systemPipeRdata
This is the released version of systemPipeRdata; for the devel version, see systemPipeRdata.
systemPipeRdata: Workflow templates and sample data
Bioconductor version: Release (3.23)
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")):
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")
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")| systemPipeRdata: Workflow templates and sample data | HTML | R Script |
| WF: Basic Generic Template | 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 | 2.16.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.6.0) |
| Imports | methods, Biostrings, BiocGenerics, jsonlite, remotes |
| System Requirements | |
| URL | https://github.com/tgirke/systemPipeRdata |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | systemPipeRdata_2.16.0.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 |