recipe bioconductor-clustifyr

Classifier for Single-cell RNA-seq Using Cell Clusters

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/clustifyr.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-clustifyr/meta.yaml

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

package bioconductor-clustifyr

versions:

1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.5.1-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends bioconductor-fgsea:

>=1.32.0,<1.33.0

depends bioconductor-s4vectors:

>=0.44.0,<0.45.0

depends bioconductor-singlecellexperiment:

>=1.28.0,<1.29.0

depends bioconductor-summarizedexperiment:

>=1.36.0,<1.37.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cowplot:

depends r-dplyr:

depends r-entropy:

depends r-ggplot2:

depends r-httr:

depends r-matrix:

depends r-matrixstats:

depends r-proxy:

depends r-rlang:

depends r-scales:

depends r-seuratobject:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-clustifyr

and update with::

   mamba update bioconductor-clustifyr

To create a new environment, run:

mamba create --name myenvname bioconductor-clustifyr

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-clustifyr:<tag>

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

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