recipe bioconductor-planttfhunter

Identification and classification of plant transcription factors

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-planttfhunter/meta.yaml

planttfhunter is used to identify plant transcription factors (TFs) from protein sequence data and classify them into families and subfamilies using the classification scheme implemented in PlantTFDB. TFs are identified using pre-built hidden Markov model profiles for DNA-binding domains. Then, auxiliary and forbidden domains are used with DNA-binding domains to classify TFs into families and subfamilies (when applicable). Currently, TFs can be classified in 58 different TF families/subfamilies.

package bioconductor-planttfhunter

(downloads) docker_bioconductor-planttfhunter

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

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-planttfhunter

and update with::

   mamba update bioconductor-planttfhunter

To create a new environment, run:

mamba create --name myenvname bioconductor-planttfhunter

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-planttfhunter:<tag>

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

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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-planttfhunter/README.html)