recipe bioconductor-metagene

A package to produce metagene plots

Homepage:

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

License:

Artistic-2.0 | file LICENSE

Recipe:

/bioconductor-metagene/meta.yaml

This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.

package bioconductor-metagene

versions:

2.31.0-0,  2.30.0-0,  2.26.0-0,  2.24.0-0,  2.20.0-0,  2.18.0-0,  2.16.0-1,  2.14.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-ensdb.hsapiens.v86:

>=2.99.0,<2.100.0

depends bioconductor-ensembldb:

>=2.24.0,<2.25.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicalignments:

>=1.36.0,<1.37.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-rsamtools:

>=2.16.0,<2.17.0

depends bioconductor-rtracklayer:

>=1.60.0,<1.61.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-ggplot2:

depends r-gplots:

depends r-magrittr:

depends r-matrixstats:

depends r-purrr:

depends r-r6:

>=2.0

depends r-stringr:

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-metagene

and update with::

   mamba update bioconductor-metagene

To create a new environment, run:

mamba create --name myenvname bioconductor-metagene

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-metagene:<tag>

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

Download stats

Link to this page

Render an 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-metagene/README.html)