recipe bioconductor-cellid

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Homepage:

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

License:

GPL-3 + file LICENSE

Recipe:

/bioconductor-cellid/meta.yaml

CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

package bioconductor-cellid

versions:

1.10.1-0,  1.8.1-0,  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-fgsea:

>=1.28.0,<1.29.0

depends bioconductor-fgsea:

>=1.28.0,<1.29.0a0

depends bioconductor-scater:

>=1.30.0,<1.31.0

depends bioconductor-scater:

>=1.30.1,<1.31.0a0

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-data.table:

depends r-fastmatch:

depends r-ggplot2:

depends r-glue:

depends r-irlba:

depends r-matrix:

depends r-matrixstats:

depends r-pbapply:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-reticulate:

depends r-rtsne:

depends r-seurat:

>=4.0.1

depends r-stringr:

depends r-tictoc:

depends r-umap:

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-cellid

and update with::

   mamba update bioconductor-cellid

To create a new environment, run:

mamba create --name myenvname bioconductor-cellid

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-cellid:<tag>

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

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