recipe bioconductor-breakpointr

Find breakpoints in Strand-seq data

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/breakpointR.html

License:

file LICENSE

Recipe:

/bioconductor-breakpointr/meta.yaml

This package implements functions for finding breakpoints, plotting and export of Strand-seq data.

package bioconductor-breakpointr

versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0, 

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.2.0-1,  1.0.0-1,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-breakpointrdata:

>=1.24.0,<1.25.0

depends bioconductor-genomeinfodb:

>=1.42.0,<1.43.0

depends bioconductor-genomicalignments:

>=1.42.0,<1.43.0

depends bioconductor-genomicranges:

>=1.58.0,<1.59.0

depends bioconductor-iranges:

>=2.40.0,<2.41.0

depends bioconductor-rsamtools:

>=2.22.0,<2.23.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-doparallel:

depends r-foreach:

depends r-ggplot2:

depends r-gtools:

requirements:

additional platforms:

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-breakpointr

and update with::

   mamba update bioconductor-breakpointr

To create a new environment, run:

mamba create --name myenvname bioconductor-breakpointr

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-breakpointr:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-breakpointr/README.html)