Files in systemPipeR
systemPipeR: NGS workflow and report generation environment

NEWS
README
DESCRIPTION
README.md
NAMESPACE
inst/CITATION
inst/unitTests/SRR446028_1.fastq
inst/unitTests/SRR446030_1.fastq
inst/unitTests/tophat.param
inst/unitTests/targets.txt
inst/unitTests/SRR446027_1.fastq
inst/unitTests/SRR446029_1.fastq
inst/unitTests/test_classes.R
inst/doc/systemPipeR.html
inst/doc/systemPipeVARseq.R
inst/doc/systemPipeChIPseq.Rnw
inst/doc/systemPipeRIBOseq.Rnw
inst/doc/systemPipeChIPseq.R inst/doc/systemPipeRIBOseq.R inst/doc/systemPipeRNAseq.pdf inst/doc/systemPipeVARseq.pdf inst/doc/systemPipeR.Rmd inst/doc/systemPipeRNAseq.R
inst/doc/systemPipeRNAseq.Rnw
inst/doc/systemPipeChIPseq.pdf
inst/doc/systemPipeVARseq.Rnw
inst/doc/systemPipeRIBOseq.pdf inst/doc/systemPipeR.R
inst/extdata/annotate_vars.param
inst/extdata/filter_sambcf.param
inst/extdata/count_rangesets.param
inst/extdata/macs2.param
inst/extdata/custom_Fct.R
inst/extdata/alignStats.xls
inst/extdata/sambcf_run.sh
inst/extdata/sambcf.param
inst/extdata/Makefile
inst/extdata/filter_vartools.param
inst/extdata/targetsPE_chip.txt
inst/extdata/vartools.param
inst/extdata/trimPE.param
inst/extdata/annotate_peaks.param
inst/extdata/torque.tmpl
inst/extdata/filter_gatk.param
inst/extdata/tophat.param
inst/extdata/bwa.param
inst/extdata/rsubread.param
inst/extdata/rundiff.param
inst/extdata/targets.txt
inst/extdata/bowtiePE.param
inst/extdata/countDFeByg.xls
inst/extdata/bowtieSE.param
inst/extdata/rpkmDFeByg.xls
inst/extdata/gatk_run.sh
inst/extdata/gsnap.param
inst/extdata/gatk.param
inst/extdata/macs2_noinput.param
inst/extdata/.BatchJobs.R
inst/extdata/targets_chip.txt
inst/extdata/trim.param
inst/extdata/targetsPE.txt
inst/extdata/slides/logo.png
inst/extdata/slides/systemPipeRslides.R
inst/extdata/slides/bibtex.bib
inst/extdata/slides/systemPipeRslides.html
inst/extdata/slides/systemPipeRslides.Rmd
inst/extdata/slides/images/SystemPipeR_Workflow.png
inst/extdata/vignette_archive/systemPipeR.pdf
inst/extdata/vignette_archive/systemPipeR.Rnw
inst/extdata/vignette_archive/systemPipeR.R vignettes/fastqReport.pdf
vignettes/heatmap1.png
vignettes/SystemPipeR_Workflow.png
vignettes/featureCounts.pdf vignettes/heatmap1.pdf
vignettes/systemPipeChIPseq.Rnw
vignettes/sample_tree.pdf
vignettes/systemPipeRIBOseq.Rnw
vignettes/featureCounts2.pdf vignettes/vennplot.pdf vignettes/GOslimbarplotMF.pdf vignettes/featurePlot.pdf vignettes/seqlogo.pdf vignettes/systemPipeR.Rmd
vignettes/bibtex.bib
vignettes/GOslimbarplotMF.png
vignettes/systemPipeRNAseq.Rnw
vignettes/systemPipeVARseq.Rnw
vignettes/DEGcounts.pdf vignettes/vennplot_var.pdf
vignettes/fastqReport.png
R/overLapper.R R/geneSetAnalysis.R R/varseq.R R/developerFct.R R/utilities.R R/AllClasses.R R/fastqQuality.R R/chipseq.R R/riboseq.R man/plotfeatureCoverage.Rd man/INTERSECTset-class.Rd man/clusterRun.Rd man/predORF.Rd man/olBarplot.Rd man/countRangeset.Rd man/writeTargetsRef.Rd man/moduleload.Rd man/featureCoverage.Rd man/alignStats.Rd man/VENNset-class.Rd man/run_DESeq2.Rd man/overLapper.Rd man/returnRPKM.Rd man/seeFastq.Rd man/catDB-class.Rd man/qsubRun.Rd man/runCommandline.Rd man/symLink2bam.Rd man/plotfeaturetypeCounts.Rd man/SYSargs-class.Rd man/genFeatures.Rd man/systemArgs.Rd man/sysargs.Rd man/run_edgeR.Rd man/preprocessReads.Rd man/filterVars.Rd man/runDiff.Rd man/GOHyperGAll.Rd man/variantReport.Rd man/catmap.Rd man/featuretypeCounts.Rd man/writeTargetsout.Rd man/readComp.Rd man/filterDEGs.Rd man/scaleRanges.Rd man/getQsubargs.Rd man/vennPlot.Rd man/mergeBamByFactor.Rd
build/vignette.rds
tests/runTests.R
systemPipeR documentation built on May 2, 2018, 4:16 a.m.