recipe bioconductor-trigger

Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-trigger/meta.yaml

Links:

biotools: trigger, doi: 10.1038/nmeth.3252

This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.

package bioconductor-trigger

(downloads) docker_bioconductor-trigger

versions:
1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1, 

1.48.0-0,  1.46.0-0,  1.44.0-1,  1.44.0-0,  1.40.0-2,  1.40.0-1,  1.40.0-0,  1.38.0-0,  1.36.0-1,  1.36.0-0,  1.34.0-0,  1.32.0-0,  1.30.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0

depends bioconductor-qvalue:

>=2.34.0,<2.35.0a0

depends bioconductor-sva:

>=3.50.0,<3.51.0

depends bioconductor-sva:

>=3.50.0,<3.51.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends r-base:

>=4.3,<4.4.0a0

depends r-corpcor:

depends r-qtl:

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-trigger

and update with::

   mamba update bioconductor-trigger

To create a new environment, run:

mamba create --name myenvname bioconductor-trigger

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-trigger:<tag>

(see `bioconductor-trigger/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-trigger/README.html)