Files in tgirke/systemPipeRdata
systemPipeRdata: NGS workflow templates and sample data

.gitignore
DESCRIPTION
NAMESPACE
NEWS
R/dataenv.R
README
README.md
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/.BatchJobs.R
inst/extdata/param/Makefile
inst/extdata/param/Makefile_chipseq
inst/extdata/param/Makefile_rnaseq
inst/extdata/param/Makefile_varseq
inst/extdata/param/annotate_peaks.param
inst/extdata/param/annotate_vars.param
inst/extdata/param/bibtex.bib
inst/extdata/param/bowtiePE.param
inst/extdata/param/bowtieSE.param
inst/extdata/param/bwa.param
inst/extdata/param/count_rangesets.param
inst/extdata/param/filter_gatk.param
inst/extdata/param/filter_sambcf.param
inst/extdata/param/filter_vartools.param
inst/extdata/param/gatk.param
inst/extdata/param/gatk_run.sh
inst/extdata/param/gsnap.param
inst/extdata/param/hisat2.param
inst/extdata/param/hisat2PE.param
inst/extdata/param/macs2.param
inst/extdata/param/macs2_noinput.param
inst/extdata/param/rsubread.param
inst/extdata/param/rundiff.param
inst/extdata/param/sambcf.param
inst/extdata/param/sambcf_run.sh
inst/extdata/param/slurm.tmpl
inst/extdata/param/targets.txt
inst/extdata/param/targetsPE.txt
inst/extdata/param/targetsPE_chip.txt
inst/extdata/param/targets_chip.txt
inst/extdata/param/tophat.param
inst/extdata/param/tophatV1.param
inst/extdata/param/torque.tmpl
inst/extdata/param/trim.param
inst/extdata/param/trimPE.param
inst/extdata/param/trim_galore.param
inst/extdata/param/trim_galore_run.sh
inst/extdata/param/vartools.param
inst/extdata/workflows/chipseq/data/dummyfile
inst/extdata/workflows/chipseq/results/fastqReport.pdf
inst/extdata/workflows/chipseq/results/fastqReport.png
inst/extdata/workflows/chipseq/results/seqlogo.pdf
inst/extdata/workflows/chipseq/results/seqlogo.png
inst/extdata/workflows/chipseq/systemPipeChIPseq.R inst/extdata/workflows/chipseq/systemPipeChIPseq.Rmd
inst/extdata/workflows/chipseq/systemPipeChIPseq.Rmd~
inst/extdata/workflows/chipseq/systemPipeChIPseq.html
inst/extdata/workflows/chipseq/systemPipeChIPseq.pdf inst/extdata/workflows/chipseq/systemPipeChIPseq_Latex.R
inst/extdata/workflows/chipseq/systemPipeChIPseq_Latex.Rnw
inst/extdata/workflows/chipseq/systemPipeChIPseq_Latex.pdf
inst/extdata/workflows/riboseq/bibtex.bib
inst/extdata/workflows/riboseq/data/dummyfile
inst/extdata/workflows/riboseq/results/DEGcounts.pdf
inst/extdata/workflows/riboseq/results/DEGcounts.png
inst/extdata/workflows/riboseq/results/GOslimbarplotMF.pdf
inst/extdata/workflows/riboseq/results/GOslimbarplotMF.png
inst/extdata/workflows/riboseq/results/fastqReport.pdf
inst/extdata/workflows/riboseq/results/fastqReport.png
inst/extdata/workflows/riboseq/results/featureCounts.pdf
inst/extdata/workflows/riboseq/results/featureCounts.png
inst/extdata/workflows/riboseq/results/featureCounts2.pdf
inst/extdata/workflows/riboseq/results/featureCounts2.png
inst/extdata/workflows/riboseq/results/featurePlot.pdf
inst/extdata/workflows/riboseq/results/featurePlot.png
inst/extdata/workflows/riboseq/results/heatmap1.pdf
inst/extdata/workflows/riboseq/results/heatmap1.png
inst/extdata/workflows/riboseq/results/sample_tree.pdf
inst/extdata/workflows/riboseq/results/sample_tree.png
inst/extdata/workflows/riboseq/results/vennplot.pdf
inst/extdata/workflows/riboseq/results/vennplot.png
inst/extdata/workflows/riboseq/systemPipeRIBOseq.R inst/extdata/workflows/riboseq/systemPipeRIBOseq.Rmd
inst/extdata/workflows/riboseq/systemPipeRIBOseq.Rmd~
inst/extdata/workflows/riboseq/systemPipeRIBOseq.html
inst/extdata/workflows/riboseq/systemPipeRIBOseq.pdf inst/extdata/workflows/riboseq/systemPipeRIBOseq_Latex.R
inst/extdata/workflows/riboseq/systemPipeRIBOseq_Latex.Rnw
inst/extdata/workflows/riboseq/systemPipeRIBOseq_Latex.pdf
inst/extdata/workflows/rnaseq/data/dummyfile
inst/extdata/workflows/rnaseq/results/DEGcounts.pdf
inst/extdata/workflows/rnaseq/results/DEGcounts.png
inst/extdata/workflows/rnaseq/results/GOslimbarplotMF.pdf
inst/extdata/workflows/rnaseq/results/GOslimbarplotMF.png
inst/extdata/workflows/rnaseq/results/fastqReport.pdf
inst/extdata/workflows/rnaseq/results/fastqReport.png
inst/extdata/workflows/rnaseq/results/featureCounts.png
inst/extdata/workflows/rnaseq/results/heatmap1.pdf
inst/extdata/workflows/rnaseq/results/heatmap1.png
inst/extdata/workflows/rnaseq/results/sample_tree.pdf
inst/extdata/workflows/rnaseq/results/sample_tree.png
inst/extdata/workflows/rnaseq/results/vennplot.pdf
inst/extdata/workflows/rnaseq/results/vennplot.png
inst/extdata/workflows/rnaseq/systemPipeRNAseq.R inst/extdata/workflows/rnaseq/systemPipeRNAseq.Rmd
inst/extdata/workflows/rnaseq/systemPipeRNAseq.html
inst/extdata/workflows/rnaseq/systemPipeRNAseq.pdf inst/extdata/workflows/rnaseq/systemPipeRNAseq_Latex.R
inst/extdata/workflows/rnaseq/systemPipeRNAseq_Latex.Rnw
inst/extdata/workflows/rnaseq/systemPipeRNAseq_Latex.pdf
inst/extdata/workflows/varseq/data/dummyfile
inst/extdata/workflows/varseq/results/dummyfile
inst/extdata/workflows/varseq/results/fastqReport.png
inst/extdata/workflows/varseq/results/plot_variant.png
inst/extdata/workflows/varseq/results/vennplot_var.png
inst/extdata/workflows/varseq/systemPipeVARseq.R inst/extdata/workflows/varseq/systemPipeVARseq.Rmd
inst/extdata/workflows/varseq/systemPipeVARseq.html
inst/extdata/workflows/varseq/systemPipeVARseq.pdf inst/extdata/workflows/varseq/systemPipeVARseq_Fct.R inst/extdata/workflows/varseq/systemPipeVARseq_Latex.R
inst/extdata/workflows/varseq/systemPipeVARseq_Latex.Rnw
inst/extdata/workflows/varseq/systemPipeVARseq_Latex.pdf inst/extdata/workflows/varseq/systemPipeVARseq_single_Latex.R
inst/extdata/workflows/varseq/systemPipeVARseq_single_Latex.Rnw
inst/extdata/workflows/varseq/systemPipeVARseq_single_Latex.pdf inst/unitTests/test_samples.R man/genWorkenvir.Rd man/pathList.Rd tests/runTests.R
vignettes/bibtex.bib
vignettes/systemPipeR_Presentation.html
vignettes/systemPipeRdata.R vignettes/systemPipeRdata.Rmd
vignettes/systemPipeRdata.html
vignettes/vignette_archive/bibtex.bib
vignettes/vignette_archive/fastqReport.pdf vignettes/vignette_archive/systemPipeR_Presentation.R vignettes/vignette_archive/systemPipeR_Presentation.Rmd
vignettes/vignette_archive/systemPipeR_Presentation.html
vignettes/vignette_archive/targets.txt
vignettes/vignette_archive/targetsPE.txt
vignettes/vignette_archive/vennplot_var.pdf
tgirke/systemPipeRdata documentation built on Oct. 18, 2017, 1:07 a.m.