recipe bioconductor-ctggem

Generating Tree Hierarchy Visualizations from Gene Expression Data

Homepage

https://bioconductor.org/packages/3.12/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

1.2.0-0,  0.99.3-0

Depends

• bioconductor-biobase >=2.50.0,<2.51.0

• bioconductor-biocgenerics >=0.36.0,<0.37.0

• bioconductor-destiny >=3.4.0,<3.5.0

• bioconductor-hsmmsinglecell >=1.10.0,<1.11.0

• bioconductor-monocle >=2.18.0,<2.19.0

• bioconductor-sincell >=1.22.0,<1.23.0

• bioconductor-summarizedexperiment >=1.20.0,<1.21.0

• bioconductor-tscan >=1.28.0,<1.29.0

• r-base >=4.0,<4.1.0a0

• r-igraph

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:

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