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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("systemPipeR")
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
Version1.8.1
https://github.com/tgirke/systemPipeR

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

Functions

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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.