recipe bioconductor-megadepth

megadepth: BigWig and BAM related utilities

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/megadepth.html

License:

Artistic-2.0

Recipe:

/bioconductor-megadepth/meta.yaml

This package provides an R interface to Megadepth by Christopher Wilks available at https://github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of a set of genomic regions across bigWig or BAM files. With this package, you can build base-pair coverage matrices for regions or annotations of your choice from BigWig files. Megadepth was used to create the raw files provided by https://bioconductor.org/packages/recount3.

package bioconductor-megadepth

(downloads) docker_bioconductor-megadepth

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.3-0,  1.0.0-1

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends r-base:

>=4.3,<4.4.0a0

depends r-cmdfun:

depends r-dplyr:

depends r-fs:

depends r-magrittr:

depends r-readr:

depends r-xfun:

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-megadepth

and update with::

   mamba update bioconductor-megadepth

To create a new environment, run:

mamba create --name myenvname bioconductor-megadepth

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-megadepth:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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