- recipe bioconductor-cageminer
Candidate Gene Miner
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.
- package bioconductor-cageminer¶
- depends bioconductor-bionero:
- depends bioconductor-genomeinfodb:
- depends bioconductor-genomicranges:
- depends bioconductor-ggbio:
- depends bioconductor-iranges:
- depends r-base:
- depends r-ggplot2:
- depends r-ggtext:
- depends r-reshape2:
- depends r-rlang:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-cageminer and update with:: mamba update bioconductor-cageminer
To create a new environment, run:
mamba create --name myenvname bioconductor-cageminer
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-cageminer:<tag> (see `bioconductor-cageminer/tags`_ for valid values for ``<tag>``)