recipe bioconductor-ctggem

Generating Tree Hierarchy Visualizations from Gene Expression Data

Homepage

https://bioconductor.org/packages/3.11/bioc/html/ctgGEM.html

License

GPL(>=2)

Recipe

/bioconductor-ctggem/meta.yaml

Cell Tree Generator for Gene Expression Matrices (ctgGEM) streamlines the building of cell-state hierarchies from single-cell gene expression data across multiple existing tools for improved comparability and reproducibility. It supports pseudotemporal ordering algorithms and visualization tools from monocle, cellTree, TSCAN, sincell, and destiny, and provides a unified output format for integration with downstream data analysis workflows and Cytoscape.

package bioconductor-ctggem

Versions

0.99.3-0

Depends

• bioconductor-biobase >=2.48.0,<2.49.0

• bioconductor-biocgenerics >=0.34.0,<0.35.0

• bioconductor-monocle >=2.16.0,<2.17.0

• bioconductor-summarizedexperiment >=1.18.0,<1.19.0

• r-base >=4.0,<4.1.0a0

• r-ggplot2

• r-igraph

• r-matrix

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-ctggem

and update with:

conda update bioconductor-ctggem

or use the docker container:

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

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

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-ctggem/README.html)