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

DESCRIPTION
NAMESPACE
R/00_function.R R/01_fastQC.R R/02_trimming.R R/03_alignment.R R/04_removeDuplicates.R R/05_realignment.R R/06_variant.call.recalibration.R R/07_variant.call.GATK.R R/08_variant.call.VarScan2.R R/09_variant.call.MuSE.R R/10_variant.call.MuTect2.R R/11_variant.call.SomaticSniper.R R/12_variant.annotation.R R/13_RNA.quantification.R R/14_CNV.R R/15_makeSet.R R/16_picard.collectmultiplemetrics.R R/17_report.R R/SEQprocess.R README.md Reference_Manual.pdf data/WGS.GATK_ex.config.R data/config.R inst/Rscript/SEQprocess.R inst/Rscript/functions_help.R
inst/example/btidx.1.bt2
inst/example/btidx.2.bt2
inst/example/btidx.3.bt2
inst/example/btidx.4.bt2
inst/example/btidx.fa
inst/example/btidx.rev.1.bt2
inst/example/btidx.rev.2.bt2
inst/example/cosmic.vcf
inst/example/example.R
inst/example/hg38.fa
inst/example/humandb/hg38_cytoBand.txt
inst/example/humandb/hg38_exac03.txt
inst/example/humandb/hg38_kgXref.txt
inst/example/humandb/hg38_knownGene.txt
inst/example/indel.vcf
inst/example/indel.vcf.idx
inst/example/mir.gff
inst/example/rawdata/test1/test1.1.fastq
inst/example/rawdata/test1/test1.2.fastq
inst/example/rawdata/test2/test2.1.fastq
inst/example/rawdata/test2/test2.2.fastq
inst/example/ref.gtf
inst/example/reference.dict
inst/example/reference.fa
inst/example/reference.fa.amb
inst/example/reference.fa.ann
inst/example/reference.fa.bwt
inst/example/reference.fa.fai
inst/example/reference.fa.pac
inst/example/reference.fa.sa
inst/example/reference.nhr
inst/example/reference.nin
inst/example/reference.nsq
inst/example/snp.vcf
inst/example/snp.vcf.idx
inst/extdata/report.rmd/SEQprocess_Report.Rmd inst/extdata/report.rmd/report_Robject.Rmd inst/extdata/report.rmd/report_align.Rmd inst/extdata/report.rmd/report_annovar.Rmd inst/extdata/report.rmd/report_cset.Rmd inst/extdata/report.rmd/report_eset.Rmd inst/extdata/report.rmd/report_qc.Rmd inst/extdata/report.rmd/report_realign.Rmd inst/extdata/report.rmd/report_rmdu.Rmd inst/extdata/report.rmd/report_trim.Rmd inst/extdata/report.rmd/report_trim.align.rmdu.Rmd inst/extdata/report.rmd/report_vset.Rmd man/MuSE.call.Rd man/MuSE.sump.Rd man/Muse.tabix2.vcf.Rd man/SEQprocess.Rd man/STAR.Rd man/bowtie2.Rd man/build.star.idx.Rd man/bwa.Rd man/cufflinks.Rd man/cutadapt.Rd man/eset2SE.Rd man/fastQC.Rd man/gatk.baserecalibrator.Rd man/gatk.combinevariants.Rd man/gatk.depthOFcoverage.Rd man/gatk.haplotypecaller.Rd man/gatk.mutect2.normal.Rd man/gatk.printreads.Rd man/gatk.realign.Rd man/gatk.targetcreator.Rd man/gatk.variantfilter.Rd man/generate.GC.Rd man/get.Robject.report.Rd man/get.annovar.report.Rd man/get.collectmetrics.report.Rd man/get.fns.Rd man/get.proc.report.Rd man/get.process.names.Rd man/get.qc.report.Rd man/get.single_end.metrics.report.Rd man/get.tophat.report.Rd man/get.trim.gal.report.Rd man/get.trim_cut.report.Rd man/gff2gr.Rd man/gtf2gr.Rd man/htseq.add.info.Rd man/htseq_count.Rd man/make.cset.Rd man/make.eset.Rd man/make.vset.Rd man/multiple.reads.pileup.Rd man/mut.type.somatic.Rd man/mutect2.Rd man/picard.addrg.Rd man/picard.collectmetrics.Rd man/picard.reorder.Rd man/picard.rmdu.Rd man/pileup2seqz.Rd man/ploidyNcellularity.Rd man/print_message.Rd man/processSomatic.Rd man/qc_aggregate.Rd man/read.pileup.gz.Rd man/refGene2gr.Rd man/report.Rd man/seqz2rda.Rd man/seqz2seg.Rd man/somaticsniper.Rd man/table.annovar.Rd man/tophat2.Rd man/trim.gal.Rd man/varscan.Rd man/vcf2annovar.Rd man/vcf2gz.Rd man/vep.Rd man/vset.preprocess.Rd vignette/vignettes.Rmd vignette/vignettes.pdf
vignette/workflowfig.png
omicsCore/SEQprocess documentation built on May 9, 2019, 8:09 p.m.