strandCheckR-package | Quantify and Filter putative double strand DNA from strand-specific RNA bam file |
checkPairedEnd | Test whether a bam file is single-end or paired-end |
filterDNA | Filter reads comming from double strand sequences from a bam File |
getStrandFromBamFile | Get the strand information of all windows from bam files |
getStrandFromReadInfo | Get the strand information of all windows from read information |
getWinOverlapEachIRange | Get the ranges of sliding windows that overlap each range of an IRanges object. |
getWinOverlapEachReadFragment | Get the window ranges that overlap each read fragment |
getWinOverlapGRanges | Get the sliding windows that overlap a GRanges object |
intersectWithFeature | Intersect the windows data frame with an annotation data frame |
plotHist | Plot the histogram of positive proportions |
plotWin | Plot the number of reads vs the proportion of '+' stranded reads. |
strandCheckR | Quantify and Filter putative double strand DNA from strand-specific RNA bam file |