Files in tgirke/systemPipeR
systemPipeR: NGS workflow and report generation environment

.Rbuildignore
.github/workflows/R-CMD-build_check.yml
DESCRIPTION
NAMESPACE
NEWS
R/AllClasses.R R/AllGenerics.R R/chipseq.R R/cmdToCWL.R R/developerFct.R R/extension_methods.R R/fastqQuality.R R/geneSetAnalysis.R R/linewise_methods.R R/linewise_utilities.R R/module.R R/overLapper.R R/plotwf.R R/riboseq.R R/sal2bash.R R/sal2rmd.R R/sysargs2_methods.R R/sysargs2_utilities.R R/sysargs_methods.R R/sysargslist_methods.R R/sysargslist_utilities.R R/utilities.R R/varseq.R
README
README.md
inst/CITATION
inst/extdata/.batchtools.conf.R
inst/extdata/.batchtools.conf.R.sge
inst/extdata/.batchtools.conf.R.torque
inst/extdata/Makefile
inst/extdata/SPR_software.csv
inst/extdata/SPRtest.Rmd
inst/extdata/alignStats.xls
inst/extdata/annotate_peaks.param
inst/extdata/annotate_vars.param
inst/extdata/batchtools.sge.tmpl
inst/extdata/batchtools.slurm.tmpl
inst/extdata/batchtools.torque.tmpl
inst/extdata/bowtiePE.param
inst/extdata/bowtieSE.param
inst/extdata/bwa.param
inst/extdata/countDFeByg.xls
inst/extdata/count_rangesets.param
inst/extdata/custom_Fct.R
inst/extdata/cwl/BUSCO/BUSCO.cwl
inst/extdata/cwl/BUSCO/BUSCO.yml
inst/extdata/cwl/BUSCO/runME
inst/extdata/cwl/BUSCO/workflow_BUSCO.cwl
inst/extdata/cwl/MACS2/MACS2-input/macs2-input.cwl
inst/extdata/cwl/MACS2/MACS2-input/macs2.yml
inst/extdata/cwl/MACS2/MACS2-noinput/macs2.cwl
inst/extdata/cwl/MACS2/MACS2-noinput/macs2.yml
inst/extdata/cwl/MACS2/macs2-input.cwl
inst/extdata/cwl/MACS2/macs2-input.yml
inst/extdata/cwl/MACS2/macs2-noinput.cwl
inst/extdata/cwl/MACS2/macs2-noinput.yml
inst/extdata/cwl/MACS2/workflow_macs2-input.cwl
inst/extdata/cwl/MACS2/workflow_macs2-noinput.cwl
inst/extdata/cwl/annotate_peaks/annotate_peaks.cwl
inst/extdata/cwl/annotate_peaks/annotate_peaks.yml
inst/extdata/cwl/annotate_peaks/workflow_annotate_peaks.cwl
inst/extdata/cwl/blast/blastp.cwl
inst/extdata/cwl/blast/blastp.yml
inst/extdata/cwl/blast/blastp/blastp.cwl
inst/extdata/cwl/blast/blastp/blastp.yml
inst/extdata/cwl/blast/makeblastdb.cwl
inst/extdata/cwl/blast/makeblastdb.yml
inst/extdata/cwl/blast/workflow_blastp.cwl
inst/extdata/cwl/blast/workflow_makeblastdb.cwl
inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl
inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml
inst/extdata/cwl/bowtie2/bowtie2-index.cwl
inst/extdata/cwl/bowtie2/bowtie2-index.yml
inst/extdata/cwl/bowtie2/bowtie2-mapping-mi.cwl
inst/extdata/cwl/bowtie2/bowtie2-mapping-mi.yml
inst/extdata/cwl/bowtie2/bowtie2-mapping-pe.cwl
inst/extdata/cwl/bowtie2/bowtie2-mapping-pe.yml
inst/extdata/cwl/bowtie2/bowtie2-mapping-se.cwl
inst/extdata/cwl/bowtie2/bowtie2-mapping-se.yml
inst/extdata/cwl/bowtie2/bowtie2-mi/bowtie2-mapping-mi.cwl
inst/extdata/cwl/bowtie2/bowtie2-mi/bowtie2-mapping-mi.yml
inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl
inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml
inst/extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.cwl
inst/extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.yml
inst/extdata/cwl/bowtie2/workflow_bowtie2-index.cwl
inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-mi.cwl
inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-pe.cwl
inst/extdata/cwl/bowtie2/workflow_bowtie2-mapping-se.cwl
inst/extdata/cwl/bwa/bwa-aln.cwl
inst/extdata/cwl/bwa/bwa-aln.yml
inst/extdata/cwl/bwa/bwa-aln/bwa-aln.cwl
inst/extdata/cwl/bwa/bwa-aln/bwa-aln.yml
inst/extdata/cwl/bwa/bwa-idx/bwa-index.cwl
inst/extdata/cwl/bwa/bwa-idx/bwa-index.yml
inst/extdata/cwl/bwa/bwa-index.cwl
inst/extdata/cwl/bwa/bwa-index.yml
inst/extdata/cwl/bwa/bwa-mem-pe.cwl
inst/extdata/cwl/bwa/bwa-mem-pe.yml
inst/extdata/cwl/bwa/bwa-mem-pe/bwa-mem-pe.cwl
inst/extdata/cwl/bwa/bwa-mem-pe/bwa-mem-pe.yml
inst/extdata/cwl/bwa/bwa-mem-se.cwl
inst/extdata/cwl/bwa/bwa-mem-se.yml
inst/extdata/cwl/bwa/bwa-mem-se/bwa-mem-se.cwl
inst/extdata/cwl/bwa/bwa-mem-se/bwa-mem-se.yml
inst/extdata/cwl/bwa/bwa-pe.cwl
inst/extdata/cwl/bwa/bwa-pe.yml
inst/extdata/cwl/bwa/bwa-pe/bwa-pe.cwl
inst/extdata/cwl/bwa/bwa-pe/bwa-pe.yml
inst/extdata/cwl/bwa/bwa-samse.cwl
inst/extdata/cwl/bwa/bwa-samse.yml
inst/extdata/cwl/bwa/bwa-samse/bwa-samse.cwl
inst/extdata/cwl/bwa/bwa-samse/bwa-samse.yml
inst/extdata/cwl/bwa/bwa-se.cwl
inst/extdata/cwl/bwa/bwa-se.yml
inst/extdata/cwl/bwa/bwa-se/bwa-se.cwl
inst/extdata/cwl/bwa/bwa-se/bwa-se.yml
inst/extdata/cwl/bwa/workflow_bwa-aln.cwl
inst/extdata/cwl/bwa/workflow_bwa-index.cwl
inst/extdata/cwl/bwa/workflow_bwa-mem-pe.cwl
inst/extdata/cwl/bwa/workflow_bwa-mem-se.cwl
inst/extdata/cwl/bwa/workflow_bwa-pe.cwl
inst/extdata/cwl/bwa/workflow_bwa-samse.cwl
inst/extdata/cwl/bwa/workflow_bwa-se.cwl
inst/extdata/cwl/count_rangesets/count_rangesets.cwl
inst/extdata/cwl/count_rangesets/count_rangesets.yml
inst/extdata/cwl/count_rangesets/workflow_count_rangesets.cwl
inst/extdata/cwl/cutadapt/cutadapt.cwl
inst/extdata/cwl/cutadapt/cutadapt.yml
inst/extdata/cwl/cutadapt/workflow_cutadapt.cwl
inst/extdata/cwl/example/example.cwl
inst/extdata/cwl/example/example.yml
inst/extdata/cwl/example/example_single.yml
inst/extdata/cwl/example/targets_example.txt
inst/extdata/cwl/example/workflow_example.cwl
inst/extdata/cwl/fastq-dump/fastq-dump.cwl
inst/extdata/cwl/fastq-dump/fastq-dump.yml
inst/extdata/cwl/fastq-dump/workflow_fastq-dump.cwl
inst/extdata/cwl/fastqc/fastqc.cwl
inst/extdata/cwl/fastqc/fastqc.yml
inst/extdata/cwl/fastqc/workflow_fastqc.cwl
inst/extdata/cwl/fastx_toolkit/fastx_clipper.cwl
inst/extdata/cwl/fastx_toolkit/fastx_clipper.yml
inst/extdata/cwl/fastx_toolkit/workflow_fastx_clipper.cwl
inst/extdata/cwl/gatk/bwa-index.cwl
inst/extdata/cwl/gatk/bwa-pe.cwl
inst/extdata/cwl/gatk/fasta_dict.cwl
inst/extdata/cwl/gatk/fasta_faidx.cwl
inst/extdata/cwl/gatk/gatk.yaml
inst/extdata/cwl/gatk/gatk_fastq2ubam.cwl
inst/extdata/cwl/gatk/gatk_fixtag.cwl
inst/extdata/cwl/gatk/gatk_genomicsDBImport.cwl
inst/extdata/cwl/gatk/gatk_genomicsDBImport.sh
inst/extdata/cwl/gatk/gatk_genotypeGVCFs.cwl
inst/extdata/cwl/gatk/gatk_haplotypecaller.cwl
inst/extdata/cwl/gatk/gatk_markduplicates.cwl
inst/extdata/cwl/gatk/gatk_mergebams.cwl
inst/extdata/cwl/gatk/gatk_select_variant.cwl
inst/extdata/cwl/gatk/gatk_sort.cwl
inst/extdata/cwl/gatk/gatk_variantFiltration.cwl
inst/extdata/cwl/gatk/gatk_variantFiltration.sh
inst/extdata/cwl/gatk/workflow_bwa-index.cwl
inst/extdata/cwl/gatk/workflow_bwa-pe.cwl
inst/extdata/cwl/gatk/workflow_fasta_dict.cwl
inst/extdata/cwl/gatk/workflow_fasta_faidx.cwl
inst/extdata/cwl/gatk/workflow_gatk_fastq2ubam.cwl
inst/extdata/cwl/gatk/workflow_gatk_fixtag.cwl
inst/extdata/cwl/gatk/workflow_gatk_genomicsDBImport.cwl
inst/extdata/cwl/gatk/workflow_gatk_genotypeGVCFs.cwl
inst/extdata/cwl/gatk/workflow_gatk_haplotypecaller.cwl
inst/extdata/cwl/gatk/workflow_gatk_markduplicates.cwl
inst/extdata/cwl/gatk/workflow_gatk_mergebams.cwl
inst/extdata/cwl/gatk/workflow_gatk_select_variant.cwl
inst/extdata/cwl/gatk/workflow_gatk_sort.cwl
inst/extdata/cwl/gatk/workflow_gatk_variantFiltration.cwl
inst/extdata/cwl/gsnap/gsnap-idx/gsnap-index.cwl
inst/extdata/cwl/gsnap/gsnap-idx/gsnap-index.yml
inst/extdata/cwl/gsnap/gsnap-index.cwl
inst/extdata/cwl/gsnap/gsnap-index.yml
inst/extdata/cwl/gsnap/gsnap-mapping-pe.cwl
inst/extdata/cwl/gsnap/gsnap-mapping-pe.yml
inst/extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.cwl
inst/extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.yml
inst/extdata/cwl/gsnap/workflow_gsnap-index.cwl
inst/extdata/cwl/gsnap/workflow_gsnap-mapping-pe.cwl
inst/extdata/cwl/gunzip/gunzip.cwl
inst/extdata/cwl/gunzip/gunzip.yml
inst/extdata/cwl/gunzip/workflow_gunzip.cwl
inst/extdata/cwl/hisat2/hisat2-idx/hisat2-index.cwl
inst/extdata/cwl/hisat2/hisat2-idx/hisat2-index.yml
inst/extdata/cwl/hisat2/hisat2-index.cwl
inst/extdata/cwl/hisat2/hisat2-index.yml
inst/extdata/cwl/hisat2/hisat2-mapping-pe.cwl
inst/extdata/cwl/hisat2/hisat2-mapping-pe.yml
inst/extdata/cwl/hisat2/hisat2-mapping-se.cwl
inst/extdata/cwl/hisat2/hisat2-mapping-se.yml
inst/extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.cwl
inst/extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.yml
inst/extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.cwl
inst/extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.yml
inst/extdata/cwl/hisat2/workflow_hisat2-index.cwl
inst/extdata/cwl/hisat2/workflow_hisat2-mapping-pe.cwl
inst/extdata/cwl/hisat2/workflow_hisat2-mapping-se.cwl
inst/extdata/cwl/kallisto/kallisto-index.cwl
inst/extdata/cwl/kallisto/kallisto.cwl
inst/extdata/cwl/kallisto/kallisto.yml
inst/extdata/cwl/kallisto/runME
inst/extdata/cwl/kallisto/workflow_kallisto-index.cwl
inst/extdata/cwl/kallisto/workflow_kallisto.cwl
inst/extdata/cwl/mergeBamByFactor/merge-bam.cwl
inst/extdata/cwl/mergeBamByFactor/merge-bam.yml
inst/extdata/cwl/mergeBamByFactor/workflow_merge-bam.cwl
inst/extdata/cwl/picard/markduplicates/picard_markduplicates.cwl
inst/extdata/cwl/picard/markduplicates/picard_markduplicates.yml
inst/extdata/cwl/picard/picard_markduplicates.cwl
inst/extdata/cwl/picard/picard_markduplicates.yml
inst/extdata/cwl/picard/workflow_picard_markduplicates.cwl
inst/extdata/cwl/preprocessReads/trim-pe.cwl
inst/extdata/cwl/preprocessReads/trim-pe.yml
inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.cwl
inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.yml
inst/extdata/cwl/preprocessReads/trim-se.cwl
inst/extdata/cwl/preprocessReads/trim-se.yml
inst/extdata/cwl/preprocessReads/trim-se/trim-se.cwl
inst/extdata/cwl/preprocessReads/trim-se/trim-se.yml
inst/extdata/cwl/preprocessReads/workflow_trim-pe.cwl
inst/extdata/cwl/preprocessReads/workflow_trim-se.cwl
inst/extdata/cwl/rsubread/rsubread-idx/rsubread-index.cwl
inst/extdata/cwl/rsubread/rsubread-idx/rsubread-index.yml
inst/extdata/cwl/rsubread/rsubread-index.cwl
inst/extdata/cwl/rsubread/rsubread-index.yml
inst/extdata/cwl/rsubread/rsubread-mapping-se.cwl
inst/extdata/cwl/rsubread/rsubread-mapping-se.yml
inst/extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.cwl
inst/extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.yml
inst/extdata/cwl/rsubread/workflow_rsubread-index.cwl
inst/extdata/cwl/rsubread/workflow_rsubread-mapping-se.cwl
inst/extdata/cwl/rundiff/rundiff.cwl
inst/extdata/cwl/rundiff/rundiff.yml
inst/extdata/cwl/rundiff/workflow_rundiff.cwl
inst/extdata/cwl/samtools/samtools-index.cwl
inst/extdata/cwl/samtools/samtools-index.yml
inst/extdata/cwl/samtools/samtools-sort.cwl
inst/extdata/cwl/samtools/samtools-sort.yml
inst/extdata/cwl/samtools/samtools-view.cwl
inst/extdata/cwl/samtools/samtools-view.yml
inst/extdata/cwl/samtools/workflow_samtools-index.cwl
inst/extdata/cwl/samtools/workflow_samtools-sort.cwl
inst/extdata/cwl/samtools/workflow_samtools-view.cwl
inst/extdata/cwl/star/runMe
inst/extdata/cwl/star/runMe_star_picard.Rmd
inst/extdata/cwl/star/star-idx/star-index.cwl
inst/extdata/cwl/star/star-idx/star-index.yml
inst/extdata/cwl/star/star-index.cwl
inst/extdata/cwl/star/star-index.yml
inst/extdata/cwl/star/star-mapping-pe.cwl
inst/extdata/cwl/star/star-mapping-pe.yml
inst/extdata/cwl/star/star-mapping-se.cwl
inst/extdata/cwl/star/star-mapping-se.yml
inst/extdata/cwl/star/star-pe/star-mapping-pe.cwl
inst/extdata/cwl/star/star-pe/star-mapping-pe.yml
inst/extdata/cwl/star/star-se/star-mapping-se.cwl
inst/extdata/cwl/star/star-se/star-mapping-se.yml
inst/extdata/cwl/star/workflow_star-index.cwl
inst/extdata/cwl/star/workflow_star-mapping-pe.cwl
inst/extdata/cwl/star/workflow_star-mapping-se.cwl
inst/extdata/cwl/star/workflow_star-pe-sam_samtools.cwl
inst/extdata/cwl/test/test.cwl
inst/extdata/cwl/test/test.yml
inst/extdata/cwl/test/workflow_test.cwl
inst/extdata/cwl/tophat2/tophat2-mapping-pe.cwl
inst/extdata/cwl/tophat2/tophat2-mapping-pe.yml
inst/extdata/cwl/tophat2/tophat2-mapping-se.cwl
inst/extdata/cwl/tophat2/tophat2-mapping-se.yml
inst/extdata/cwl/tophat2/tophat2-pe/tophat2-mapping-pe.cwl
inst/extdata/cwl/tophat2/tophat2-pe/tophat2-mapping-pe.yml
inst/extdata/cwl/tophat2/tophat2-se/tophat2-mapping-se.cwl
inst/extdata/cwl/tophat2/tophat2-se/tophat2-mapping-se.yml
inst/extdata/cwl/tophat2/workflow_tophat2-mapping-pe.cwl
inst/extdata/cwl/tophat2/workflow_tophat2-mapping-se.cwl
inst/extdata/cwl/trim_galore/trim_galore-pe.cwl
inst/extdata/cwl/trim_galore/trim_galore-pe.yml
inst/extdata/cwl/trim_galore/trim_galore-pe/trim_galore-pe.cwl
inst/extdata/cwl/trim_galore/trim_galore-pe/trim_galore-pe.yml
inst/extdata/cwl/trim_galore/trim_galore-se.cwl
inst/extdata/cwl/trim_galore/trim_galore-se.yml
inst/extdata/cwl/trim_galore/trim_galore-se/trim_galore-se.cwl
inst/extdata/cwl/trim_galore/trim_galore-se/trim_galore-se.yml
inst/extdata/cwl/trim_galore/workflow_trim_galore-pe.cwl
inst/extdata/cwl/trim_galore/workflow_trim_galore-se.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-pe.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-pe.yml
inst/extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.yml
inst/extdata/cwl/trimmomatic/trimmomatic-se.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-se.yml
inst/extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.yml
inst/extdata/cwl/trimmomatic/workflow_trimmomatic-pe.cwl
inst/extdata/cwl/trimmomatic/workflow_trimmomatic-se.cwl
inst/extdata/cwl/varseq/annotate.cwl
inst/extdata/cwl/varseq/combine.cwl
inst/extdata/cwl/varseq/filter.cwl
inst/extdata/cwl/varseq/varseq.yml
inst/extdata/cwl/varseq/workflow_annotate.cwl
inst/extdata/cwl/varseq/workflow_combine.cwl
inst/extdata/cwl/varseq/workflow_filter.cwl
inst/extdata/cwl/workflow-bcftools/bcftools-call.cwl
inst/extdata/cwl/workflow-bcftools/bcftools.cwl
inst/extdata/cwl/workflow-bcftools/bcftools.yml
inst/extdata/cwl/workflow-bcftools/samtools-index.cwl
inst/extdata/cwl/workflow-bcftools/samtools-sort.cwl
inst/extdata/cwl/workflow-bcftools/samtools_markduplicates.cwl
inst/extdata/cwl/workflow-bcftools/workflow_bcftools.cwl
inst/extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.cwl
inst/extdata/cwl/workflow-bwa-aln/workflow_bwa-aln-se.yml
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.cwl
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-pe/workflow_hisat2-pe.yml
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.cwl
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.yml
inst/extdata/cwl/workflow-hisat2/workflow_hisat2-pe.cwl
inst/extdata/cwl/workflow-hisat2/workflow_hisat2-pe.yml
inst/extdata/cwl/workflow-hisat2/workflow_hisat2-se.cwl
inst/extdata/cwl/workflow-hisat2/workflow_hisat2-se.yml
inst/extdata/docopt.R/gsnap/gsnap.doc.R inst/extdata/docopt.R/gsnap/gsnap_idx.doc.R inst/extdata/docopt.R/rsubread/rsubread.doc.R inst/extdata/docopt.R/rsubread/rsubread_idx.doc.R inst/extdata/docopt.R/test/test.doc.R
inst/extdata/filter_gatk.param
inst/extdata/filter_sambcf.param
inst/extdata/filter_vartools.param
inst/extdata/gatk.param
inst/extdata/gatk_run.sh
inst/extdata/gsnap.param
inst/extdata/hisat2.param
inst/extdata/hisat2PE.param
inst/extdata/macs2.param
inst/extdata/macs2_noinput.param
inst/extdata/rpkmDFeByg.xls
inst/extdata/rsubread.param
inst/extdata/rundiff.param
inst/extdata/sambcf.param
inst/extdata/sambcf_run.sh
inst/extdata/spr_simple_lw.Rmd inst/extdata/spr_simple_wf.Rmd inst/extdata/systemPipeTEST.Rmd
inst/extdata/targets.txt
inst/extdata/targetsPE.txt
inst/extdata/targetsPE_chip.txt
inst/extdata/targets_chip.txt
inst/extdata/toolsCollection.Rmd
inst/extdata/tophat.param
inst/extdata/trim.param
inst/extdata/trimPE.param
inst/extdata/trim_galore.param
inst/extdata/trim_galore_run.sh
inst/extdata/vartools.param
inst/extdata/wf_demo.Rmd
inst/htmlwidgets/lib/plotwf/full.render.js
inst/htmlwidgets/lib/plotwf/plotwf.css
inst/htmlwidgets/lib/plotwf/viz.js
inst/htmlwidgets/plotwf.js
inst/htmlwidgets/plotwf.yaml
man/EnvModules-class.Rd man/GOHyperGAll.Rd man/INTERSECTset-class.Rd man/LineWise-class.Rd man/ParamFiles.Rd man/SPRdata.Rd man/SPRproject.Rd man/SYSargs-class.Rd man/SYSargs2-class.Rd man/SYSargsList-class.Rd man/VENNset-class.Rd man/add-methods.Rd man/alignStats.Rd man/catDB-class.Rd man/catmap.Rd man/check.output.Rd man/clusterRun.Rd man/config.param.Rd man/configWF.Rd man/countRangeset.Rd man/createParamFiles.Rd man/evalCode.Rd man/featureCoverage.Rd man/featuretypeCounts.Rd man/filterDEGs.Rd man/filterVars.Rd man/genFeatures.Rd man/importWF.Rd man/loadWorkflow.Rd man/mergeBamByFactor.Rd man/moduleload.Rd man/olBarplot.Rd man/olRanges.Rd man/output_update.Rd man/overLapper.Rd man/plotWF.Rd man/plotfeatureCoverage.Rd man/plotfeaturetypeCounts.Rd man/predORF.Rd man/preprocessReads.Rd man/readComp.Rd man/renderReport.Rd man/returnRPKM.Rd man/runCommandline.Rd man/runDiff.Rd man/runWF.Rd man/run_DESeq2.Rd man/run_edgeR.Rd man/scaleRanges.Rd man/seeFastq.Rd man/subsetWF.Rd man/symLink2bam.Rd man/sysargs.Rd man/systemArgs.Rd man/systemPipeR-package.Rd man/targets.as.df.Rd man/tryCMD.Rd man/tryPath.Rd man/variantReport.Rd man/vennPlot.Rd man/writeTargetsRef.Rd man/writeTargetsout.Rd tests/testthat.R tests/testthat/test-01-SYSargs.R tests/testthat/test-02-SYSargs2.R tests/testthat/test-03-SYSargsList.R tests/testthat/test-04-LineWise.R tests/testthat/test-05-catDB.R tests/testthat/test-06-VENNset.R tests/testthat/test-07-features.R tests/testthat/test-08-cmd2cwl.R tests/testthat/test-utilities.R
vignettes/GOslimbarplotMF.png
vignettes/SPR_CWL_hello.png
vignettes/SPR_steps.Rmd
vignettes/SYS_WF.png
vignettes/SYSargs2.png
vignettes/SYSdir.png
vignettes/SystemPipeR_Workflow.png
vignettes/bibtex.bib
vignettes/directory.png
vignettes/fastqReport.png
vignettes/heatmap1.png
vignettes/plotwf.Rmd
vignettes/sysargslist.png
vignettes/systemPipeR.Rmd vignettes/systemPipeR_CWL.Rmd vignettes/systemPipeR_classes.Rmd vignettes/systemPipeR_workflows.Rmd
vignettes/utilities.png
tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.