Files in systemPipeR
systemPipeR: NGS workflow and report generation environment
NEWS
README.md
NAMESPACE
README
DESCRIPTION
R/overLapper.R
R/SYSargsList.R
R/chipseq.R
R/utilities.R
R/AllClasses.R
R/module.R
R/fastqQuality.R
R/varseq.R
R/AllClasses2.R
R/developerFct.R
R/riboseq.R
R/geneSetAnalysis.R
inst/CITATION
inst/doc/systemPipeR_workflows.html
inst/doc/systemPipeR.Rmd
inst/doc/systemPipeR_workflows.Rmd
inst/doc/systemPipeR.R
inst/doc/systemPipeR.html
inst/doc/systemPipeR_workflows.R
inst/extdata/alignStats.xls
inst/extdata/filter_sambcf.param
inst/extdata/sambcf_run.sh
inst/extdata/countDFeByg.xls
inst/extdata/custom_Fct.R
inst/extdata/vartools.param
inst/extdata/filter_gatk.param
inst/extdata/sambcf.param
inst/extdata/rpkmDFeByg.xls
inst/extdata/batchtools.sge.tmpl
inst/extdata/targetsPE.txt
inst/extdata/bwa.param
inst/extdata/batchtools.slurm.tmpl
inst/extdata/macs2.param
inst/extdata/filter_vartools.param
inst/extdata/SYS_software.csv
inst/extdata/trim_galore.param
inst/extdata/rsubread.param
inst/extdata/macs2_noinput.param
inst/extdata/trim.param
inst/extdata/count_rangesets.param
inst/extdata/batchtools.torque.tmpl
inst/extdata/rundiff.param
inst/extdata/.batchtools.conf.R
inst/extdata/targets.txt
inst/extdata/targets_chip.txt
inst/extdata/tophat.param
inst/extdata/gatk_run.sh
inst/extdata/trim_galore_run.sh
inst/extdata/bowtiePE.param
inst/extdata/annotate_vars.param
inst/extdata/gatk.param
inst/extdata/hisat2PE.param
inst/extdata/gsnap.param
inst/extdata/annotate_peaks.param
inst/extdata/hisat2.param
inst/extdata/targetsPE_chip.txt
inst/extdata/bowtieSE.param
inst/extdata/Makefile
inst/extdata/trimPE.param
inst/extdata/cwl/hisat2/hisat2-idx/hisat2-index.cwl
inst/extdata/cwl/hisat2/hisat2-idx/hisat2-index.yml
inst/extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.yml
inst/extdata/cwl/hisat2/hisat2-pe/hisat2-mapping-pe.cwl
inst/extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.cwl
inst/extdata/cwl/hisat2/hisat2-se/hisat2-mapping-se.yml
inst/extdata/cwl/mergeBamByFactor/merge-bam.cwl
inst/extdata/cwl/mergeBamByFactor/merge-bam.yml
inst/extdata/cwl/preprocessReads/trim-se/trim-se.yml
inst/extdata/cwl/preprocessReads/trim-se/trim-se.cwl
inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.cwl
inst/extdata/cwl/preprocessReads/trim-pe/trim-pe.yml
inst/extdata/cwl/count_rangesets/count_rangesets.yml
inst/extdata/cwl/count_rangesets/count_rangesets.cwl
inst/extdata/cwl/rsubread/rsubread-idx/rsubread-index.yml
inst/extdata/cwl/rsubread/rsubread-idx/rsubread-index.cwl
inst/extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.cwl
inst/extdata/cwl/rsubread/rsubread-se/rsubread-mapping-se.yml
inst/extdata/cwl/gatk/gatk.yaml
inst/extdata/cwl/gatk/gatk_fixtag.cwl
inst/extdata/cwl/gatk/gatk_variantFiltration.cwl
inst/extdata/cwl/gatk/gatk_select_variant.cwl
inst/extdata/cwl/gatk/fasta_faidx.cwl
inst/extdata/cwl/gatk/gatk_fastq2ubam.cwl
inst/extdata/cwl/gatk/gatk_sort.cwl
inst/extdata/cwl/gatk/bwa-pe.cwl
inst/extdata/cwl/gatk/gatk_genomicsDBImport.sh
inst/extdata/cwl/gatk/gatk_mergebams.cwl
inst/extdata/cwl/gatk/gatk_genomicsDBImport.cwl
inst/extdata/cwl/gatk/gatk_variantFiltration.sh
inst/extdata/cwl/gatk/fasta_dict.cwl
inst/extdata/cwl/gatk/gatk_markduplicates.cwl
inst/extdata/cwl/gatk/bwa-index.cwl
inst/extdata/cwl/gatk/gatk_haplotypecaller.cwl
inst/extdata/cwl/gatk/gatk_genotypeGVCFs.cwl
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.yml
inst/extdata/cwl/tophat2/tophat2-se/tophat2-mapping-se.cwl
inst/extdata/cwl/varseq/annotate.cwl
inst/extdata/cwl/varseq/filter.cwl
inst/extdata/cwl/varseq/varseq.yml
inst/extdata/cwl/varseq/combine.cwl
inst/extdata/cwl/rundiff/rundiff.yml
inst/extdata/cwl/rundiff/rundiff.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.cwl
inst/extdata/cwl/trimmomatic/trimmomatic-se/trimmomatic-se.yml
inst/extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.yml
inst/extdata/cwl/trimmomatic/trimmomatic-pe/trimmomatic-pe.cwl
inst/extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.yml
inst/extdata/cwl/gsnap/gsnap-pe/gsnap-mapping-pe.cwl
inst/extdata/cwl/gsnap/gsnap-idx/gsnap-index.cwl
inst/extdata/cwl/gsnap/gsnap-idx/gsnap-index.yml
inst/extdata/cwl/MACS2/MACS2-noinput/macs2.yml
inst/extdata/cwl/MACS2/MACS2-noinput/macs2.cwl
inst/extdata/cwl/MACS2/MACS2-input/macs2-input.cwl
inst/extdata/cwl/MACS2/MACS2-input/macs2.yml
inst/extdata/cwl/bwa/bwa-se/bwa-se.yml
inst/extdata/cwl/bwa/bwa-se/bwa-se.cwl
inst/extdata/cwl/bwa/bwa-idx/bwa-index.yml
inst/extdata/cwl/bwa/bwa-idx/bwa-index.cwl
inst/extdata/cwl/bwa/bwa-pe/bwa-pe.cwl
inst/extdata/cwl/bwa/bwa-pe/bwa-pe.yml
inst/extdata/cwl/annotate_peaks/annotate-peaks.yml
inst/extdata/cwl/annotate_peaks/annotate-peaks.cwl
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.yml
inst/extdata/cwl/workflow-hisat2/workflow-hisat2-se/workflow_hisat2-se.cwl
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/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/trim_galore-se.yml
inst/extdata/cwl/trim_galore/trim_galore-se/trim_galore-se.cwl
inst/extdata/cwl/workflow-bcftools/samtools-sort.cwl
inst/extdata/cwl/workflow-bcftools/bcftools.cwl
inst/extdata/cwl/workflow-bcftools/samtools_markduplicates.cwl
inst/extdata/cwl/workflow-bcftools/bcftools-call.cwl
inst/extdata/cwl/workflow-bcftools/bcftools.yml
inst/extdata/cwl/workflow-bcftools/workflow_bcftools.cwl
inst/extdata/cwl/workflow-bcftools/samtools-index.cwl
inst/extdata/cwl/samtools/samtools-sort.cwl
inst/extdata/cwl/samtools/samtools-sort.yml
inst/extdata/cwl/samtools/samtools-view.yml
inst/extdata/cwl/samtools/samtools-view.cwl
inst/extdata/cwl/samtools/samtools-index.yml
inst/extdata/cwl/samtools/samtools-index.cwl
inst/extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.yml
inst/extdata/cwl/bowtie2/bowtie2-se/bowtie2-mapping-se.cwl
inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl
inst/extdata/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml
inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml
inst/extdata/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl
inst/extdata/docopt.R/rsubread/rsubread_idx.doc.R
inst/extdata/docopt.R/rsubread/rsubread.doc.R
inst/extdata/docopt.R/gsnap/gsnap_idx.doc.R
inst/extdata/docopt.R/gsnap/gsnap.doc.R
inst/unitTests/test_classes.R
inst/unitTests/SRR446028_1.fastq
inst/unitTests/targets.txt
inst/unitTests/tophat.param
inst/unitTests/SRR446029_1.fastq
inst/unitTests/SRR446027_1.fastq
inst/unitTests/SRR446030_1.fastq
build/vignette.rds
tests/runTests.R
vignettes/SYS_WF.png
vignettes/heatmap1.png
vignettes/sysargslist.png
vignettes/systemPipeR.Rmd
vignettes/fastqReport.png
vignettes/systemPipeR_workflows.Rmd
vignettes/SYSargs2.png
vignettes/GOslimbarplotMF.png
vignettes/SystemPipeR_Workflow.png
vignettes/utilities.png
vignettes/directory.png
vignettes/SYSdir.png
vignettes/bibtex.bib
man/tryPath.Rd
man/getQsubargs.Rd
man/plotfeaturetypeCounts.Rd
man/catmap.Rd
man/sysargs.Rd
man/seeFastq.Rd
man/qsubRun.Rd
man/SYSargs2Pipe-methods.Rd
man/INTERSECTset-class.Rd
man/targets.as.df.Rd
man/EnvModules-class.Rd
man/alignStats.Rd
man/olRanges.Rd
man/SYSargsList-class.Rd
man/createWF.Rd
man/renderReport.Rd
man/countRangeset.Rd
man/SYSargs2-class.Rd
man/run_track.Rd
man/moduleload.Rd
man/output_update.Rd
man/config.param.Rd
man/plotWF.Rd
man/vennPlot.Rd
man/preprocessReads.Rd
man/overLapper.Rd
man/SYSargs2Pipe-class.Rd
man/renderWF.Rd
man/featureCoverage.Rd
man/evalCode.Rd
man/module.Rd
man/featuretypeCounts.Rd
man/subsetWF.Rd
man/olBarplot.Rd
man/tryCL.Rd
man/runDiff.Rd
man/plotfeatureCoverage.Rd
man/returnRPKM.Rd
man/run_edgeR.Rd
man/predORF.Rd
man/runCommandline.Rd
man/loadWorkflow.Rd
man/VENNset-class.Rd
man/genFeatures.Rd
man/SYSargs-class.Rd
man/systemArgs.Rd
man/readComp.Rd
man/filterVars.Rd
man/writeTargetsout.Rd
man/filterDEGs.Rd
man/symLink2bam.Rd
man/initWF.Rd
man/runWF.Rd
man/sysargslist-methods.Rd
man/clusterRun.Rd
man/configWF.Rd
man/mergeBamByFactor.Rd
man/writeTargetsRef.Rd
man/catDB-class.Rd
man/GOHyperGAll.Rd
man/sysargs2-methods.Rd
man/run_DESeq2.Rd
man/scaleRanges.Rd
man/variantReport.Rd
