recipe bioconductor-scdd

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-scdd/meta.yaml

This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

package bioconductor-scdd

versions:

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0, 

1.26.0-0,  1.24.0-0,  1.22.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.6.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-ebseq:

>=2.0.0,<2.1.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scran:

>=1.30.0,<1.31.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-arm:

depends r-base:

>=4.3,<4.4.0a0

depends r-fields:

depends r-ggplot2:

depends r-mclust:

depends r-outliers:

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-scdd

and update with::

   mamba update bioconductor-scdd

To create a new environment, run:

mamba create --name myenvname bioconductor-scdd

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-scdd:<tag>

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

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