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:

/bioconductor-singler/meta.yaml

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:

2.4.0-0,  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, 

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-beachmat:

>=2.18.0,<2.19.0

depends bioconductor-beachmat:

>=2.18.0,<2.19.0a0

depends bioconductor-biocneighbors:

>=1.20.0,<1.21.0

depends bioconductor-biocneighbors:

>=1.20.0,<1.21.0a0

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-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

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:

depends r-rcpp:

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-singler

and update with::

   mamba update bioconductor-singler

To create a new environment, run:

mamba create --name myenvname bioconductor-singler

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-singler:<tag>

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

Download stats

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-singler/README.html)