systemPipeR: systemPipeR: NGS workflow and report generation environment
Version 1.10.0

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.

AuthorThomas Girke
Bioconductor views Alignment ChIPSeq Coverage DataImport GeneExpression GeneSetEnrichment Genetics Infrastructure MethylSeq QualityControl RNASeq RiboSeq SNP Sequencing
Date of publicationNone
MaintainerThomas Girke <thomas.girke@ucr.edu>
LicenseArtistic-2.0
Version1.10.0
URL https://github.com/tgirke/systemPipeR
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")

Getting started

README.md
_systemPipeR_: NGS workflow and report generation environment

Popular man pages

genFeatures: Generate feature ranges from TxDb
GOHyperGAll: GO term enrichment analysis for large numbers of gene sets
olBarplot: Bar plot for intersect sets
predORF: Predict ORFs
symLink2bam: Symbolic links for IGV
variantReport: Generate Variant Report
vennPlot: Plot 2-5 way Venn diagrams
See all...

All man pages Function index File listing

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

Functions

AffyID2GeneID Source code
GOCluster_Report Man page Source code
GOHyperGAll Man page Source code
GOHyperGAll_Simplify Man page Source code
GOHyperGAll_Subset Man page Source code
INTERSECTset-class Man page
SYSargs-class Man page
SampleName Man page
SampleName,SYSargs-method Man page
SampleName-methods Man page
VENNset-class Man page
[,SYSargs,ANY,ANY,ANY-method Man page
alignStats Man page Source code
allAnnot Source code
as.list,INTERSECTset-method Man page
as.list,VENNset-method Man page
catDB-class Man page
catlist Man page
catlist,catDB-method Man page
catlist-methods Man page
catmap Man page
catmap,catDB-method Man page
catmap-methods Man page
clusterRun Man page Source code
codingReport Source code
coerce,list,INTERSECTset-method Man page
coerce,list,SYSargs-method Man page
coerce,list,VENNset-method Man page
coerce,list,catDB-method Man page
combineVarReports Man page Source code
complexitylevels Man page
complexitylevels,INTERSECTset-method Man page
complexitylevels,VENNset-method Man page
complexitylevels-methods Man page
cores Man page
cores,SYSargs-method Man page
cores-methods Man page
countRangeset Man page Source code
featureCoverage Man page Source code
featuretypeCounts Man page Source code
filterDEGs Man page Source code
filterVars Man page Source code
genFeatures Man page Source code
gene2GOlist Source code
getQsubargs Man page Source code
getSRAfastq Source code
goBarplot Man page Source code
idconv Man page
idconv,catDB-method Man page
idconv-methods Man page
infile1 Man page
infile1,SYSargs-method Man page
infile1-methods Man page
infile2 Man page
infile2,SYSargs-method Man page
infile2-methods Man page
intersectlist Man page
intersectlist,INTERSECTset-method Man page
intersectlist-methods Man page
intersectmatrix Man page
intersectmatrix,INTERSECTset-method Man page
intersectmatrix,VENNset-method Man page
intersectmatrix-methods Man page
length,INTERSECTset-method Man page
length,SYSargs-method Man page
length,VENNset-method Man page
makeCATdb Man page Source code
mergeBamByFactor Man page Source code
modulelist Man page Source code
moduleload Man page Source code
modules Man page
modules,SYSargs-method Man page
modules-methods Man page
names,INTERSECTset-method Man page
names,SYSargs-method Man page
names,VENNset-method Man page
names,catDB-method Man page
olBarplot Man page Source code
other Man page
other,SYSargs-method Man page
other-methods Man page
outfile1 Man page
outfile1,SYSargs-method Man page
outfile1-methods Man page
outpaths Man page
outpaths,SYSargs-method Man page
outpaths-methods Man page
overLapper Man page Source code
plotfeatureCoverage Man page Source code
plotfeaturetypeCounts Man page Source code
predORF Man page Source code
preprocessReads Man page Source code
qsubRun Man page Source code
readComp Man page Source code
readGOorg Source code
reference Man page
reference,SYSargs-method Man page
reference-methods Man page
resizeFeature Source code
results Man page
results,SYSargs-method Man page
results-methods Man page
returnRPKM Man page Source code
runCommandline Man page Source code
runDiff Man page Source code
run_DESeq2 Man page Source code
run_edgeR Man page Source code
sampleDFgene2GO Source code
scaleRanges Man page Source code
seeFastq Man page Source code
seeFastqPlot Man page Source code
setlist Man page
setlist,INTERSECTset-method Man page
setlist,VENNset-method Man page
setlist-methods Man page
show,INTERSECTset-method Man page
show,SYSargs-method Man page
show,VENNset-method Man page
show,catDB-method Man page
software Man page
software,SYSargs-method Man page
software-methods Man page
subsetReadsByMappingRegion Source code
symLink2bam Man page Source code
sysargs Man page
sysargs,SYSargs-method Man page
sysargs-methods Man page
systemArgs Man page Source code
targetsheader Man page
targetsheader,SYSargs-method Man page
targetsheader-methods Man page
targetsin Man page
targetsin,SYSargs-method Man page
targetsin-methods Man page
targetsout Man page
targetsout,SYSargs-method Man page
targetsout-methods Man page
varSummary Man page Source code
variantReport Man page Source code
vennPlot Man page Source code
vennlist Man page
vennlist,VENNset-method Man page
vennlist-methods Man page
writeTargetsRef Man page Source code
writeTargetsout Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/chipseq.R
R/developerFct.R
R/fastqQuality.R
R/geneSetAnalysis.R
R/overLapper.R
R/riboseq.R
R/utilities.R
R/varseq.R
README
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/systemPipeChIPseq.R
inst/doc/systemPipeChIPseq.Rnw
inst/doc/systemPipeChIPseq.pdf
inst/doc/systemPipeR.R
inst/doc/systemPipeR.Rmd
inst/doc/systemPipeR.html
inst/doc/systemPipeRIBOseq.R
inst/doc/systemPipeRIBOseq.Rnw
inst/doc/systemPipeRIBOseq.pdf
inst/doc/systemPipeRNAseq.R
inst/doc/systemPipeRNAseq.Rnw
inst/doc/systemPipeRNAseq.pdf
inst/doc/systemPipeVARseq.R
inst/doc/systemPipeVARseq.Rnw
inst/doc/systemPipeVARseq.pdf
inst/extdata
inst/extdata/.BatchJobs.R
inst/extdata/Makefile
inst/extdata/alignStats.xls
inst/extdata/annotate_peaks.param
inst/extdata/annotate_vars.param
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/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/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/slides
inst/extdata/slides/bibtex.bib
inst/extdata/slides/images
inst/extdata/slides/images/SystemPipeR_Workflow.png
inst/extdata/slides/logo.png
inst/extdata/slides/systemPipeRslides.R
inst/extdata/slides/systemPipeRslides.Rmd
inst/extdata/slides/systemPipeRslides.html
inst/extdata/slides/systemPipeRslides_cache
inst/extdata/slides/systemPipeRslides_cache/html
inst/extdata/targets.txt
inst/extdata/targetsPE.txt
inst/extdata/targetsPE_chip.txt
inst/extdata/targets_chip.txt
inst/extdata/tophat.param
inst/extdata/torque.tmpl
inst/extdata/trim.param
inst/extdata/trimPE.param
inst/extdata/vartools.param
inst/extdata/vignette_archive
inst/extdata/vignette_archive/systemPipeR.R
inst/extdata/vignette_archive/systemPipeR.Rnw
inst/extdata/vignette_archive/systemPipeR.pdf
inst/unitTests
inst/unitTests/SRR446027_1.fastq
inst/unitTests/SRR446028_1.fastq
inst/unitTests/SRR446029_1.fastq
inst/unitTests/SRR446030_1.fastq
inst/unitTests/targets.txt
inst/unitTests/test_classes.R
inst/unitTests/tophat.param
man
man/GOHyperGAll.Rd
man/INTERSECTset-class.Rd
man/SYSargs-class.Rd
man/VENNset-class.Rd
man/alignStats.Rd
man/catDB-class.Rd
man/catmap.Rd
man/clusterRun.Rd
man/countRangeset.Rd
man/featureCoverage.Rd
man/featuretypeCounts.Rd
man/filterDEGs.Rd
man/filterVars.Rd
man/genFeatures.Rd
man/getQsubargs.Rd
man/mergeBamByFactor.Rd
man/moduleload.Rd
man/olBarplot.Rd
man/overLapper.Rd
man/plotfeatureCoverage.Rd
man/plotfeaturetypeCounts.Rd
man/predORF.Rd
man/preprocessReads.Rd
man/qsubRun.Rd
man/readComp.Rd
man/returnRPKM.Rd
man/runCommandline.Rd
man/runDiff.Rd
man/run_DESeq2.Rd
man/run_edgeR.Rd
man/scaleRanges.Rd
man/seeFastq.Rd
man/symLink2bam.Rd
man/sysargs.Rd
man/systemArgs.Rd
man/variantReport.Rd
man/vennPlot.Rd
man/writeTargetsRef.Rd
man/writeTargetsout.Rd
tests
tests/runTests.R
vignettes
vignettes/DEGcounts.pdf
vignettes/GOslimbarplotMF.pdf
vignettes/GOslimbarplotMF.png
vignettes/SystemPipeR_Workflow.png
vignettes/bibtex.bib
vignettes/fastqReport.pdf
vignettes/fastqReport.png
vignettes/featureCounts.pdf
vignettes/featureCounts2.pdf
vignettes/featurePlot.pdf
vignettes/heatmap1.pdf
vignettes/heatmap1.png
vignettes/sample_tree.pdf
vignettes/seqlogo.pdf
vignettes/systemPipeChIPseq.Rnw
vignettes/systemPipeR.Rmd
vignettes/systemPipeRIBOseq.Rnw
vignettes/systemPipeRNAseq.Rnw
vignettes/systemPipeVARseq.Rnw
vignettes/vennplot.pdf
vignettes/vennplot_var.pdf
systemPipeR documentation built on May 20, 2017, 9:18 p.m.

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