cageminer
This is the released version of cageminer; for the devel version, see cageminer.
Candidate Gene Miner
Bioconductor version: Release (3.23)
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
Author: Fabrício Almeida-Silva [aut, cre]
, Thiago Venancio [aut]
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
citation("cageminer")):
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")
BiocManager::install("cageminer")
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("cageminer")| Mining high-confidence candidate genes with cageminer | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation |
| Version | 1.18.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | ggplot2, rlang, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO |
| System Requirements | |
| URL | https://github.com/almeidasilvaf/cageminer |
| Bug Reports | https://support.bioconductor.org/t/cageminer |
See More
| Suggests | testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown, covr, sessioninfo |
| 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 | cageminer_1.18.0.tar.gz |
| Windows Binary (x86_64) | cageminer_1.18.0.zip |
| macOS Binary (big-sur-x86_64) | cageminer_1.18.0.tgz |
| macOS Binary (sonoma-arm64) | cageminer_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cageminer |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cageminer |
| Bioc Package Browser | https://code.bioconductor.org/browse/cageminer/ |
| Package Short Url | https://bioconductor.org/packages/cageminer/ |
| Package Downloads Report | Download Stats |