geneslator
This is the development version of geneslator; to use it, please install the devel version of Bioconductor.
Geneslator, a tool for accurate gene name conversion
Bioconductor version: Development (3.24)
Geneslator is a comprehensive R package that performs gene identifier conversion and ortholog mapping. The tool integrates multiple cross-organism databases (NCBI, Ensembl, UniProt, GO, KEGG, Reactome, Wikipathways) and organism-specific resources within a single, coherent framework. Geneslator currently supports the following organisms: human, mouse, rat, yeast, worm, fly, zebrafish and arabidopsis.
Author: Giovanni Micale [aut, cre]
, Giulia Cavallaro [aut]
, Grete Francesca Privitera [aut]
Maintainer: Giovanni Micale <giovanni.micale at unict.it>
citation("geneslator")):
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("geneslator")
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("geneslator")| Geneslator R package for gene annotation | HTML | R Script |
| Reference Manual |
Details
| biocViews | AnnotationData, Arabidopsis_thaliana, Caenorhabditis_elegans, Danio_rerio, Drosophila_melanogaster, Homo_sapiens, Mus_musculus, OrgDb, Organism, OrganismDb, PackageType, Rattus_norvegicus, Saccharomyces_cerevisiae, zebrafish |
| Version | 0.99.10 |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | AnnotationDbi, methods, IRanges, utils, jsonlite, DBI, curl, zen4R, BiocFileCache, KEGGREST |
| System Requirements | |
| URL | https://github.com/knowmics-lab/geneslator |
| Bug Reports | https://github.com/knowmics-lab/geneslator/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | geneslator_0.99.10.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/geneslator/ |
| Package Downloads Report | Download Stats |