recipe bioconductor-comapr

Crossover analysis and genetic map construction

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/comapr.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-comapr/meta.yaml

comapr detects crossover intervals for single gametes from their haplotype states sequences and stores the crossovers in GRanges object. The genetic distances can then be calculated via the mapping functions using estimated crossover rates for maker intervals. Visualisation functions for plotting interval-based genetic map or cumulative genetic distances are implemented, which help reveal the variation of crossovers landscapes across the genome and across individuals.

package bioconductor-comapr

versions:

1.4.0-0,  1.2.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-gviz:

>=1.44.0,<1.45.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-dplyr:

depends r-foreach:

depends r-ggplot2:

depends r-gridextra:

depends r-matrix:

depends r-plotly:

depends r-plyr:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-rlang:

depends r-scales:

depends r-tidyr:

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-comapr

and update with::

   mamba update bioconductor-comapr

To create a new environment, run:

mamba create --name myenvname bioconductor-comapr

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-comapr:<tag>

(see `bioconductor-comapr/tags`_ for valid values for ``<tag>``)

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Link to this page

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