Man pages for dvera/rage
R-based Analysis of GEnomic data

bam.2.bedConvert bam files to bed files.
bam.2.samConvert bam files to sam files
bam.catConcatenate bam files
bam.countCount reads in bam files
bam.indexIndex bam files
bam.mergeMerge sorted bam files
bam.multicovCalculate coverage of multiple bams files over intervals in a...
bam.parselengthsParse reads in bam files by insert size.
bam.sortSort bams by position or name
bb.2.bedConvert bigBed files to bed files
bed.2.bbConvert bed files to bigBed files
bed.2.bgConvert bed files to bedGraph files
bed.coverageCalculate coverage of a set of bed files over intervals in a...
bed.genomecovCalculate coverage of a set of bed files at each base of the...
bed.histPlot a histogram of interval sizes in bed files
bed.mergeMerge overlapping interavls within an individual bed file.
bed.parselengthsParse intervals in bed files by size.
bed.sizesRetreive interval sizes in bed files
bed.sortSort beds by chromosome and position
bg.2.bwConvert bedGraph files to bigWig files
bg.histPlot a histogram of scores sizes in bedGraph files
bg.mapPerform calculations on bedGraph scores over the inverals in...
bg.scoresRetreive scores in bedGraph files
macs2Perform peak-calling with MACS2
mat.makeCreate a matrix of data aligned at a set of features.
sam.2.bamConvert sam files to bam files
sam.statsGet summary statistics for bam files
dvera/rage documentation built on May 13, 2017, 9:50 a.m.