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

GPL2 / GPL-2

Recipe

/r-dartr/meta.yaml

package r-dartr

(downloads) docker_r-dartr

Versions

1.1.11-0, 1.0.5-1, 1.0.5-0, 1.0-0

Depends bioconductor-qvalue

Depends bioconductor-snprelate

Depends r-adegenet

>=2.0.0

Depends r-ape

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-data.table

Depends r-directlabels

Depends r-dismo

Depends r-doparallel

Depends r-foreach

Depends r-gdistance

Depends r-ggplot2

Depends r-hierfstat

Depends r-igraph

Depends r-leaflet

Depends r-mass

Depends r-mmod

Depends r-pca3d

Depends r-pegas

Depends r-plyr

Depends r-popgenreport

Depends r-reshape2

Depends r-rgdal

Depends r-rrblup

Depends r-seqinr

Depends r-snpassoc

Depends r-sp

Depends r-stampp

Depends r-stringr

Depends r-tidyr

Depends r-vegan

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install r-dartr

and update with:

conda update r-dartr

or use the docker container:

docker pull quay.io/biocontainers/r-dartr:<tag>

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