recipe bioconductor-celaref

Single-cell RNAseq cell cluster labelling by reference

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/celaref.html

License:

GPL-3

Recipe:

/bioconductor-celaref/meta.yaml

After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).

package bioconductor-celaref

versions:

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0, 

1.20.0-0,  1.18.0-0,  1.16.0-0,  1.12.0-0,  1.10.0-0,  1.8.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.0.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-delayedarray:

>=0.28.0,<0.29.0

depends bioconductor-mast:

>=1.28.0,<1.29.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-ggplot2:

depends r-magrittr:

depends r-matrix:

depends r-readr:

depends r-rlang:

depends r-tibble:

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-celaref

and update with::

   mamba update bioconductor-celaref

To create a new environment, run:

mamba create --name myenvname bioconductor-celaref

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-celaref:<tag>

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

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