Man pages for UofABioinformaticsHub/rnaCleanR
Calculate strandness information of a bam file
| checkPairedEnd | Test whether a bam file is single-end or paired-end |
| dot-calculateStrandCoverage | Calculate the strand information based on coverage |
| dot-calculateStrandNbReads | Calculate the strand information based on the number of reads |
| dot-concatenateAlignments | Concatenate a list of Alignments into One |
| dot-getWinInSequence | Get window data frame with the correct sequence name and... |
| dot-keptProbaWin | Get the probability of being kept for each window |
| dot-keptReadFragment | Calculate the read fragments to be kept |
| dot-sequenceInfoInPartition | Calculate the first/last base/read of each sequence within... |
| dot-summarizeHist | Summarize the histogram of strand proportions from the input... |
| filterDNA | Filter reads comming from double strand sequences from a bam... |
| getStrandFromBamFile | Get the strand information of all windows from bam files |
| getStrandFromReadInfo | Get the strand information of all windows from read... |
| getWinOverlapEachIRange | Get the ranges of sliding windows that overlap each range of... |
| 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... |
| plotHist | Plot the histogram of positive proportions |
| plotWin | Plot the number of reads vs the proportion of '+' stranded... |
| strandCheckR-package | Quantify and Filter putative double strand DNA from... |
