recipe bioconductor-muscat

Multi-sample multi-group scRNA-seq data analysis tools

Homepage

https://bioconductor.org/packages/3.14/bioc/html/muscat.html

License

GPL-3

Recipe

/bioconductor-muscat/meta.yaml

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

package bioconductor-muscat

Versions

1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

Depends

• bioconductor-biocparallel >=1.28.0,<1.29.0

• bioconductor-complexheatmap >=2.10.0,<2.11.0

• bioconductor-deseq2 >=1.34.0,<1.35.0

• bioconductor-edger >=3.36.0,<3.37.0

• bioconductor-limma >=3.50.0,<3.51.0

• bioconductor-s4vectors >=0.32.0,<0.33.0

• bioconductor-scater >=1.22.0,<1.23.0

• bioconductor-scuttle >=1.4.0,<1.5.0

• bioconductor-singlecellexperiment >=1.16.0,<1.17.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-variancepartition >=1.24.0,<1.25.0

• r-base >=4.1,<4.2.0a0

• r-blme

• r-data.table

• r-dplyr

• r-ggplot2

• r-glmmtmb

• r-lme4

• r-lmertest

• r-matrix

• r-matrixstats

• r-progress

• r-purrr

• r-scales

• r-sctransform

• r-viridis

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-muscat

and update with:

conda update bioconductor-muscat

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-muscat:<tag>

(see bioconductor-muscat/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-muscat/README.html)