# Calculate strandness information of a bam file

## Documentation for package ‘strandCheckR’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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