DESCRIPTION
add bootMoa which is used for determining the components representing significant concordant structures. Bootstrap method is used, similar to bootMbpca
moa can return raw results from svd this can be used for bootstrap to determine the number of significant components
add multiple test correction for mogsa
fix un-matched title in vignette
14 Feb 2019: limma 3.39.9 - The old function ebayes(), which was deprecated a year ago in favor of eBayes(), is now removed.
14 Feb 2019: limma 3.39.8 - Further simplifications and improvements to the arrayWeights() code when method="genebygene". - New argument 'prior.n' for arrayWeights() to control the prior weight with which the array weights are squeezed towards unity.
12 Feb 2019: limma 3.39.7 - The fitted() and residuals() methods for MArrayLM objects now give an informative error message if the object contains contrasts instead of the original coefficients.
Rename arrayWeightsSimple.R to arrayWeightsREML.R
bump
bump
bump
Make NA checking for list glpolygon output in densityplot more robust
Fix conditionals with potential length > 1
minor C++ changes
update TCGAsampleSelect documentation
bump version
update filename translation function
Update spillover_ng tests to remove unnecessary pregating
Update reference compensation matrix used by flowStat tests
add pkg man page
Add existing package check to all Bioconductor repos - extended to check annotation, experiment, and workflows before was only checking CRAN and software
v1.11.18 minor internal modification
v1.11.16 optimization of ExpressionSet instance handling
v1.15.18 minor internal modification
v1.15.16 optimization of pData and fData modifications; Biobase as depends
new accession to modelSelection parameters and possibility to aviod testing specific rates for variability
bug fixed in anaDiff with Firefox
Changed a bug in the examples.
Version bumped back down because off illegal version bump (oops)</div>
Version bump, Release 1.0.0 Ready!</div>
test
Added some more unit tests
Never use 'revert'!
Version bump
Revert "More tweaks to H5Dread" This reverts commit b6571876ab2a67b70d079811b11c0f6756604544.
More tweaks to H5Dread
fix mCSEAIntegrate
Pigengene: dOrderW2
Pigengene: dOrderW
Add informative error message when a subset of estimated GMM have singular covariance matrices + add generic for plot function + minor doc updates
more description of purpose
paper draft 3
Merge branch 'master' of https://github.com/compbiocore/RSeqAn
updated DOIs
Update README.md
Update README.md
Update README.md
Update paper.md
Update paper.md
forgot spaces in yaml
merging
Update README.md added link to vignette as well as direct c++ code in usage
updated date and bibliography in yaml and added direct source code in extdata
updated affiliations
fixed tables
Merge branch 'paper'
finished paper and add cache to travis
paper is done
paper bibliography
first draft of paper
version bump
correctly subset gene/sample names
update URL and bump version
remove custom URL
include copy of NEWS
update README and pkgdown.yml
update .travis.yml file
version bump
include pkgdown yml file
add text to NEWS.md and change inst/NEWS type
updates to extra vignette
Extend Annotated (for metadata), closes #208
v1.11.14 minor internal modification
v1.15.14 minor internal modification
change version Merge branch 'master' of git.bioconductor.org:packages/bioCancer # Conflicts: # DESCRIPTION</div>
Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/</div>
v1.11.12 minor modification in example with ExpressionSet
v1.15.12 minor modification in examples defining ExpressionSet instances
minor version bump to 1.1.2
bug fix in getCurves: the extend = 'pc1' option was broken in a non-obvious way (if endpoints of lineages are near 0 in dimensions 2+)
Merge pull request #29 from rcannood/develop Fix travis issues
remove suggested package from install
Vignette requires more suggested packages
attempt to get biocstyle installed
install bioccheck differently
also warm up bioc devel cache?
also install biocstyle
probably don't need these args if script is being overwritten
override after success in prepare cache
third try
second attempt
try building without init
solve issue with vignette not being built due to missing bib file
remove html
undoing previous commit. Changing the header did not fix Travis' mysterious inability to see slingshot.html sitting in inst/doc/.
modified header of slingshot.Rmd (per suggestion on SO), rebuild vignette
v1.11.10 minor update of example
update migration_notes.md
Version Bump
Fixed an error with non-matching seqlevels
bug fix in cgdsr URL
resync with Rsmatools 1.99.1 and Rhtslib 1.15.3
Fix a bug and update citation
Compile and link C code against Rhtslib instead of Rsamtools
resync with Rsmatools 1.99.1 and Rhtslib 1.15.3
Fix for Solaris Do not build standalone executables (e.g. bgzip, tabix, etc...). They're not needed and seem to cause problems on Solaris.
commented on substr and added sym2CellOnto in vignette
added sym2CellOnto function
Documentation update - see NEWS
Fix ensemble import. Add IDR. See NEWs
12 Feb 2019: limma 3.39.6 - Major rewrite of arrayWeights() to improve speed and stability. The arrayWeightsSimple() function has been removed and its functionality incorporated into arrayWeights(), including the new 'var.group' argument to simplify specification of the variance design matrix.
Added package logos to vignette
Response to Issue #2: added dgCMatrix export method and an array transposition in import
bug fix: fixed bug introduced in previous patches when running create_sequences('RNA')
version bump
bug fix: create_sequences(alphabet=RNA) now works with difreq/trifreq
version bump
bug fix: create_sequences() not working properly with difreq or trifreq provided
more tests: compare_motifs() + convert_type()
expanded add_multifreq() and compare_motifs() tests
updated vignette
ctmarks app seems stable now
Revert R version requirement change
Fix fetchExtendedChromInfoFromUCSC("hg38") A recent change on the UCSC side broke fetchExtendedChromInfoFromUCSC("hg38"), the workhorse behind Seqinfo("hg38"). See https://support.bioconductor.org/p/117808/#117831 for the details. With this fix, hg38 is still strictly mapped to GRCh38 and not to a patched version of it (what assembly hg38 is based on exactly has become somewhat unclear on the UCSC side).
embed samtools sources directly, since Rsamtools has moved to htslib
revised ctmarks app with helpText
close connections in BatchtoolsParam unit tests - requires an explicit garbage collection
(port) clean up Makevars
clean up Makevars on non-Windows
better random number management on load - don't create .Random.seed if not already present
changes to accommodate new Rsamtools that uses Rhtslib; patch supplied by Hervé Pagès
version
fix argument
fix the problem of compound/unannotated nodes causing graph merge fail
compound nodes
version
topTable updates: show medians, sort columns
prototype definition and slots are consistent now, thanks to the reminder sent by Lori Shepherd
check works now with devtools::check()
Fixed bugs
version bump & update news
headTabix: use fread.gzipped only when user wants to get more than 1e6 rows
test-1-read: check if methylRawDB is same when directory is given or not, i.e. test wether directory affects object
methylRaw: check for content in tabix file, break if not
add some sections to methDiff.R
calculateDiffMeth: dealing with case of full model not being different from reduced model; print warning and set NaN to 1
pool: check length of treatment and number of sample is same
improve validity checks for methylDB objects
fread.gzipped: rewrite building of shell command with system2 to mimic R.Utils::gunzip
add test for methylRawList Constructor
test-1-read: check if methylRawDB is same when directory is given or not, i.e. test wether directory affects object
getCorrelation: reduce code duplication and overhead by introducing S3 functions to be called by S4 methods
update NEWS and versionbump to 1.9.2
fread.gzipped: return df
headTabix: use fread.gzipped directly on the tabix file should fix issue https://github.com/al2na/methylKit/issues/141
fread.gzipped: update function to check compression based on file content and allow to decompress .bgz files
Update README.md
Update README.md add codecov support
Add codecov
Update README.md
modified simulated data and updated NEWS file
Bug in preproccessInputData solved (DESeqResults to data.frame)
version bump
use UTF8
add users who provided valuable feedback to the acknowlegement
parseKGML2DataFrame: edgeData and KEGGedgeData can be of different length. Now the solution is to expand the shorter one. users are encouraged to report any bug
add readme
version bump
use devtools::check for checking
renaming
import url.exists
replace RUnit with testthat, add RCurl
test existence of the URL before downloading, thanks to the suggestion of Juliane Manitz, author of the kangar00 package on CRAN
use testthat instead of RUnit as the test engine
build ignore updated for git
too long a line was truncated into shorter lines
fixed documentation
reduced size of PROonto.rda
update with graphNEL support
downsized TwoSzabo data set
adding a try() around Seqinfo
also give the validity score during custom gene set extractprojection()
new feature in 1.15.12 for vstBlind
v1.1.22
version bump
bug fix: scan_sequences() now works for motifs with pseudocount of 0
fixed tests from last commit
updated news
renamed tests, added some
document() changed some documentation
added spell check test
v1.11.8 minor vignette update
v1.11.4 error message when using a character now fixed
testthat directory and eset slot in opls class
v1.11.2 getEset method
1.15.11 : add sum as aggregation function
v1.15.8 BiocCheck OK
v1.15.8; opls-eset: scores, loadings, VIP, etc. in pData and fData from getEset; parPaletteVc argument in plot-opls
oops, forgot closing curly bracket
Remove knet_win32_init()/knet_win32_destroy() calls on Windows
Disable applyPileups() examples and a few more of its tests
new version 1.15.10 to fix a bug in agregation stats
version 1.15.9, fix bug in agregationStats
minor change: fixed spelling mistakes + added lang field to desc
fixed merge conflict.
changed the function of filterLowCountGenes.
version bump
fixed windows build issues
Merge branch 'master' of github.com:FertigLab/CoGAPS
missing documentation
fix downloads link
add link to travis in status button
fix embedded travis status
embed travis status in readme
bump version
fix comment
fix up merge errors; remove incomplete hdf5 code
merge
version bump
add test to check that 'none' gets converted to NULL when passed for distributed
properly set distributed to NULL in initialize method
extra paranthesis
don't check file extension if data is not a file path
allow 'none' for distributed method
version bump
ignore build files
allow for RDS files to be passed in
added check for params@distributed
added blank Hdf5Parser class
implemented policy based design for sparse/dense storage in the GibbsSampler
link against Rhdf5 library
replace names with patientID
TCGAsampleSelect works with vector of sample codes
Merge remote-tracking branch 'origin/dev'
add package argument to data calls
version bump
update table of data type descriptions
Update README.md
Update README.md
minor change: increased character param security + bug fix: method documentation for motif_tree()
version 1.23.3-2
Consistent naming of RDS output files.
Use tempdir() to avoid polluting the working dir.
Response to Issue #3: Prioritze rowData over empty Granges objects
Merge branch 'master' of git.bioconductor.org:packages/LoomExperiment
Added cbind to LoomGraphs documentation
Reorganized text in sections and comments. Mentioned how to get per-gene corrected values.
Bumped version number, date.
Made heatmap of log-fold changes for the brain data.
Forgot to add references.
Added paragraph about experimental strategies.
Reorganized text, elaborated on the doublet score interpretation.
Support for qnamePrefixEnd and qnameSuffixStart params in interest().
new feature: motif_peaks()
motif_peaks() work nearing final state, ready to merge
cleaned up code
cpp code for linbin and peakfinder functions
Merge branch 'master' into experimental
motif_peaks() R code all done
documentation first draft
now exporting motif_peaks
Merge branch 'master' into experimental
motif_peaks() has matured a bit
initial motif_peaks() function created
initial motif_peaks() function created
basic implementation for finding significant motif peaks in sequence data
added create_cluster()
basic cluster framework set up
init experimental branch
update .Rbuildignore
added RNAdynamics vignette
More ENUM fixes
Merge branch 'master' of github.com:grimbough/rhdf5
Fix bug introduced in read ENUM/factor
Skip test creating large vectors on Travis
(port) configure file to add -lrt linking
version bump and configure script - closes #93 closes #94
add configure.ac, src/Makevars.in to check librt for shm_open and link to it if needed
added new features, more tests and documentation (#70) * added new features, more tests and documentation * fixed space * made docs more clear and spaces
docfixes and fix to kozaksequenceScore (#69)
small securityfix for windowPerGroup (#68) * small securityfix for windowPerGroup * small fix for merge
remove one migration leftover
fix invalid VCF files
Migrate to Rhtslib (htslib 1.7) and to Rsamtools 1.99.0
minor tweak to src/Makevars[.win] files
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