recipe bioconductor-targetscore

TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-targetscore/meta.yaml

Links:

biotools: targetscore, doi: 10.1093/bioinformatics/btt599

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

package bioconductor-targetscore

(downloads) docker_bioconductor-targetscore

versions:
1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0, 

1.44.0-0,  1.40.0-0,  1.38.0-0,  1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-matrix:

depends r-pracma:

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-targetscore

and update with::

   mamba update bioconductor-targetscore

To create a new environment, run:

mamba create --name myenvname bioconductor-targetscore

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-targetscore:<tag>

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