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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 2.19.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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 | DiffBind |
| 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_2.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | systemPipeR_2.19.0.tgz |
| macOS Binary (sonoma-arm64) | systemPipeR_2.19.0.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 |