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

bowtie2bowtie2
build.star.idxSTAR
bwabwa
cufflinkscufflinks
cutadaptcutadapt
eset2SEeset2SE
fastQCfastQC
gatk.baserecalibratorgatk.baserecalibrator
gatk.combinevariantsgatk.combinevariants
gatk.depthOFcoveragegatk.depthOFcoverage
gatk.haplotypecallergatk.haplotypecaller
gatk.mutect2.normalgatk.mutect2.normal
gatk.printreadsgatk.printreads
gatk.realigngatk.realign
gatk.targetcreatorgatk.targetcreator
gatk.variantfiltergatk.variantfilter
generate.GCgenerate.GC
get.annovar.reportget.annovar.report
get.collectmetrics.reportget.collectmetrics.report
get.fnsget.fns
get.process.namesget.process.names
get.proc.reportget.proc.report
get.qc.reportget.qc.report
get.Robject.reportget.Robject.report
get.single_end.metrics.reportget.single.end.metrics.report
get.tophat.reportget.tophat.report
get.trim_cut.reportget.trim_cut.report
get.trim.gal.reportget.trim.gal.report
gff2grgff2gr
gtf2grgtf2gr
htseq.add.infohtseq.add.info
htseq_counthtseq_count
make.csetmake.cset
make.esetmake.eset
make.vsetmake.vset
multiple.reads.pileupmultiple.reads.pileup
MuSE.callMuSE.call
MuSE.sumpMuSE.sump
Muse.tabix2.vcfVCFtabix
mutect2mutect2
mut.type.somaticmut.type.somatic
picard.addrgpicard.addrg
picard.collectmetricspicard.collectmetrics
picard.reorderpicard.reorder
picard.rmdupicard.rmdu
pileup2seqzgenerate.seqz
ploidyNcellularityploidyNcellularity
print_messageprint_message
processSomaticprocessSomatic
qc_aggregateqc_aggregate
read.pileup.gzread.pileup.gz
refGene2grrefGene2gr
reportreport
SEQprocessSEQprocess
seqz2rdaseqz2rda
seqz2segseqz2seg
somaticsnipersomaticsniper
STARSTAR
table.annovartable.annovar
tophat2tophat2
trim.galtrim.gal
varscanvarscan
vcf2annovarvcf2annovar
vcf2gzvcf2gz
vepVairant Effect Predictor (VEP)
vset.preprocessvset.preprocess
omicsCore/SEQprocess documentation built on May 9, 2019, 8:09 p.m.