This is the development version of cageminer; to use it, please install the devel version of Bioconductor.
Candidate Gene Miner
Bioconductor version: Development (3.14)
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.
Maintainer: Fabrício Almeida-Silva <fabricio_almeidasilva at hotmail.com>
Citation (from within R,
To install this package, start R (version
“4.1”) and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("cageminer")
For older versions of R, please refer to the appropriate
To view documentation for the version of this package installed
in your system, start R and enter:
|Mining high-confidence candidate genes with cageminer|
|biocViews||FunctionalGenomics, FunctionalPrediction, GeneExpression, GenomeWideAssociation, Network, NetworkEnrichment, SNP, Software, VariantAnnotation|
|In Bioconductor since||BioC 3.14 (R-4.1)|
|Depends||R (>= 4.1)|
|Imports||ggplot2, ggbio, ggtext, GenomeInfoDb, GenomicRanges, IRanges, reshape2, methods, BioNERO|
|Suggests||testthat (>= 3.0.0), SummarizedExperiment, knitr, BiocStyle, rmarkdown|
|Depends On Me|
|Links To Me|
Installation instructions to use this
package in your R session.
Read more here: Source link