omicsCore/SEQprocess
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

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Vignettes
Functions
153
Source code
24
Man pages
66
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omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.
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API

API for omicsCore/SEQprocess
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Global functions
MuSE.call Man page Source code
MuSE.sump Man page Source code
Muse.tabix2.vcf Man page
SEQprocess Man page Source code
STAR Man page Source code
bowtie2 Man page Source code
build.star.idx Man page Source code
bwa Man page Source code
cufflinks Man page Source code
cutadapt Man page Source code
eset2SE Man page Source code
fastQC Man page Source code
gatk.applyBQSR Source code
gatk.baserecalibrator Man page Source code
gatk.baserecalibrator.o Source code Source code Source code
gatk.combinevariants Man page Source code
gatk.depthOFcoverage Man page Source code
gatk.haplotypecaller Man page Source code
gatk.mutect2.normal Man page Source code
gatk.printreads Man page
gatk.printreads.o Source code Source code Source code
gatk.realign Man page Source code
gatk.targetcreator Man page Source code
gatk.variantfilter Man page Source code
generate.GC Man page Source code
get.Robject.report Man page Source code
get.annovar.report Man page Source code
get.collectmetrics.report Man page Source code
get.fns Man page Source code
get.proc.report Man page Source code
get.process.names Man page Source code
get.qc.report Man page Source code
get.single_end.metrics.report Man page Source code
get.tophat.report Man page Source code
get.trim.gal.report Man page Source code
get.trim_cut.report Man page Source code
gff2gr Man page Source code
gtf2gr Man page Source code
htseq.add.info Man page Source code
htseq_count Man page Source code
make.cset Man page Source code
make.eset Man page Source code
make.vset Man page Source code
multiple.reads.pileup Man page Source code
mut.type.somatic Man page Source code
mutect2 Man page Source code
picard.addrg Man page Source code
picard.collectmetrics Man page Source code
picard.reorder Man page Source code
picard.rmdu Man page Source code
pileup2seqz Man page Source code
ploidyNcellularity Man page Source code
print_message Man page Source code
processSomatic Man page Source code
qc_aggregate Man page
read.pileup.gz Man page Source code
refGene2gr Man page Source code
report Man page Source code
run.annotation Source code
run.bowtie2 Source code
run.bwa Source code
run.cnv Source code
run.gatk Source code
run.make.vset Source code
run.muse Source code
run.mutect2 Source code
run.realign Source code
run.rseq.abundance Source code
run.somaticsniper Source code
run.star Source code
run.tophat2 Source code
run.trim Source code
run.varscan Source code
seqz2rda Man page Source code
seqz2seg Man page Source code
somaticsniper Man page Source code
tabix.vcf Man page Source code
table.annovar Man page Source code
tophat2 Man page Source code
trim.gal Man page Source code
varscan Man page Source code
vcf2annovar Man page Source code
vcf2gz Man page Source code
vep Man page Source code
vset.preprocess Man page Source code
omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.

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