bed2GR | Read genomic ranges from bed files (zero based coordinates) |
countBamInGRanges | Count reads from a bam file in genomic ranges |
coverageBamInGRanges | Coverage profile from a bam file across genomic ranges |
extract | Helper function to extract text using regular expressions |
get.count.matrix | Get a count matrix from bam files that match a certain... |
get.htseq.count.matrix | Get a count matrix from htseq-count files that match a... |
get.rpkm | Normalize to reads per kilobase per million sequences |
gff2GR | Read gene annotations in gff format |
GR2gff | Export GRanges to gff format |
GR2gtf | Export GRanges to gtf format |
gtf2GR | Read gene annotations in gtf format |
macs2GRange | Transform a MACS output peakfile into a GRanges object |
makeGffAttributes | Helper function to generate the gff attributes field |
makeGtfAttributes | Helper function to generate the gtf attributes field |
merge.peaks | Merge MACS peaks calls from files in a directory |
plot.spp.qc | Plot SPP quality metrics |
seqQTL | Package for preprocessing sequencing based traits for QTL... |
spp.qc.summary | Summary of SPP quality metrics from files in a directory |
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