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>
citation("systemPipeR")):
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")| Overview | HTML | R Script |
| systemPipeR: Workflows collection | 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 | 2.6.3 |
| 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 |
| Linking To | |
| 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) |
| 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. |
| Enhances | |
| URL | https://systempipe.org/ https://github.com/tgirke/systemPipeR |
See More
| 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 |