Man pages for RamsinghLab/ATACseeker
Utilities for ATACseq QC, differential accessibility, and integration

addMtGeneLabelSet gene names for bp ranges. Original code by Stephen Turner...
atacPairedEndpull in (filter and assemble as an object) some or all of the...
ATACseeker-packageA short title line describing what the package does
callMTcall mitochondrial variants from the results of...
collectStatscollect various cross-correlation and window size stats for...
fragmentLengthsget fragment sizes for a GAlignmentPairs object (can be slow)
fragPlotPlot fragment size density for a set of samples.
get5primeCutsget the 5' cut sites from a GAlignmentPairs (usually of an...
getComplexitycomplexity estimates from a GAlignmentPairs object, formatted...
getEndsconvert a galp into a gr of 5' cuts
getEstsComplexity estimation for ATACseq libraries.
getFeatureCountsutility fn for getComplexity and preseqR
getMTgrab the mitochondrial reads from a BAM and estimate their...
getQCobtain QC information used by csaw from paired-end BAM files
plotComplexityplot results from preseq (complexity estimation around...
plotCoverageutility fn from Patrick Abouyoun's 2010 seminar
plotMTplot mitochondrial variant calls in the context of...
plotStrandedconvenience function
processUcscCytobandutility function to pull in UCSC cytoband / arm files this is...
shrinkPairsThis seems to work better than anything else for "shifting"...
tssQcPlotwhat you would expect. not terribly novel; maybe use...
RamsinghLab/ATACseeker documentation built on April 15, 2018, 4:19 p.m.