recipe bioconductor-demuxmix

Demultiplexing oligo-barcoded scRNA-seq data using regression mixture models

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-demuxmix/meta.yaml

A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

package bioconductor-demuxmix

(downloads) docker_bioconductor-demuxmix

versions:

1.4.0-0,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-gridextra:

depends r-mass:

depends r-matrix:

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-demuxmix

and update with::

   mamba update bioconductor-demuxmix

To create a new environment, run:

mamba create --name myenvname bioconductor-demuxmix

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-demuxmix:<tag>

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