Man pages for UofABioinformaticsHub/rnaCleanR
Calculate strandness information of a bam file

checkPairedEndTest whether a bam file is single-end or paired-end
dot-calculateStrandCoverageCalculate the strand information based on coverage
dot-calculateStrandNbReadsCalculate the strand information based on the number of reads
dot-concatenateAlignmentsConcatenate a list of Alignments into One
dot-getWinInSequenceGet window data frame with the correct sequence name and...
dot-keptProbaWinGet the probability of being kept for each window
dot-keptReadFragmentCalculate the read fragments to be kept
dot-sequenceInfoInPartitionCalculate the first/last base/read of each sequence within...
dot-summarizeHistSummarize the histogram of strand proportions from the input...
filterDNAFilter reads comming from double strand sequences from a bam...
getStrandFromBamFileGet the strand information of all windows from bam files
getStrandFromReadInfoGet the strand information of all windows from read...
getWinOverlapEachIRangeGet the ranges of sliding windows that overlap each range of...
getWinOverlapEachReadFragmentGet the window ranges that overlap each read fragment
getWinOverlapGRangesGet the sliding windows that overlap a GRanges object
intersectWithFeatureIntersect the windows data frame with an annotation data...
plotHistPlot the histogram of positive proportions
plotWinPlot the number of reads vs the proportion of '+' stranded...
strandCheckR-packageQuantify and Filter putative double strand DNA from...
UofABioinformaticsHub/rnaCleanR documentation built on Feb. 6, 2019, 5:59 a.m.