recipe bioconductor-cotan

COexpression Tables ANalysis

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-cotan/meta.yaml

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

package bioconductor-cotan

versions:

2.2.1-0,  2.0.4-0,  1.2.0-0

depends bioconductor-complexheatmap:

>=2.18.0,<2.19.0

depends r-assertthat:

depends r-base:

>=4.3,<4.4.0a0

depends r-circlize:

depends r-dendextend:

depends r-dplyr:

depends r-factoextra:

depends r-ggplot2:

depends r-ggrepel:

depends r-ggthemes:

depends r-irlba:

depends r-matrix:

depends r-paralleldist:

depends r-parallelly:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rfast:

depends r-rlang:

depends r-scales:

depends r-seurat:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-umap:

depends r-withr:

depends r-zeallot:

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-cotan

and update with::

   mamba update bioconductor-cotan

To create a new environment, run:

mamba create --name myenvname bioconductor-cotan

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-cotan:<tag>

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

Download stats

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