pairedGSEA
This is the development version of pairedGSEA; for the stable release version, see pairedGSEA.
Paired DGE and DGS analysis for gene set enrichment analysis
Bioconductor version: Development (3.24)
pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.
Author: Søren Helweg Dam [cre, aut]
, Lars Rønn Olsen [aut]
, Kristoffer Vitting-Seerup [aut]
Maintainer: Søren Helweg Dam <sohdam at dtu.dk>
citation("pairedGSEA")):
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("pairedGSEA")
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("pairedGSEA")| User Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, GeneSetEnrichment, ImmunoOncology, Pathways, RNASeq, Software, Transcription |
| Version | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4.0) |
| Imports | DESeq2, DEXSeq, limma, fgsea, msigdbr, sva, SummarizedExperiment, S4Vectors, BiocParallel, ggplot2, aggregation, stats, utils, methods, showtext |
| System Requirements | |
| URL | https://github.com/shdam/pairedGSEA |
| Bug Reports | https://github.com/shdam/pairedGSEA/issues |
See More
| Suggests | writexl, readxl, readr, rhdf5, plotly, testthat (>= 3.0.0), knitr, rmarkdown, BiocStyle, covr |
| 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 | pairedGSEA_1.13.0.tar.gz |
| Windows Binary (x86_64) | pairedGSEA_1.13.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | pairedGSEA_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | pairedGSEA_1.13.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/pairedGSEA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/pairedGSEA |
| Bioc Package Browser | https://code.bioconductor.org/browse/pairedGSEA/ |
| Package Short Url | https://bioconductor.org/packages/pairedGSEA/ |
| Package Downloads Report | Download Stats |