rgsepd
This is the development version of rgsepd; for the stable release version, see rgsepd.
Gene Set Enrichment / Projection Displays
Bioconductor version: Development (3.24)
R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.
Author: Karl Stamm
Maintainer: Karl Stamm <karl.stamm at gmail.com>
citation("rgsepd")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("rgsepd")
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("rgsepd")| An Introduction to the rgsepd package | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Software |
| Version | 1.45.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.2.0), DESeq2, goseq(>= 1.28) |
| Imports | gplots, biomaRt, org.Hs.eg.db, GO.db, SummarizedExperiment, AnnotationDbi |
| System Requirements | |
| URL |
See More
| Suggests | boot, tools, BiocGenerics, knitr, xtable |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | rgsepd_1.45.0.tar.gz |
| Windows Binary (x86_64) | rgsepd_1.45.0.zip |
| macOS Binary (big-sur-x86_64) | rgsepd_1.45.0.tgz |
| macOS Binary (sonoma-arm64) | rgsepd_1.45.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rgsepd |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rgsepd |
| Bioc Package Browser | https://code.bioconductor.org/browse/rgsepd/ |
| Package Short Url | https://bioconductor.org/packages/rgsepd/ |
| Package Downloads Report | Download Stats |