Greenleaf lab master #2
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* bugfix remove sys.time for weird error in R 4.0 * bug fix new uwot save and loading features * deprecated * version number * handle error where spurious fragments seem to be 1 tile above max * update bugfixes * let quantCut in plotTrajectory be null * grepExclude in plotTrajectoryHeatmap * bugfix integrative analysis coaccessibility and peak2genelinks * change file locking location groupcoverages * throw error if no peakset for adding annotations * make it so predictionScore is not needed for peak2gene links * update addPeakSet * updated description * bugfix named list * update error handling plotEnrichHeatmap * update error messages tilematrix * handle error with bsgenomes * width is end - start + 1 * bugfix checkCairo in iterativeLSI * update archr verbosity and logging for markerfeatures * bugfix + documentation * update subsetting to metadata * handling case n = 1 for deviations matrix * bugfix ordering of scTrack * handle error where no barcodes passing on a small chromosome/scaffold * bugfix validBSgenome * fix missing paren * fix missing paren * add feature for supplying custom gene list for rna integration * add sanity check to partial matrix * update cellsInArrow in case user overrides sample in ArchRProj * Add null option for genesUse to validInput * bugfix NA in combined vars * add checks for genes symbol to be not a list Co-authored-by: Ryan Corces <ryancorces@gmail.com>
…its from subsetted cells because it will keep stability
Remove issue reports for feature requests and documentation. These have been moved to discussions
offsetPlus and offsetMinus only apply when input is a bam file.
…into release_1.0.2
…print checks if the error actually occurs.
Fixes backwards compatibility problem with .loadUWOT
check for existence of each file individually rather than the download directory. Add new .downloadFiles() function to handle file download and checking to see if files downloaded properly.
…load Dev better download
the variable `error` doesnt exist / hasnt been declared anywhere. pretty sure this should be `throwError = FALSE`
if the GRangesList given to features in plotBrowserTrack does not have names, then the call to data.frame errors out. This fix ensures that namex isnt null or blank.
more robust checking of if files exist and have been properly downloaded GreenleafLab#1478
Update auto-comment.yml
…reenleafLab-master
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