SeqGSEA
This is the development version of SeqGSEA; for the stable release version, see SeqGSEA.
Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing
Bioconductor version: Development (3.24)
The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene's differential expression and splicing, respectively.
Author: Xi Wang <Xi.Wang at newcastle.edu.au>
Maintainer: Xi Wang <Xi.Wang at dkfz.de>
citation("SeqGSEA")):
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("SeqGSEA")
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("SeqGSEA")| Gene set enrichment analysis of RNA-Seq data with the SeqGSEA package | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | GPL (>= 3) |
| Depends | Biobase, doParallel, DESeq2 |
| Imports | methods, biomaRt |
| System Requirements | |
| URL |
See More
| Suggests | GenomicRanges |
| 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 | SeqGSEA_1.53.0.tar.gz |
| Windows Binary (x86_64) | SeqGSEA_1.53.0.zip |
| macOS Binary (big-sur-x86_64) | SeqGSEA_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | SeqGSEA_1.53.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SeqGSEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SeqGSEA |
| Bioc Package Browser | https://code.bioconductor.org/browse/SeqGSEA/ |
| Package Short Url | https://bioconductor.org/packages/SeqGSEA/ |
| Package Downloads Report | Download Stats |