systemPipeR

DOI: 10.18129/B9.bioc.systemPipeR  

systemPipeR: workflow management and report generation environment

Bioconductor version: Release (3.17)

systemPipeR is a generic 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 a consistently implemented sample annotation infrastructure. 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.

Author: Thomas Girke

Maintainer: Thomas Girke <thomas.girke at ucr.edu>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("systemPipeR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("systemPipeR")

 

HTML	R Script	Overview
HTML	R Script	systemPipeR: Workflows collection
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, ReportWriting, RiboSeq, SNP, Sequencing, Software, WorkflowManagement, WorkflowStep
Version	2.6.3
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	Artistic-2.0
Depends	Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods
Imports	GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures(>= 1.31.3), VariantAnnotation(>= 1.25.11)
SystemRequirements	systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system.
Enhances
URL	https://systempipe.org/ https://github.com/tgirke/systemPipeR
Depends On Me
Imports Me	DiffBind
Suggests Me	systemPipeRdata, systemPipeShiny, systemPipeTools
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	systemPipeR_2.6.3.tar.gz
Windows Binary	systemPipeR_2.6.3.zip
macOS Binary (x86_64)	systemPipeR_2.6.3.tgz
macOS Binary (arm64)	systemPipeR_2.6.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/systemPipeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/systemPipeR
Bioc Package Browser	https://code.bioconductor.org/browse/systemPipeR/
Package Short Url	https://bioconductor.org/packages/systemPipeR/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive