recipe bioconductor-gigsea

Genotype Imputed Gene Set Enrichment Analysis

Homepage:

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

License:

LGPL-3

Recipe:

/bioconductor-gigsea/meta.yaml

We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.

package bioconductor-gigsea

(downloads) docker_bioconductor-gigsea

versions:
1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0, 

1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-locfdr:

depends r-mass:

depends r-matrix:

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-gigsea

and update with::

   mamba update bioconductor-gigsea

To create a new environment, run:

mamba create --name myenvname bioconductor-gigsea

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-gigsea:<tag>

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

Download stats

Link to this page

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

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-gigsea/README.html)