recipe r-dartr

Functions are provided that facilitate the import and analysis of SNP (single nucleotide polymorphism) and silicodart (presence/absence) data. The main focus is on data generated by DarT (Diversity Arrays Technology). However, once SNP or related fragment presence/absence data from any source is imported into a genlight object many of the functions can be used. Functions are available for input and output of SNP and silicodart data, for reporting on and filtering on various criteria (e.g. CallRate, Heterozygosity, Reproducibility, maximum allele frequency). Advanced filtering is based on Linkage Disequilibrium and HWE (Hardy-Weinberg equilibrium). Other functions are available for visualization after PCoA (Principle Coordinate Analysis), or to facilitate transfer of data between genlight/genind objects and newhybrids, related, phylip, structure, faststructure packages.

Homepage:

https://CRAN.R-project.org/package=dartR

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-dartr/meta.yaml

package r-dartr

versions:

2.9.7-1,  2.9.7-0,  2.0.4-1,  2.0.4-0,  2.0.3-0,  1.9.9.1-1,  1.9.9.1-0,  1.9.6-0,  1.9.4-0, 

2.9.7-1,  2.9.7-0,  2.0.4-1,  2.0.4-0,  2.0.3-0,  1.9.9.1-1,  1.9.9.1-0,  1.9.6-0,  1.9.4-0,  1.1.11-2,  1.1.11-1,  1.1.11-0,  1.0.5-1,  1.0.5-0,  1.0-0

depends bioconductor-snprelate:

depends r-adegenet:

>=2.0.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-crayon:

depends r-dartr.data:

depends r-data.table:

depends r-dplyr:

depends r-fields:

depends r-foreach:

depends r-ggplot2:

depends r-gridextra:

depends r-mass:

depends r-patchwork:

depends r-plyr:

depends r-popgenreport:

depends r-raster:

depends r-reshape2:

depends r-shiny:

depends r-sp:

>=1.6.1

depends r-stampp:

depends r-stringr:

depends r-tidyr:

depends r-vegan:

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 r-dartr

and update with::

   mamba update r-dartr

To create a new environment, run:

mamba create --name myenvname r-dartr

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/r-dartr:<tag>

(see `r-dartr/tags`_ for valid values for ``<tag>``)

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