systemPipeR
This is the development version of systemPipeR; for the stable release version, see systemPipeR.
systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis
Bioconductor version: Development (3.23)
systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke at ucr.edu>
citation("systemPipeR")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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")| Overview | HTML | R Script |
| systemPipeR: Workflow Templates | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, ReportWriting, RiboSeq, SNP, Sequencing, Software, WorkflowManagement, WorkflowStep |
| Version | 2.17.2 |
| In Bioconductor since | BioC 3.0 (R-3.1) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0), Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods |
| Imports | GenomicRanges, SummarizedExperiment, ggplot2, yaml, stringr, magrittr, S4Vectors, crayon, BiocGenerics, htmlwidgets |
| System Requirements | 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. |
| URL | https://github.com/tgirke/systemPipeR |
See More
| Suggests | BiocStyle, knitr, rmarkdown, systemPipeRdata, GenomicAlignments, grid, dplyr, testthat, rjson, annotate, AnnotationDbi, kableExtra, GO.db, GenomeInfoDb, DT, rtracklayer, limma, edgeR, DESeq2, IRanges, batchtools, GenomicFeatures, txdbmaker, GenomeInfoDbData, VariantAnnotation(>= 1.25.11) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | systemPipeShiny, systemPipeTools, systemPipeRdata |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeR_2.17.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | systemPipeR_2.17.1.tgz |
| macOS Binary (sonoma-arm64) | |
| 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 |