recipe bioconductor-scmultiome

Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets

Homepage:

https://bioconductor.org/packages/3.18/data/experiment/html/scMultiome.html

License:

CC BY-SA 4.0

Recipe:

/bioconductor-scmultiome/meta.yaml

Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.

package bioconductor-scmultiome

versions:

1.2.0-0,  1.0.0-0

depends bioconductor-annotationhub:

>=3.10.0,<3.11.0

depends bioconductor-data-packages:

>=20231203

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-experimenthub:

>=2.10.0,<2.11.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-hdf5array:

>=1.30.0,<1.31.0

depends bioconductor-multiassayexperiment:

>=1.28.0,<1.29.0

depends bioconductor-rhdf5:

>=2.46.0,<2.47.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-singlecellexperiment:

>=1.24.0,<1.25.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends curl:

depends r-azurestor:

depends r-base:

>=4.3,<4.4.0a0

depends r-checkmate:

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-scmultiome

and update with::

   mamba update bioconductor-scmultiome

To create a new environment, run:

mamba create --name myenvname bioconductor-scmultiome

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-scmultiome:<tag>

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

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