recipe bioconductor-scdesign3

A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/scDesign3.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-scdesign3/meta.yaml

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real data. Using a unified probabilistic model for single-cell and spatial omics data, scDesign3 infers biologically meaningful parameters; assesses the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations; and generates in silico negative and positive controls for benchmarking computational tools.

package bioconductor-scdesign3

versions:

1.0.0-0

depends bioconductor-biocparallel:

>=1.36.0,<1.37.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-gamlss:

depends r-gamlss.dist:

depends r-ggplot2:

depends r-irlba:

depends r-matrix:

depends r-matrixstats:

depends r-mclust:

depends r-mgcv:

depends r-mvtnorm:

depends r-pbmcapply:

depends r-rvinecopulib:

depends r-tibble:

depends r-umap:

depends r-viridis:

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-scdesign3

and update with::

   mamba update bioconductor-scdesign3

To create a new environment, run:

mamba create --name myenvname bioconductor-scdesign3

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-scdesign3:<tag>

(see `bioconductor-scdesign3/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-scdesign3/README.html)