Package Recipe 'bioconductor-cotan'

recipe bioconductor-cotan

COexpression Tables ANalysis

Homepage:: https://bioconductor.org/packages/3.20/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:

2.10.3-0, 2.10.1-0, 2.6.0-0, 2.2.1-0, 2.0.4-0, 1.2.0-0

Depends:

on bioconductor-biocsingular >=1.26.0,<1.27.0
on bioconductor-complexheatmap >=2.26.0,<2.27.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-assertthat
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-dendextend
on r-dplyr
on r-ggdist
on r-ggplot2
on r-ggrepel
on r-ggthemes
on r-matrix
on r-paralleldist
on r-parallelly
on r-proxy
on r-rcolorbrewer
on r-rfast
on r-rlang
on r-rspectra
on r-scales
on r-seurat
on r-stringr
on r-tibble
on r-tidyr
on r-withr
on r-zeallot

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-cotan

to add into an existing workspace instead, run:

pixi add bioconductor-cotan

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-cotan

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-cotan

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-cotan:<tag>

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-cotan/README.html)