recipe bioconductor-smartid

Scoring and Marker Selection Method Based on Modified TF-IDF

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-smartid/meta.yaml

This package enables automated selection of group specific signature, especially for rare population. The package is developed for generating specifc lists of signature genes based on Term Frequency-Inverse Document Frequency (TF-IDF) modified methods. It can also be used as a new gene-set scoring method or data transformation method. Multiple visualization functions are implemented in this package.

package bioconductor-smartid

(downloads) docker_bioconductor-smartid

versions:

1.2.0-0

depends bioconductor-sparsematrixstats:

>=1.18.0,<1.19.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-matrix:

depends r-mclust:

depends r-mixtools:

depends r-tidyr:

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-smartid

and update with::

   mamba update bioconductor-smartid

To create a new environment, run:

mamba create --name myenvname bioconductor-smartid

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-smartid:<tag>

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