Package Recipe 'r-dartr'

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:

2.9.9.5-0, 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,

2.9.9.5-0, 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:

on bioconductor-snprelate
on libxml2
on r-adegenet >=2.0.0
on r-ape
on r-base >=4.4,<4.5.0a0
on r-crayon
on r-dartr.data
on r-data.table
on r-dplyr
on r-fields
on r-foreach
on r-ggplot2
on r-gridextra
on r-gsubfn
on r-mass
on r-patchwork
on r-plyr
on r-popgenreport
on r-purrr
on r-raster
on r-reshape2
on r-shiny
on r-sp >=1.6.1
on r-stampp
on r-stringr
on r-terra >=1.8_5
on r-tidyr

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 r-dartr

to add into an existing workspace instead, run:

pixi add r-dartr

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 r-dartr

Alternatively, to install into a new environment, run:

conda create -n envname r-dartr

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/r-dartr:<tag>

(see r-dartr/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¶

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