recipe bioconductor-scvir

experimental inferface from R to scvi-tools

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-scvir/meta.yaml

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

package bioconductor-scvir

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-basilisk:

>=1.14.0,<1.15.0

depends bioconductor-biocfilecache:

>=2.10.0,<2.11.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-matrixgenerics:

>=1.14.0,<1.15.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-scater:

>=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-base:

>=4.3,<4.4.0a0

depends r-pheatmap:

depends r-reticulate:

depends r-shiny:

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-scvir

and update with::

   mamba update bioconductor-scvir

To create a new environment, run:

mamba create --name myenvname bioconductor-scvir

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-scvir:<tag>

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

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