recipe bioconductor-scarray

Large-scale single-cell RNA-seq data manipulation with GDS files

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/SCArray.html

License:

GPL-3

Recipe:

/bioconductor-scarray/meta.yaml

Provides large-scale single-cell RNA-seq data manipulation using Genomic Data Structure (GDS) files. It combines dense and sparse matrices stored in GDS files and the Bioconductor infrastructure framework (SingleCellExperiment and DelayedArray) to provide out-of-memory data storage and large-scale manipulation using the R programming language.

package bioconductor-scarray

versions:

1.8.2-0,  1.6.0-1,  1.6.0-0,  1.2.1-1,  1.2.1-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.34.0,<1.35.0

depends bioconductor-biocsingular:

>=1.16.0,<1.17.0

depends bioconductor-delayedarray:

>=0.26.0,<0.27.0

depends bioconductor-delayedmatrixstats:

>=1.22.0,<1.23.0

depends bioconductor-gdsfmt:

>=1.36.0,<1.37.0

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 libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-matrix:

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-scarray

and update with::

   mamba update bioconductor-scarray

To create a new environment, run:

mamba create --name myenvname bioconductor-scarray

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-scarray:<tag>

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

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