recipe bioconductor-cageminer

Candidate Gene Miner

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/cageminer.html

License:

GPL-3

Recipe:

/bioconductor-cageminer/meta.yaml

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

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-bionero >=1.6.0,<1.7.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-ggbio >=1.46.0,<1.47.0

• bioconductor-iranges >=2.32.0,<2.33.0

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-ggtext

• r-reshape2

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-cageminer

and update with:

conda update bioconductor-cageminer

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-cageminer:<tag>

(see bioconductor-cageminer/tags for valid values for <tag>)

Download stats

Link to this page

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