recipe bioconductor-lea

LEA: an R package for Landscape and Ecological Association Studies

Homepage:

https://bioconductor.org/packages/3.20/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:
3.22.0-0,  3.18.0-0,  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, 

3.22.0-0,  3.18.0-0,  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:

  • on libblas >=3.9.0,<4.0a0

  • on libgcc >=14

  • on liblapack >=3.9.0,<4.0a0

  • on liblzma >=5.8.2,<6.0a0

  • on libzlib >=1.3.1,<2.0a0

  • on r-base >=4.5,<4.6.0a0

Additional platforms:

Installation

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-lea

to add into an existing workspace instead, run:

pixi add bioconductor-lea

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-lea

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-lea

with envname being the name of the desired environment.

Container

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

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)