- recipe bioconductor-singler
Reference-Based Single-Cell RNA-Seq Annotation
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/SingleR.html
- License:
GPL-3 + file LICENSE
- Recipe:
Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
- package bioconductor-singler¶
- versions:
2.8.0-0,2.4.0-0,2.2.0-0,2.0.0-1,2.0.0-0,1.8.1-1,1.8.1-0,1.8.0-0,1.6.1-0,2.8.0-0,2.4.0-0,2.2.0-0,2.0.0-1,2.0.0-0,1.8.1-1,1.8.1-0,1.8.0-0,1.6.1-0,1.4.1-0,1.4.0-0,1.2.2-0,1.2.1-0,1.0.0-0- depends bioconductor-assorthead:
>=1.0.0,<1.1.0- depends bioconductor-assorthead:
>=1.0.0,<1.1.0a0- depends bioconductor-beachmat:
>=2.22.0,<2.23.0- depends bioconductor-beachmat:
>=2.22.0,<2.23.0a0- depends bioconductor-biocneighbors:
>=2.0.0,<2.1.0- depends bioconductor-biocneighbors:
>=2.0.0,<2.1.0a0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0- depends bioconductor-biocparallel:
>=1.40.0,<1.41.0a0- depends bioconductor-biocsingular:
>=1.22.0,<1.23.0- depends bioconductor-biocsingular:
>=1.22.0,<1.23.0a0- depends bioconductor-delayedarray:
>=0.32.0,<0.33.0- depends bioconductor-delayedarray:
>=0.32.0,<0.33.0a0- depends bioconductor-delayedmatrixstats:
>=1.28.0,<1.29.0- depends bioconductor-delayedmatrixstats:
>=1.28.0,<1.29.0a0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0- depends bioconductor-s4vectors:
>=0.44.0,<0.45.0a0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0- depends bioconductor-summarizedexperiment:
>=1.36.0,<1.37.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libcxx:
>=18- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.4,<4.5.0a0- depends r-matrix:
- depends r-rcpp:
- requirements:
- additional platforms:
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-singler and update with:: mamba update bioconductor-singler
To create a new environment, run:
mamba create --name myenvname bioconductor-singler
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-singler:<tag> (see `bioconductor-singler/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-singler/README.html)
