recipe bioconductor-ewce

Expression Weighted Celltype Enrichment

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-ewce/meta.yaml

Used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

package bioconductor-ewce

versions:

1.14.0-0,  1.10.2-0,  1.8.2-0,  1.6.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-delayedarray:

>=0.32.0,<0.33.0

depends bioconductor-ewcedata:

>=1.14.0,<1.15.0

depends bioconductor-limma:

>=3.62.0,<3.63.0

depends bioconductor-orthogene:

>=1.12.0,<1.13.0

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-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-hgnchelper:

depends r-matrix:

depends r-reshape2:

depends r-rnomni:

>=1.0

depends r-stringr:

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-ewce

and update with::

   mamba update bioconductor-ewce

To create a new environment, run:

mamba create --name myenvname bioconductor-ewce

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-ewce:<tag>

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

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