- recipe bioconductor-rgadem
de novo motif discovery
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/rGADEM.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: rgadem, doi: 10.1371/journal.pone.0016432
rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.
- package bioconductor-rgadem¶
- versions:
2.50.0-0
,2.48.0-0
,2.46.0-1
,2.46.0-0
,2.42.0-2
,2.42.0-1
,2.42.0-0
,2.40.0-0
,2.38.0-1
,2.50.0-0
,2.48.0-0
,2.46.0-1
,2.46.0-0
,2.42.0-2
,2.42.0-1
,2.42.0-0
,2.40.0-0
,2.38.0-1
,2.38.0-0
,2.36.0-0
,2.34.0-0
,2.32.0-1
,2.30.0-0
,2.28.0-0
,2.26.0-0
,2.24.0-0
,2.22.0-0
- depends bioconductor-biostrings:
>=2.70.0,<2.71.0
- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0
- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0
- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0
- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0
- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0
- depends bioconductor-iranges:
>=2.36.0,<2.37.0
- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0
- depends bioconductor-seqlogo:
>=1.68.0,<1.69.0
- depends bioconductor-seqlogo:
>=1.68.0,<1.69.0a0
- depends libblas:
>=3.9.0,<4.0a0
- depends libgcc-ng:
>=12
- depends liblapack:
>=3.9.0,<4.0a0
- depends r-base:
>=4.3,<4.4.0a0
- 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-rgadem and update with:: mamba update bioconductor-rgadem
To create a new environment, run:
mamba create --name myenvname bioconductor-rgadem
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-rgadem:<tag> (see `bioconductor-rgadem/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-rgadem/README.html)