recipe bioconductor-pwmenrich

PWM enrichment analysis

Homepage:

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

License:

LGPL (>= 2)

Recipe:

/bioconductor-pwmenrich/meta.yaml

Links:

biotools: pwmenrich, doi: 10.1038/nmeth.3252

A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

package bioconductor-pwmenrich

(downloads) docker_bioconductor-pwmenrich

versions:
4.42.0-0,  4.38.0-0,  4.36.0-0,  4.34.0-0,  4.30.0-0,  4.28.1-0,  4.26.0-1,  4.26.0-0,  4.23.0-0, 

4.42.0-0,  4.38.0-0,  4.36.0-0,  4.34.0-0,  4.30.0-0,  4.28.1-0,  4.26.0-1,  4.26.0-0,  4.23.0-0,  4.22.0-0,  4.20.0-1,  4.18.0-0,  4.16.0-0,  4.14.0-0

depends bioconductor-biocgenerics:

>=0.52.0,<0.53.0

depends bioconductor-biostrings:

>=2.74.0,<2.75.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-seqlogo:

>=1.72.0,<1.73.0

depends r-base:

>=4.4,<4.5.0a0

depends r-evd:

depends r-gdata:

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-pwmenrich

and update with::

   mamba update bioconductor-pwmenrich

To create a new environment, run:

mamba create --name myenvname bioconductor-pwmenrich

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-pwmenrich:<tag>

(see `bioconductor-pwmenrich/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-pwmenrich/README.html)