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

.Rbuildignore

.gitignore

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

SEQprocess.Rproj

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

vignette/workflowfig.png

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.

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

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

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

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

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

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