systemPipeR
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see systemPipeR.
systemPipeR: NGS workflow and report generation environment
Bioconductor version: 3.13
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.
Author: Thomas Girke
Maintainer: Thomas Girke <thomas.girke at ucr.edu>
citation("systemPipeR")):
Installation
To install this package, start R (version "4.1") 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")| systemPipeR and CWL | HTML | R Script |
| systemPipeR: Workflow design and reporting generation environment | HTML | R Script |
| systemPipeR: Workflows collection | HTML | R Script |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, ReportWriting, RiboSeq, SNP, Sequencing, Software, Workflow |
| Version | 1.26.3 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | Artistic-2.0 |
| Depends | Rsamtools(>= 1.31.2), Biostrings, ShortRead(>= 1.37.1), methods |
| Imports | GenomicRanges, GenomicFeatures(>= 1.31.3), SummarizedExperiment, VariantAnnotation(>= 1.25.11), rjson, ggplot2, limma, edgeR, DESeq2, GOstats, GO.db, annotate, pheatmap, batchtools, yaml, stringr, assertthat, magrittr, DOT, rsvg, IRanges, testthat, S4Vectors, crayon |
| 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://systempipe.org/ |
See More
| Suggests | BiocGenerics, ape, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager, systemPipeRdata, GenomicAlignments, grid, DT, dplyr, kableExtra |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | DiffBind, RNASeqR |
| Suggests Me | systemPipeRdata, systemPipeShiny, systemPipeTools |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeR_1.26.3.tar.gz |
| Windows Binary | systemPipeR_1.26.3.zip |
| macOS 10.13 (High Sierra) | systemPipeR_1.26.3.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 3.13 | Source Archive |