recipe bioconductor-metagene2

A package to produce metagene plots

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/metagene2.html

License:

Artistic-2.0

Recipe:

/bioconductor-metagene2/meta.yaml

This package produces metagene plots to compare coverages of sequencing experiments at selected groups of genomic regions. It can be used for such analyses as assessing the binding of DNA-interacting proteins at promoter regions or surveying antisense transcription over the length of a gene. The metagene2 package can manage all aspects of the analysis, from normalization of coverages to plot facetting according to experimental metadata. Bootstraping analysis is used to provide confidence intervals of per-sample mean coverages.

package bioconductor-metagene2

versions:

1.18.0-0,  1.16.0-0,  1.14.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-purrr:

depends r-r6:

>=2.0

depends r-reshape2:

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-metagene2

and update with::

   mamba update bioconductor-metagene2

To create a new environment, run:

mamba create --name myenvname bioconductor-metagene2

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-metagene2:<tag>

(see `bioconductor-metagene2/tags`_ for valid values for ``<tag>``)

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