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
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
