recipe bioconductor-lea

LEA: an R package for Landscape and Ecological Association Studies

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-lea/meta.yaml

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.

package bioconductor-lea

(downloads) docker_bioconductor-lea

versions:
3.14.0-0,  3.12.2-0,  3.10.0-1,  3.10.0-0,  3.6.0-2,  3.6.0-1,  3.6.0-0,  3.4.0-0,  3.2.0-1, 

3.14.0-0,  3.12.2-0,  3.10.0-1,  3.10.0-0,  3.6.0-2,  3.6.0-1,  3.6.0-0,  3.4.0-0,  3.2.0-1,  3.2.0-0,  3.0.0-0,  2.8.0-0,  2.6.0-1,  2.6.0-0,  2.4.0-0

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

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-lea

and update with::

   mamba update bioconductor-lea

To create a new environment, run:

mamba create --name myenvname bioconductor-lea

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-lea:<tag>

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