API for dvera/rage
R-based Analysis of GEnomic data

Global functions
bam.2.bed Man page Source code
bam.2.sam Man page Source code
bam.cat Man page Source code
bam.count Man page Source code
bam.index Man page Source code
bam.merge Man page Source code
bam.multicov Man page Source code
bam.parselengths Man page Source code
bam.rmdup Source code
bam.sort Man page Source code
bb.2.bed Man page Source code
bcftools.call Source code
bcftools.filter Source code
bcftools.merge Source code
bcftools.query Source code
bcftools.view.incomplete Source code
bcl2fastq Source code
bed.2.bb Man page Source code
bed.2.bg Man page Source code
bed.avglengths Source code
bed.breadth Source code
bed.cat Source code
bed.centers Source code
bed.clip Source code
bed.closest Source code
bed.closest2 Source code
bed.coverage Man page Source code
bed.dist Source code
bed.ends Source code
bed.genomecov Man page Source code
bed.hist Man page Source code
bed.intersect Source code
bed.liftover Source code
bed.makewindows Source code
bed.merge Man page Source code
bed.overhangs Source code
bed.overlap Source code
bed.parselengths Man page Source code
bed.parsestrands Source code
bed.recenter Source code
bed.recenter2 Source code
bed.removechrom Source code
bed.sample Source code
bed.shuffle Source code
bed.sizes Man page Source code
bed.slop Source code
bed.sort Man page Source code
bed.spacing Source code
bed.structures Source code
bed.subtract Source code
bed.summary Source code
bed.wigaverages Source code
bed.words Source code
bg.2.bed Source code
bg.2.bw Man page Source code
bg.2.wig Source code
bg.acf Source code
bg.conform Source code
bg.cor.plot Source code
bg.cors Source code
bg.diff Source code
bg.discardOverlaps Source code
bg.dist Source code
bg.hist Man page Source code
bg.iqr Source code
bg.ks Source code
bg.loess Source code
bg.map Man page Source code
bg.normalize.iqr Source code
bg.ops Source code
bg.plot Source code
bg.plotchroms Source code
bg.ppois Source code
bg.qnorm Source code
bg.qnorm2 Source code
bg.quantiles Source code
bg.scores Man page Source code
bg.selectscores Source code
bg.sort Source code
bg.threshold Source code
bg.transform Source code
bg.unify Source code
bg.uniondiff Source code
bg.ztest Source code
bgzip Source code
bowtie Source code
bowtie2 Source code
bw.2.bg Source code
bw.2.wig Source code
bwa.aln Source code
bwa.index Source code
bwa.sampe Source code
bwa.samse Source code
cfbg.make Source code
counts2matrix Source code
cranex Source code
cuffdiff Source code
cuffdiff.2.clusters Source code
cuffdiff.2.matrix Source code
cuffdiff2kegg Source code
cuffdiff2list Source code
cufflinks Source code
cufflinks.2.counts Source code
cutadapt.paired Source code
deg.2.heatmap Source code
deindex Source code
dge.heatmap Source code
dge.log2 Source code
dz.2.wig Source code
edger Source code
fastq.bwasw Source code
fastq.clip Source code
fastq.clip.fastx Source code
fastq.clip.paired Source code
fastq.consensus Source code
fastq.correct Source code
fastq.count Source code
fastq.fastqc Source code
fastq.filter Source code
fastq.forcemerge Source code
fastq.merge Source code
fastq.qc Source code
fastqp.plots Source code
fastx.qualitytrimmer Source code
fastx.trimmer Source code
filelines Source code
files Source code
files2 Source code
findfiles Source code
get.prefix Source code
get.suffix Source code
getfullpaths Source code
gff.2.bed Source code
gff.2.bed2 Source code
gff.2.bg Source code
gtf.2.fa Source code
gunzip Source code
hisat Source code
hub.add Source code
hub.bam Source code
hub.bed Source code
hub.modify Source code
hub.vcf Source code
hub.wig Source code
kallisto.quant Source code
lsl Source code
lslS Source code
lslSr Source code
lslt Source code
lsltr Source code
macs2 Man page Source code
mat.cor Source code
mat.heatmap Source code
mat.hist Source code
mat.iqr Source code
mat.loess Source code
mat.make Man page Source code
mat.normalize.iqr Source code
mat.ops Source code
mat.plotaverages Source code
mat.plotaverages2 Source code
mat.plotmats Source code
mat.plotrows Source code
mat.qnorm Source code
mat.strandtosense Source code
mat.tilegrid Source code
mat.window Source code
mat2bg Source code
np.2.bed Source code
rage.hist Source code
rage.run Source code
randomStrings Source code
read.bgs Source code
read.fmat Source code
read.mat Source code
read.tsv Source code
remove.prefix Source code
remove.suffix Source code
removeext Source code
removeheader Source code
renamefiles Source code
renamefiles2 Source code
rere Source code
rerere Source code
resizeWindow Source code
rot Source code
rotcol Source code
rotlist Source code
rotrow Source code
rotvec Source code
sam.2.bam Man page Source code
sam.stats Man page Source code
samplesheet.2.deindexsheet Source code
samtools.mpileup Source code
samtools.view Source code
scats Source code
scatterdens Source code
seqtk.seq Source code
seqtk.trimfq Source code
shead Source code
sless Source code
sra.2.fastq Source code
stail Source code
stringtie Source code
tabix Source code
tophat Source code
tophat.2.matrix Source code
uniquefilename Source code
vcf.2.bed Source code
vcf.2.bg Source code
vcf.2.fasta Source code
wig.2.bw Source code
write.mat Source code
write.tsv Source code
dvera/rage documentation built on May 13, 2017, 9:50 a.m.