gesel
This is the development version of gesel; to use it, please install the devel version of Bioconductor.
Search for Interesting Gene Sets
Bioconductor version: Development (3.24)
Query the gesel indices to identify interesting gene sets. Users can test for enrichment in their own list of genes and/or search by text in the set names or descriptions. The indices can be hosted remotely or on a local filesystem.
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("gesel")):
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("gesel")
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("gesel")| Working with the Gesel database | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DataImport, GeneSetEnrichment, Pathways, Software |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | utils, methods, rappdirs, httr2, Rcpp |
| System Requirements | |
| URL | https://github.com/gesel-inc/gesel-R |
| Bug Reports | https://github.com/gesel-inc/gesel-R/issues |
See More
| Suggests | BiocStyle, knitr, testthat, rmarkdown, S4Vectors, IRanges |
| Linking To | assorthead, Rcpp |
| 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 | gesel_0.99.5.tar.gz |
| Windows Binary (x86_64) | gesel_0.99.5.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | gesel_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | gesel_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/gesel |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gesel |
| Bioc Package Browser | https://code.bioconductor.org/browse/gesel/ |
| Package Short Url | https://bioconductor.org/packages/gesel/ |
| Package Downloads Report | Download Stats |