systemPipeRdata
This is the development version of systemPipeRdata; for the stable release version, see systemPipeRdata.
systemPipeRdata: Workflow templates and sample data
Bioconductor version: Development (3.20)
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("systemPipeRdata")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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")| Basic Generic Template | HTML | R Script |
| systemPipeRdata: Workflow templates and sample data | HTML | R Script |
| WF: Basic Single Cell Template | HTML | R Script |
| WF: BLAST Template | HTML | R Script |
| WF: Cheminformatics Drug Similarity Template | HTML | R Script |
| WF: ChIP-Seq Workflow Template | 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, DataImport, ExperimentData, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, Infrastructure, MethylSeq, QualityControl, RNASeq, RiboSeq, SNP, Sequencing, WorkflowStep |
| Version | 2.9.3 |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | methods, Biostrings, BiocGenerics, jsonlite, remotes |
| System Requirements | |
| URL | https://github.com/tgirke/systemPipeRdata https://systempipe.org/ |
See More
| Suggests | GenomicFeatures, GenomicRanges, IRanges, Rsamtools, ShortRead, rtracklayer, RUnit, BiocStyle, knitr, rmarkdown, systemPipeR, kableExtra, magrittr, dplyr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | systemPipeR, systemPipeShiny |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeRdata_2.9.3.tar.gz |
| Windows Binary | |
| macOS Binary (x86_64) | |
| macOS Binary (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 |