Package: systemPipeR 2.11.2

Thomas Girke

systemPipeR: systemPipeR: workflow management and report generation environment

systemPipeR is a multipurpose data analysis workflow environment that unifies R with command-line tools. It enables scientists to analyze many types of large- or small-scale data on local or distributed computer systems with a high level of reproducibility, scalability and portability. At its core is a command-line interface (CLI) that adopts the Common Workflow Language (CWL). This design allows users to choose for each analysis step the optimal R or command-line software. It supports both end-to-end and partial execution of workflows with built-in restart functionalities. Efficient management of complex analysis tasks is accomplished by a flexible workflow control container class. Handling of large numbers of input samples and experimental designs is facilitated by consistent sample annotation mechanisms. As a multi-purpose workflow toolkit, systemPipeR enables users to run existing workflows, customize them or design entirely new ones while taking advantage of widely adopted data structures within the Bioconductor ecosystem. Another important core functionality is the generation of reproducible scientific analysis and technical reports. For result interpretation, systemPipeR offers a wide range of plotting functionality, while an associated Shiny App offers many useful functionalities for interactive result exploration. The vignettes linked from this page include (1) a general introduction, (2) a description of technical details, and (3) a collection of workflow templates.

Authors:Thomas Girke

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NEWS

# Install 'systemPipeR' in R:

install.packages('systemPipeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tgirke/systempiper/issues

On BioConductor:systemPipeR-2.11.2(bioc 3.20)systemPipeR-2.10.0(bioc 3.19)

bioconductor-package

161 exports 4.17 score 99 dependencies 3 dependents 27 mentions

Last updated 10 days agofrom:7f2b0c6dbd

Exports:addResources alignStats appendCodeLine<-appendParam appendParam2 appendStep<-as.list baseCommand catlist catmap check.outfiles check.output clt clusterRun cmdlist cmdToCwl cmdToCwl<-codeChunkStart codeLine combineVarReports complexitylevels config.param configWF copyEnvir cores countRangeset createParam createParamFiles cwlFilesUpdate dependency dependency<-evalCode featureCoverage featuretypeCounts files filterDEGs filterVars genFeatures getColumn goBarplot GOCluster_Report GOHyperGAll GOHyperGAll_Simplify GOHyperGAll_Subset idconv importWF infile1 infile2 input inputvars intersectlist intersectmatrix linewise LineWise listCmdModules listCmdTools loadWF loadWorkflow makeCATdb mergeBamByFactor module moduleAvail moduleClear moduleInit modulelist moduleload modules moduleUnload olBarplot olRanges other outfile1 outfiles outpaths output output_update overLapper plotfeatureCoverage plotfeaturetypeCounts plotWF plotwfOutput predORF preprocessReads printParam printParam2 projectInfo readComp reference removeParam2 renameParam renameParam2 renameStep<-renderLogs renderPlotwf renderReport renderWF replaceCodeLine<-replaceParam replaceParam2 replaceStep<-results returnRPKM rmdPath run_DESeq2 run_edgeR runCommandline runDiff runInfo runWF sal2bash sal2rmd SampleName scaleRanges SE SE<-seeFastq seeFastqPlot setlist show showDF software SPRproject status statusWF stepName stepsWF subset subsetParam subsetWF symLink2bam sysargs sysargs2 sysargslist SYSargsList systemArgs targets targets.as.df targets.as.list targetsheader targetsin targetsout targetsWF trimbatch tryCL tryCMD tryPath updateColumn<-updateWF variantReport varSummary vennlist vennPlot viewEnvir wf write_SYSargsList writeParamFiles writeTargets writeTargetsout writeTargetsRef yamlinput yamlinput<-

Dependencies:abind askpass base64enc BH Biobase BiocGenerics BiocParallel Biostrings bitops bslib cachem cli codetools colorspace cpp11 crayon curl DelayedArray deldir digest evaluate fansi farver fastmap fontawesome formatR fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httr hwriter interp IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig png pwalign R6 rappdirs RColorBrewer Rcpp RcppEigen Rhtslib rlang rmarkdown Rsamtools S4Arrays S4Vectors sass scales ShortRead snow SparseArray stringi stringr SummarizedExperiment sys tibble tinytex UCSC.utils utf8 vctrs viridisLite withr xfun XVector yaml zlibbioc

systemPipeR: Workflow Environment for Data Analysis and Report Generation

Author: Le Zhang, Daniela Cassol, and Thomas Girke

Rendered fromsystemPipeR.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2024-07-01
Started: 2015-07-27

systemPipeR: Workflows collection

Author: Daniela Cassol ([email protected]) and Thomas Girke ([email protected])

Rendered fromsystemPipeR_workflows.Rmdusingknitr::rmarkdownon Jul 01 2024.

Last update: 2022-04-24
Started: 2019-10-15

Help page	Topics
systemPipeR package for Workflow Environment	systemPipeR-package
Extension accessor methods for SummarizedExperiment object	addAssay addAssay,SummarizedExperiment-method addAssay-methods addMetadata addMetadata,SummarizedExperiment-method addMetadata-methods
Alignment statistics	alignStats
Class '"catDB"'	catDB-class catlist,catDB-method catmap,catDB-method coerce,list,catDB-method idconv,catDB-method names,catDB-method show,catDB-method
catDB accessor methods	catlist catlist-methods catmap catmap-methods idconv idconv-methods
Checking if the outfiles files exist	check.outfiles check.output
Submit command-line tools to cluster	clusterRun
Adding param file	config.param
Workflow Steps Selection	configWF
Read counting for several range sets	countRangeset
createParam	createParam createParamFiles writeParamFiles
Update CWL description files	cwlFilesUpdate
Class '"EnvModules"'	$,EnvModules-method available_modules,EnvModules-method coerce,EnvModules,list-method coerce,list,EnvModules-method default_modules,EnvModules-method EnvModules,EnvModules-method EnvModules-class loaded_modules,EnvModules-method modulecmd,EnvModules-method names,EnvModules-method show,EnvModules-method [,EnvModules,ANY,ANY,ANY-method [[,EnvModules,ANY,ANY-method [[,EnvModules,ANY,missing-method [[<-,EnvModules,ANY,ANY,ANY-method [[<-,EnvModules,ANY,ANY-method [[<-,EnvModules-method
Toggles option 'eval' on the RMarkdown files	evalCode
Genome read coverage by transcript models	featureCoverage
Plot read distribution across genomic features	featuretypeCounts
Filter and plot DEG results	filterDEGs
Filter VCF files	filterVars
Generate feature ranges from TxDb	genFeatures
GO term enrichment analysis for large numbers of gene sets	goBarplot GOCluster_Report GOHyperGAll GOHyperGAll_Simplify GOHyperGAll_Subset makeCATdb
Import R Markdown file as workflow	importWF
Class '"INTERSECTset"'	as.list,INTERSECTset-method coerce,list,INTERSECTset-method complexitylevels,INTERSECTset-method intersectlist,INTERSECTset-method intersectmatrix,INTERSECTset-method INTERSECTset-class length,INTERSECTset-method names,INTERSECTset-method setlist,INTERSECTset-method show,INTERSECTset-method
Class '"LineWise"'	$,LineWise-method appendCodeLine,LineWise-method appendCodeLine<-,LineWise-method codeChunkStart codeChunkStart,LineWise-method codeLine,LineWise-method coerce,LineWise,list-method coerce,list,LineWise-method dependency,LineWise-method files,LineWise-method length,LineWise-method LineWise linewise linewise,LineWise-method LineWise-class names,LineWise-method replaceCodeLine,LineWise-method replaceCodeLine<-,LineWise-method rmdPath rmdPath,LineWise-method runInfo,LineWise-method show,LineWise-method status,LineWise-method stepName,LineWise-method [,LineWise,ANY,ANY,ANY-method [[,LineWise,ANY,missing-method [[<-,LineWise,ANY,ANY,ANY-method [[<-,LineWise,ANY,ANY-method
List/check the existence of command-line tools of a workflow	listCmdModules listCmdTools
Constructs SYSargs2 object from CWL param and targets files	loadWF loadWorkflow renderWF updateWF
Merge BAM files based on factor	mergeBamByFactor
Interface to allow full use of the Environment Modules system for Unix	module moduleAvail moduleClear moduleInit modulelist moduleload moduleUnload
Bar plot for intersect sets	olBarplot
Identify Range Overlaps for IRanges and GRanges Object	olRanges
Updates the output files paths in the 'SYSargs2' object	output_update
Set Intersect and Venn Diagram Functions	complexitylevels complexitylevels-methods intersectlist intersectlist-methods intersectmatrix intersectmatrix-methods overLapper setlist setlist-methods vennlist vennlist-methods
Plot feature coverage results	plotfeatureCoverage
Plot read distribution across genomic features	plotfeaturetypeCounts
Visualize SPR workflow and status	plotWF plotwfOutput renderPlotwf
Predict ORFs	predORF
Run custom read preprocessing functions	preprocessReads
Accessories function to modify the Command-line Version 1	appendParam printParam renameParam replaceParam subsetParam
Accessories function to modify the Command-line Version 2	appendParam2 printParam2 removeParam2 renameParam2 replaceParam2
Import sample comparisons from targets file	readComp
Render RMarkdown Logs Report	renderLogs
Render RMarkdown Report	renderReport
RPKM Normalization	returnRPKM
Runs DESeq2	run_DESeq2
Runs edgeR	run_edgeR
Execute SYSargs and SYSargs2	runCommandline
Differential abundance analysis for many range sets	runDiff
Execute SYSargsList	runWF
Translate SYSargsList back to a bash workflow	sal2bash
Translate SYSargsList back to a workflow template Rmarkdown file	sal2rmd
Scale spliced ranges to genome coordinates	scaleRanges
Quality reports for FASTQ files	seeFastq seeFastqPlot
Create an HTML table using DT package with fixed columns	showDF
Workflow Project Initiation	SPRproject
Subsetting SYSargs2 class slots	subsetWF
Symbolic links for IGV	symLink2bam
SYSargs accessor methods	cores cores-methods infile1 infile1-methods infile2 infile2-methods modules-methods other other-methods outfile1 outfile1-methods outpaths outpaths-methods reference reference-methods results results-methods SampleName-methods software software-methods sysargs sysargs-methods targetsheader-methods targetsin targetsin-methods targetsout targetsout-methods
Class '"SYSargs"'	coerce,list,SYSargs-method cores,SYSargs-method infile1,SYSargs-method infile2,SYSargs-method length,SYSargs-method modules,SYSargs-method names,SYSargs-method other,SYSargs-method outfile1,SYSargs-method outpaths,SYSargs-method reference,SYSargs-method results,SYSargs-method SampleName,SYSargs-method show,SYSargs-method software,SYSargs-method sysargs,SYSargs-method SYSargs-class targetsheader,SYSargs-method targetsin,SYSargs-method targetsout,SYSargs-method [,SYSargs,ANY,ANY,ANY-method
Class '"SYSargs2"'	$,SYSargs2-method baseCommand,SYSargs2-method clt clt,SYSargs2-method cmdlist,SYSargs2-method cmdToCwl cmdToCwl,SYSargs2-method cmdToCwl<- cmdToCwl<-,SYSargs2-method coerce,list,SYSargs2-method coerce,SYSargs2,list-method files files,SYSargs2-method infile1,SYSargs2-method infile2,SYSargs2-method input input,SYSargs2-method inputvars inputvars,SYSargs2-method internal_outfiles internal_outfiles,SYSargs2-method length,SYSargs2-method modules modules,SYSargs2-method names,SYSargs2-method output output,SYSargs2-method SampleName,SYSargs2-method show,SYSargs2-method status status,SYSargs2-method sysargs2 sysargs2,SYSargs2-method SYSargs2-class targets targets,SYSargs2-method targetsheader,SYSargs2-method wf wf,SYSargs2-method yamlinput,SYSargs2-method yamlinput<-,SYSargs2,ANY,ANY-method yamlinput<-,SYSargs2-method [,SYSargs2,ANY,ANY,ANY-method [[,SYSargs2,ANY,missing-method [[<-,SYSargs2,ANY,ANY,ANY-method [[<-,SYSargs2,ANY,ANY-method
SYSargsList Constructor	SYSargsList
Class '"SYSargsList"'	$,SYSargsList-method addResources addResources,SYSargsList-method appendCodeLine<- appendCodeLine<-,SYSargsList-method appendStep<- appendStep<-,SYSargsList-method baseCommand baseCommand,SYSargsList-method cmdlist cmdlist,SYSargsList-method codeLine codeLine,SYSargsList-method coerce,list,SYSargsList-method coerce,SYSargsList,list-method copyEnvir copyEnvir,SYSargsList-method dependency dependency,SYSargsList-method dependency<- dependency<-,SYSargsList-method getColumn getColumn,SYSargsList-method length,SYSargsList-method names,SYSargsList-method outfiles outfiles,SYSargsList-method projectInfo projectInfo,SYSargsList-method renameStep<- renameStep<-,SYSargsList-method replaceCodeLine<- replaceCodeLine<-,SYSargsList-method replaceStep<- replaceStep<-,SYSargsList-method runInfo runInfo,SYSargsList-method SampleName SampleName,SYSargsList-method SE SE,SYSargsList-method SE<- SE<-,SYSargsList-method show,SYSargsList-method statusWF statusWF,SYSargsList-method stepName stepName,SYSargsList-method stepsWF stepsWF,SYSargsList-method subset subset,SYSargsList-method sysargslist sysargslist,SYSargsList-method SYSargsList-class targetsheader targetsheader,SYSargsList-method targetsWF targetsWF,SYSargsList-method targets_connection targets_connection,SYSargsList-method updateColumn<- updateColumn<-,SYSargsList-method viewEnvir viewEnvir,SYSargsList-method yamlinput yamlinput,SYSargsList-method yamlinput<- yamlinput<-,SYSargsList-method [,SYSargsList,ANY,ANY,ANY-method [[,SYSargsList,ANY,missing-method [[<-,SYSargsList,ANY,ANY,ANY-method [[<-,SYSargsList,ANY,ANY-method
Constructs SYSargs object from param and targets files	systemArgs
Convert targets to list or data.frame	targets.as.df targets.as.list
Genome read coverage by transcript models	trimbatch
Collect information about the third-party software	tryCL tryCMD
Validation of the files or directories	tryPath
Generate Variant Report	combineVarReports variantReport varSummary
Plot 2-5 way Venn diagrams	vennPlot
Class '"VENNset"'	as.list,VENNset-method coerce,list,VENNset-method complexitylevels,VENNset-method intersectmatrix,VENNset-method length,VENNset-method names,VENNset-method setlist,VENNset-method show,VENNset-method vennlist,VENNset-method VENNset-class
Writeout SYSargsList object	write_SYSargsList
Write updated targets out to file from 'SYSargsList'	writeTargets
Write updated targets out to file	writeTargetsout
Generate targets file with reference	writeTargetsRef

Package: systemPipeR 2.11.2

systemPipeR: systemPipeR: workflow management and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

systemPipeR: Workflows collection

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