recipe bioconductor-muscat

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

Homepage:

https://bioconductor.org/packages/3.18/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:

1.16.0-0,  1.14.0-0,  1.12.0-0,  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:

>=1.36.0,<1.37.0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends bioconductor-deseq2:

>=1.42.0,<1.43.0

depends bioconductor-edger:

>=4.0.0,<4.1.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-scuttle:

>=1.12.0,<1.13.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-variancepartition:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-blme:

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-glmmtmb:

depends r-lme4:

depends r-lmertest:

depends r-matrix:

depends r-matrixstats:

depends r-progress:

depends r-purrr:

depends r-scales:

depends r-sctransform:

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-muscat

and update with::

   mamba update bioconductor-muscat

To create a new environment, run:

mamba create --name myenvname bioconductor-muscat

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-muscat:<tag>

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

Download stats

Link to this page

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