recipe bioconductor-cepo

Cepo for the identification of differentially stable genes

Homepage:

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

License:

MIT + file LICENSE

Recipe:

/bioconductor-cepo/meta.yaml

Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

package bioconductor-cepo

versions:

1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-delayedarray:

>=0.26.0,<0.27.0

depends bioconductor-delayedmatrixstats:

>=1.22.0,<1.23.0

depends bioconductor-gseabase:

>=1.62.0,<1.63.0

depends bioconductor-hdf5array:

>=1.28.0,<1.29.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-patchwork:

depends r-reshape2:

depends r-rlang:

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-cepo

and update with::

   mamba update bioconductor-cepo

To create a new environment, run:

mamba create --name myenvname bioconductor-cepo

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-cepo:<tag>

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