systemPipeR: systemPipeR: NGS workflow and report generation environment

R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.

Author
Thomas Girke
Date of publication
None
Maintainer
Thomas Girke <thomas.girke@ucr.edu>
License
Artistic-2.0
Version
1.8.1
URLs

View on Bioconductor

Man pages

alignStats
Alignment statistics
catDB-class
Class '"catDB"'
catmap
catDB accessor methods
clusterRun
Submit command-line tools to cluster
countRangeset
Read counting for several range sets
featureCoverage
Genome read coverage by transcript models
featuretypeCounts
Plot read distribution across genomic features
filterDEGs
Filter and plot DEG results
filterVars
Filter VCF files
genFeatures
Generate feature ranges from TxDb
getQsubargs
Arguments for qsub
GOHyperGAll
GO term enrichment analysis for large numbers of gene sets
INTERSECTset-class
Class '"INTERSECTset"'
mergeBamByFactor
Merge BAM files based on factor
moduleload
Interface to module system
olBarplot
Bar plot for intersect sets
overLapper
Set Intersect and Venn Diagram Functions
plotfeatureCoverage
Plot feature coverage results
plotfeaturetypeCounts
Plot read distribution across genomic features
predORF
Predict ORFs
preprocessReads
Run custom read preprocessing functions
qsubRun
Submit command-line tools to cluster
readComp
Import sample comparisons from targets file
returnRPKM
RPKM Normalization
runCommandline
Execute SYSargs
run_DESeq2
Runs DESeq2
runDiff
Differential abundance analysis for many range sets
run_edgeR
Runs edgeR
scaleRanges
Scale spliced ranges to genome coordinates
seeFastq
Quality reports for FASTQ files
symLink2bam
Symbolic links for IGV
sysargs
SYSargs accessor methods
SYSargs-class
Class '"SYSargs"'
systemArgs
Constructs SYSargs object from param and targets files
variantReport
Generate Variant Report
vennPlot
Plot 2-5 way Venn diagrams
VENNset-class
Class '"VENNset"'
writeTargetsout
Write updated targets out to file
writeTargetsRef
Generate targets file with reference

Files in this package

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