systemPipeRdata

This is the development version of systemPipeRdata; for the stable release version, see systemPipeRdata.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2

systemPipeRdata: Workflow templates and sample data

Bioconductor version: Development (3.24)

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

Author: Thomas Girke

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

Citation (from within R, enter citation("systemPipeRdata")):

Thomas Girke. systemPipeRdata: systemPipeRdata: Workflow templates and sample data. doi:10.18129/B9.bioc.systemPipeRdata, R package version 2.17.1, https://bioconductor.org/packages/systemPipeRdata.

Generated from the package metadata; it may differ from the package's own citation.

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("systemPipeRdata")

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("systemPipeRdata")

WF: Basic Generic Template	HTML	R Script
WF: BLAST Template	HTML	R Script
WF: Cheminformatics Drug Similarity Template	HTML	R Script
WF: Basic Single Cell Template	HTML	R Script
WF: ChIP-Seq Workflow Template	HTML	R Script
systemPipeRdata: Workflow templates and sample data	HTML	R Script
WF: RIBO-Seq Workflow Template	HTML	R Script
WF: RNA-Seq Workflow Template	HTML	R Script
WF: VAR-Seq Template	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, ExperimentHubSoftware, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep
Version	2.17.1
In Bioconductor since	BioC 3.2 (R-3.2) (11 years)
License	Artistic-2.0
Depends	R (>= 3.6.0)
Imports	methods, Biostrings, BiocGenerics, jsonlite, remotes, BiocFileCache
System Requirements
URL	https://github.com/tgirke/systemPipeRdata

Suggests	GenomicFeatures, DT, txdbmaker, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr, gert
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	systemPipeR, systemPipeShiny
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	systemPipeRdata_2.17.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/systemPipeRdata
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/systemPipeRdata
Package Short Url	https://bioconductor.org/packages/systemPipeRdata/
Package Downloads Report	Download Stats