- recipe bioconductor-scarray
Large-scale single-cell RNA-seq data manipulation with GDS files
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/SCArray.html
- License:
GPL-3
- Recipe:
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:
1.10.0-0,1.8.2-0,1.6.0-1,1.6.0-0,1.2.1-1,1.2.1-0,1.2.0-0,1.0.0-0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biocsingular:
>=1.18.0,<1.19.0- depends bioconductor-biocsingular:
>=1.18.0,<1.19.0a0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0- depends bioconductor-delayedarray:
>=0.28.0,<0.29.0a0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0- depends bioconductor-delayedmatrixstats:
>=1.24.0,<1.25.0a0- depends bioconductor-gdsfmt:
>=1.38.0,<1.39.0- depends bioconductor-gdsfmt:
>=1.38.0,<1.39.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0- depends bioconductor-singlecellexperiment:
>=1.24.0,<1.25.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- 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
myenvnamebeing 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>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-scarray/README.html)
