Man pages for matthiasheinig/seqQTL
Package for preprocessing sequencing based traits for QTL analysis

bed2GRRead genomic ranges from bed files (zero based coordinates)
countBamInGRangesCount reads from a bam file in genomic ranges
coverageBamInGRangesCoverage profile from a bam file across genomic ranges
extractHelper function to extract text using regular expressions
get.count.matrixGet a count matrix from bam files that match a certain...
get.htseq.count.matrixGet a count matrix from htseq-count files that match a...
get.rpkmNormalize to reads per kilobase per million sequences
gff2GRRead gene annotations in gff format
GR2gffExport GRanges to gff format
GR2gtfExport GRanges to gtf format
gtf2GRRead gene annotations in gtf format
macs2GRangeTransform a MACS output peakfile into a GRanges object
makeGffAttributesHelper function to generate the gff attributes field
makeGtfAttributesHelper function to generate the gtf attributes field
merge.peaksMerge MACS peaks calls from files in a directory
plot.spp.qcPlot SPP quality metrics
seqQTLPackage for preprocessing sequencing based traits for QTL...
spp.qc.summarySummary of SPP quality metrics from files in a directory
matthiasheinig/seqQTL documentation built on May 21, 2017, 11:03 p.m.