Files in tgirke/systemPipeRdata
systemPipeRdata: Workflow templates and sample data
..Rproj
.Rbuildignore
.github/bash/update_cwl.sh
.github/bash/update_docoptR.sh
.github/bash/update_inst.sh
.github/depends.Rds
.github/ref_vignette/vignette_version.txt
.github/workflows/actions.yml
.github/workflows/update_cwl.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/dataenv.R
R/getSubsetReads.R
README.md
_pkgdown.yml
changelog
docs/404.html
docs/articles/index.html
docs/articles/results/DEGcounts.png
docs/articles/results/GOslimbarplotMF.png
docs/articles/results/coverage.png
docs/articles/results/directory.png
docs/articles/results/fastqReport.png
docs/articles/results/featureCounts.png
docs/articles/results/featureCounts2.png
docs/articles/results/featurePlot.png
docs/articles/results/heatmap1.png
docs/articles/results/plot_variant.png
docs/articles/results/rstudio.png
docs/articles/results/sample_tree.png
docs/articles/results/seqlogo.png
docs/articles/results/vennplot.png
docs/articles/results/vennplot_var.png
docs/articles/systemPipeChIPseq.html
docs/articles/systemPipeChIPseq_files/anchor-sections-1.0/anchor-sections.css
docs/articles/systemPipeChIPseq_files/anchor-sections-1.0/anchor-sections.js
docs/articles/systemPipeRIBOseq.html
docs/articles/systemPipeRIBOseq_files/anchor-sections-1.0/anchor-sections.css
docs/articles/systemPipeRIBOseq_files/anchor-sections-1.0/anchor-sections.js
docs/articles/systemPipeRNAseq.html
docs/articles/systemPipeRNAseq_files/anchor-sections-1.0/anchor-sections.css
docs/articles/systemPipeRNAseq_files/anchor-sections-1.0/anchor-sections.js
docs/articles/systemPipeRdata.html
docs/articles/systemPipeRdata_files/anchor-sections-1.0/anchor-sections.css
docs/articles/systemPipeRdata_files/anchor-sections-1.0/anchor-sections.js
docs/articles/systemPipeVARseq.html
docs/articles/systemPipeVARseq_files/anchor-sections-1.0/anchor-sections.css
docs/articles/systemPipeVARseq_files/anchor-sections-1.0/anchor-sections.js
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/availableWF.html
docs/reference/genWorkenvir.html
docs/reference/getSubsetReads.html
docs/reference/index.html
docs/reference/pathList.html
docs/sitemap.xml
external_data_store.txt
inst/extdata/annotation/GO/GOannotationsBiomart_mod.txt
inst/extdata/annotation/GO/catdb.RData
inst/extdata/annotation/tair10.dict
inst/extdata/annotation/tair10.fasta
inst/extdata/annotation/tair10.fasta.fai
inst/extdata/annotation/tair10.gff
inst/extdata/annotation/tair10.sqlite
inst/extdata/bam/SRR446027_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446027_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446028_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446028_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446029_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446029_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446030_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446030_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446031_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446031_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446032_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446032_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446033_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446033_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446034_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446034_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446035_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446035_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446036_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446036_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446037_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446037_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446038_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446038_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446039_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446039_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446040_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446040_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446041_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446041_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446042_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446042_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446043_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446043_1.fastq.gz.hisat.bam.bai
inst/extdata/bam/SRR446044_1.fastq.gz.hisat.bam
inst/extdata/bam/SRR446044_1.fastq.gz.hisat.bam.bai
inst/extdata/fastq/SRR446027_1.fastq.gz
inst/extdata/fastq/SRR446027_2.fastq.gz
inst/extdata/fastq/SRR446028_1.fastq.gz
inst/extdata/fastq/SRR446028_2.fastq.gz
inst/extdata/fastq/SRR446029_1.fastq.gz
inst/extdata/fastq/SRR446029_2.fastq.gz
inst/extdata/fastq/SRR446030_1.fastq.gz
inst/extdata/fastq/SRR446030_2.fastq.gz
inst/extdata/fastq/SRR446031_1.fastq.gz
inst/extdata/fastq/SRR446031_2.fastq.gz
inst/extdata/fastq/SRR446032_1.fastq.gz
inst/extdata/fastq/SRR446032_2.fastq.gz
inst/extdata/fastq/SRR446033_1.fastq.gz
inst/extdata/fastq/SRR446033_2.fastq.gz
inst/extdata/fastq/SRR446034_1.fastq.gz
inst/extdata/fastq/SRR446034_2.fastq.gz
inst/extdata/fastq/SRR446035_1.fastq.gz
inst/extdata/fastq/SRR446035_2.fastq.gz
inst/extdata/fastq/SRR446036_1.fastq.gz
inst/extdata/fastq/SRR446036_2.fastq.gz
inst/extdata/fastq/SRR446037_1.fastq.gz
inst/extdata/fastq/SRR446037_2.fastq.gz
inst/extdata/fastq/SRR446038_1.fastq.gz
inst/extdata/fastq/SRR446038_2.fastq.gz
inst/extdata/fastq/SRR446039_1.fastq.gz
inst/extdata/fastq/SRR446039_2.fastq.gz
inst/extdata/fastq/SRR446040_1.fastq.gz
inst/extdata/fastq/SRR446040_2.fastq.gz
inst/extdata/fastq/SRR446041_1.fastq.gz
inst/extdata/fastq/SRR446041_2.fastq.gz
inst/extdata/fastq/SRR446042_1.fastq.gz
inst/extdata/fastq/SRR446042_2.fastq.gz
inst/extdata/fastq/SRR446043_1.fastq.gz
inst/extdata/fastq/SRR446043_2.fastq.gz
inst/extdata/fastq/SRR446044_1.fastq.gz
inst/extdata/fastq/SRR446044_2.fastq.gz
inst/extdata/param/.batchtools.conf.R
inst/extdata/param/.batchtools.conf.R.sge
inst/extdata/param/.batchtools.conf.R.torque
inst/extdata/param/SraRunTable_SRP010938.txt
inst/extdata/param/batchtools.sge.tmpl
inst/extdata/param/batchtools.slurm.tmpl
inst/extdata/param/batchtools.torque.tmpl
inst/extdata/param/bibtex.bib
inst/extdata/param/cwl/BUSCO/BUSCO.cwl
inst/extdata/param/cwl/BUSCO/BUSCO.yml
inst/extdata/param/cwl/BUSCO/runME
inst/extdata/param/cwl/BUSCO/workflow_BUSCO.cwl
inst/extdata/param/cwl/MACS2/MACS2-input/macs2-input.cwl
inst/extdata/param/cwl/MACS2/MACS2-input/macs2.yml
inst/extdata/param/cwl/MACS2/MACS2-noinput/macs2.cwl
inst/extdata/param/cwl/MACS2/MACS2-noinput/macs2.yml
inst/extdata/param/cwl/MACS2/macs2-input.cwl
inst/extdata/param/cwl/MACS2/macs2-input.yml
inst/extdata/param/cwl/MACS2/macs2-noinput.cwl
inst/extdata/param/cwl/MACS2/macs2-noinput.yml
inst/extdata/param/cwl/MACS2/workflow_macs2-input.cwl
inst/extdata/param/cwl/MACS2/workflow_macs2-noinput.cwl
inst/extdata/param/cwl/annotate_peaks/annotate_peaks.cwl
inst/extdata/param/cwl/annotate_peaks/annotate_peaks.yml
inst/extdata/param/cwl/annotate_peaks/workflow_annotate_peaks.cwl
inst/extdata/param/cwl/blast/blastdbcmd.cwl
inst/extdata/param/cwl/blast/blastdbcmd.yml
inst/extdata/param/cwl/blast/blastn.cwl
inst/extdata/param/cwl/blast/blastn.yml
inst/extdata/param/cwl/blast/makeblastdb.cwl
inst/extdata/param/cwl/blast/makeblastdb.yml
inst/extdata/param/cwl/blast/workflow_blastn.cwl
inst/extdata/param/cwl/blast/workflow_makeblastdb.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-idx/bowtie2-index.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-idx/bowtie2-index.yml
inst/extdata/param/cwl/bowtie2/bowtie2-index.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-index.yml
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-mi.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-mi.yml
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-pe.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-pe.yml
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-se.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-mapping-se.yml
inst/extdata/param/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.cwl
inst/extdata/param/cwl/bowtie2/bowtie2-pe/bowtie2-mapping-pe.yml
inst/extdata/param/cwl/bowtie2/workflow_bowtie2-index.cwl
inst/extdata/param/cwl/bowtie2/workflow_bowtie2-mapping-mi.cwl
inst/extdata/param/cwl/bowtie2/workflow_bowtie2-mapping-pe.cwl
inst/extdata/param/cwl/bowtie2/workflow_bowtie2-mapping-se.cwl
inst/extdata/param/cwl/bwa/bwa-aln.cwl
inst/extdata/param/cwl/bwa/bwa-aln.yml
inst/extdata/param/cwl/bwa/bwa-index.cwl
inst/extdata/param/cwl/bwa/bwa-index.yml
inst/extdata/param/cwl/bwa/bwa-mem-pe.cwl
inst/extdata/param/cwl/bwa/bwa-mem-pe.yml
inst/extdata/param/cwl/bwa/bwa-mem-se.cwl
inst/extdata/param/cwl/bwa/bwa-mem-se.yml
inst/extdata/param/cwl/bwa/bwa-pe.cwl
inst/extdata/param/cwl/bwa/bwa-pe.yml
inst/extdata/param/cwl/bwa/bwa-samse.cwl
inst/extdata/param/cwl/bwa/bwa-samse.yml
inst/extdata/param/cwl/bwa/bwa-se.cwl
inst/extdata/param/cwl/bwa/bwa-se.yml
inst/extdata/param/cwl/bwa/workflow_bwa-aln.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-index.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-mem-pe.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-mem-se.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-pe.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-samse.cwl
inst/extdata/param/cwl/bwa/workflow_bwa-se.cwl
inst/extdata/param/cwl/count_rangesets/count_rangesets.cwl
inst/extdata/param/cwl/count_rangesets/count_rangesets.yml
inst/extdata/param/cwl/count_rangesets/workflow_count_rangesets.cwl
inst/extdata/param/cwl/cutadapt/cutadapt.cwl
inst/extdata/param/cwl/cutadapt/cutadapt.yml
inst/extdata/param/cwl/cutadapt/workflow_cutadapt.cwl
inst/extdata/param/cwl/example/example.cwl
inst/extdata/param/cwl/example/example.yml
inst/extdata/param/cwl/example/example_single.yml
inst/extdata/param/cwl/example/targets_example.txt
inst/extdata/param/cwl/example/workflow_example.cwl
inst/extdata/param/cwl/fastq-dump/fastq-dump.cwl
inst/extdata/param/cwl/fastq-dump/fastq-dump.yml
inst/extdata/param/cwl/fastq-dump/workflow_fastq-dump.cwl
inst/extdata/param/cwl/fastqc/fastqc-se.cwl
inst/extdata/param/cwl/fastqc/fastqc-se.yml
inst/extdata/param/cwl/fastqc/fastqc.cwl
inst/extdata/param/cwl/fastqc/fastqc.yml
inst/extdata/param/cwl/fastqc/workflow_fastqc.cwl
inst/extdata/param/cwl/fastx_toolkit/fastx_clipper.cwl
inst/extdata/param/cwl/fastx_toolkit/fastx_clipper.yml
inst/extdata/param/cwl/fastx_toolkit/workflow_fastx_clipper.cwl
inst/extdata/param/cwl/gatk/bwa-index.cwl
inst/extdata/param/cwl/gatk/bwa-pe.cwl
inst/extdata/param/cwl/gatk/fasta_dict.cwl
inst/extdata/param/cwl/gatk/fasta_faidx.cwl
inst/extdata/param/cwl/gatk/gatk.yaml
inst/extdata/param/cwl/gatk/gatk_fastq2ubam.cwl
inst/extdata/param/cwl/gatk/gatk_fixtag.cwl
inst/extdata/param/cwl/gatk/gatk_genomicsDBImport.cwl
inst/extdata/param/cwl/gatk/gatk_genomicsDBImport.sh
inst/extdata/param/cwl/gatk/gatk_genotypeGVCFs.cwl
inst/extdata/param/cwl/gatk/gatk_haplotypecaller.cwl
inst/extdata/param/cwl/gatk/gatk_markduplicates.cwl
inst/extdata/param/cwl/gatk/gatk_mergebams.cwl
inst/extdata/param/cwl/gatk/gatk_select_variant.cwl
inst/extdata/param/cwl/gatk/gatk_sort.cwl
inst/extdata/param/cwl/gatk/gatk_variantFiltration.cwl
inst/extdata/param/cwl/gatk/gatk_variantFiltration.sh
inst/extdata/param/cwl/gatk/workflow_bwa-index.cwl
inst/extdata/param/cwl/gatk/workflow_bwa-pe.cwl
inst/extdata/param/cwl/gatk/workflow_fasta_dict.cwl
inst/extdata/param/cwl/gatk/workflow_fasta_faidx.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_fastq2ubam.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_fixtag.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_genomicsDBImport.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_genotypeGVCFs.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_haplotypecaller.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_markduplicates.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_mergebams.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_select_variant.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_sort.cwl
inst/extdata/param/cwl/gatk/workflow_gatk_variantFiltration.cwl
inst/extdata/param/cwl/gsnap/gsnap-index.cwl
inst/extdata/param/cwl/gsnap/gsnap-index.yml
inst/extdata/param/cwl/gsnap/gsnap-mapping-pe.cwl
inst/extdata/param/cwl/gsnap/gsnap-mapping-pe.yml
inst/extdata/param/cwl/gsnap/workflow_gsnap-index.cwl
inst/extdata/param/cwl/gsnap/workflow_gsnap-mapping-pe.cwl
inst/extdata/param/cwl/gunzip/gunzip.cwl
inst/extdata/param/cwl/gunzip/gunzip.yml
inst/extdata/param/cwl/gunzip/gzip.cwl
inst/extdata/param/cwl/gunzip/gzip.yml
inst/extdata/param/cwl/gunzip/targets_gunzip.txt
inst/extdata/param/cwl/gunzip/workflow_gunzip.cwl
inst/extdata/param/cwl/gunzip/workflow_gzip.cwl
inst/extdata/param/cwl/hisat2/hisat2-index.cwl
inst/extdata/param/cwl/hisat2/hisat2-index.yml
inst/extdata/param/cwl/hisat2/hisat2-mapping-pe.cwl
inst/extdata/param/cwl/hisat2/hisat2-mapping-pe.yml
inst/extdata/param/cwl/hisat2/hisat2-mapping-se.cwl
inst/extdata/param/cwl/hisat2/hisat2-mapping-se.yml
inst/extdata/param/cwl/hisat2/workflow_hisat2-index.cwl
inst/extdata/param/cwl/hisat2/workflow_hisat2-mapping-pe.cwl
inst/extdata/param/cwl/hisat2/workflow_hisat2-mapping-se.cwl
inst/extdata/param/cwl/kallisto/kallisto-index.cwl
inst/extdata/param/cwl/kallisto/kallisto.cwl
inst/extdata/param/cwl/kallisto/kallisto.yml
inst/extdata/param/cwl/kallisto/runME
inst/extdata/param/cwl/kallisto/workflow_kallisto-index.cwl
inst/extdata/param/cwl/kallisto/workflow_kallisto.cwl
inst/extdata/param/cwl/mergeBamByFactor/merge-bam.cwl
inst/extdata/param/cwl/mergeBamByFactor/merge-bam.yml
inst/extdata/param/cwl/mergeBamByFactor/workflow_merge-bam.cwl
inst/extdata/param/cwl/picard/picard_markduplicates.cwl
inst/extdata/param/cwl/picard/picard_markduplicates.yml
inst/extdata/param/cwl/picard/workflow_picard_markduplicates.cwl
inst/extdata/param/cwl/preprocessReads/preprocessReads-pe.cwl
inst/extdata/param/cwl/preprocessReads/preprocessReads-pe.yml
inst/extdata/param/cwl/preprocessReads/preprocessReads-pe_riboseq.yml
inst/extdata/param/cwl/preprocessReads/preprocessReads-se.cwl
inst/extdata/param/cwl/preprocessReads/preprocessReads-se.yml
inst/extdata/param/cwl/preprocessReads/trim-pe.cwl
inst/extdata/param/cwl/preprocessReads/trim-pe.yml
inst/extdata/param/cwl/preprocessReads/trim-pe/trim-pe.cwl
inst/extdata/param/cwl/preprocessReads/trim-pe/trim-pe.yml
inst/extdata/param/cwl/preprocessReads/trim-se.cwl
inst/extdata/param/cwl/preprocessReads/trim-se.yml
inst/extdata/param/cwl/preprocessReads/trim-se/trim-se.cwl
inst/extdata/param/cwl/preprocessReads/trim-se/trim-se.yml
inst/extdata/param/cwl/preprocessReads/workflow_trim-pe.cwl
inst/extdata/param/cwl/preprocessReads/workflow_trim-se.cwl
inst/extdata/param/cwl/repo_version.txt
inst/extdata/param/cwl/rsubread/rsubread-index.cwl
inst/extdata/param/cwl/rsubread/rsubread-index.yml
inst/extdata/param/cwl/rsubread/rsubread-mapping-se.cwl
inst/extdata/param/cwl/rsubread/rsubread-mapping-se.yml
inst/extdata/param/cwl/rsubread/workflow_rsubread-index.cwl
inst/extdata/param/cwl/rsubread/workflow_rsubread-mapping-se.cwl
inst/extdata/param/cwl/rundiff/rundiff.cwl
inst/extdata/param/cwl/rundiff/rundiff.yml
inst/extdata/param/cwl/rundiff/workflow_rundiff.cwl
inst/extdata/param/cwl/samtools/samtools-index.cwl
inst/extdata/param/cwl/samtools/samtools-index.yml
inst/extdata/param/cwl/samtools/samtools-sort.cwl
inst/extdata/param/cwl/samtools/samtools-sort.yml
inst/extdata/param/cwl/samtools/samtools-view.cwl
inst/extdata/param/cwl/samtools/samtools-view.yml
inst/extdata/param/cwl/samtools/workflow_samtools-index.cwl
inst/extdata/param/cwl/samtools/workflow_samtools-sort.cwl
inst/extdata/param/cwl/samtools/workflow_samtools-view.cwl
inst/extdata/param/cwl/star/runMe
inst/extdata/param/cwl/star/star-index.cwl
inst/extdata/param/cwl/star/star-index.yml
inst/extdata/param/cwl/star/star-mapping-pe.cwl
inst/extdata/param/cwl/star/star-mapping-pe.yml
inst/extdata/param/cwl/star/star-mapping-se.cwl
inst/extdata/param/cwl/star/star-mapping-se.yml
inst/extdata/param/cwl/star/workflow_star-index.cwl
inst/extdata/param/cwl/star/workflow_star-mapping-pe.cwl
inst/extdata/param/cwl/star/workflow_star-mapping-se.cwl
inst/extdata/param/cwl/star/workflow_star-pe-sam_samtools.cwl
inst/extdata/param/cwl/test/test.cwl
inst/extdata/param/cwl/test/test.yml
inst/extdata/param/cwl/test/workflow_test.cwl
inst/extdata/param/cwl/tophat2/tophat2-mapping-pe.cwl
inst/extdata/param/cwl/tophat2/tophat2-mapping-pe.yml
inst/extdata/param/cwl/tophat2/tophat2-mapping-se.cwl
inst/extdata/param/cwl/tophat2/tophat2-mapping-se.yml
inst/extdata/param/cwl/tophat2/workflow_tophat2-mapping-pe.cwl
inst/extdata/param/cwl/tophat2/workflow_tophat2-mapping-se.cwl
inst/extdata/param/cwl/trim_galore/trim_galore-pe.cwl
inst/extdata/param/cwl/trim_galore/trim_galore-pe.yml
inst/extdata/param/cwl/trim_galore/trim_galore-se.cwl
inst/extdata/param/cwl/trim_galore/trim_galore-se.yml
inst/extdata/param/cwl/trim_galore/workflow_trim_galore-pe.cwl
inst/extdata/param/cwl/trim_galore/workflow_trim_galore-se.cwl
inst/extdata/param/cwl/trimmomatic/trimmomatic-pe.cwl
inst/extdata/param/cwl/trimmomatic/trimmomatic-pe.yml
inst/extdata/param/cwl/trimmomatic/trimmomatic-se.cwl
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