recipe bioconductor-scrnaseq

Collection of Public Single-Cell RNA-Seq Datasets

Homepage:

https://bioconductor.org/packages/3.17/data/experiment/html/scRNAseq.html

License:

CC0

Recipe:

/bioconductor-scrnaseq/meta.yaml

Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

package bioconductor-scrnaseq

(downloads) docker_bioconductor-scrnaseq

versions:
2.14.0-02.12.0-02.8.0-12.8.0-02.6.1-02.4.0-12.4.0-02.3.17-02.2.0-0

2.14.0-02.12.0-02.8.0-12.8.0-02.6.1-02.4.0-12.4.0-02.3.17-02.2.0-01.99.8-01.10.0-11.8.0-01.6.0-0

depends bioconductor-annotationdbi:

>=1.62.0,<1.63.0

depends bioconductor-annotationhub:

>=3.8.0,<3.9.0

depends bioconductor-biocgenerics:

>=0.46.0,<0.47.0

depends bioconductor-data-packages:

>=20230706

depends bioconductor-ensembldb:

>=2.24.0,<2.25.0

depends bioconductor-experimenthub:

>=2.8.0,<2.9.0

depends bioconductor-genomicfeatures:

>=1.52.0,<1.53.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-singlecellexperiment:

>=1.22.0,<1.23.0

depends bioconductor-summarizedexperiment:

>=1.30.0,<1.31.0

depends curl:

depends r-base:

>=4.3,<4.4.0a0

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-scrnaseq

and update with::

   mamba update bioconductor-scrnaseq

To create a new environment, run:

mamba create --name myenvname bioconductor-scrnaseq

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-scrnaseq:<tag>

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

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