recipe bioconductor-garfield

GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/garfield.html

License:

GPL-3

Recipe:

/bioconductor-garfield/meta.yaml

GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).

package bioconductor-garfield

(downloads) docker_bioconductor-garfield

versions:
1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0, 

1.30.0-1,  1.30.0-0,  1.28.0-0,  1.26.0-2,  1.26.0-1,  1.26.0-0,  1.22.0-2,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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-garfield

and update with::

   mamba update bioconductor-garfield

To create a new environment, run:

mamba create --name myenvname bioconductor-garfield

with myenvname being 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-garfield:<tag>

(see `bioconductor-garfield/tags`_ for valid values for ``<tag>``)

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Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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