recipe bioconductor-ctggem

Generating Tree Hierarchy Visualizations from Gene Expression Data

Homepage:

https://bioconductor.org/packages/3.14/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:

1.6.0-0,  1.2.0-1,  1.2.0-0,  0.99.3-0

Depends:

• bioconductor-biobase >=2.54.0,<2.55.0

• bioconductor-biocgenerics >=0.40.0,<0.41.0

• bioconductor-monocle >=2.22.0,<2.23.0

• bioconductor-sincell >=1.26.0,<1.27.0

• bioconductor-summarizedexperiment >=1.24.0,<1.25.0

• bioconductor-tscan >=1.32.0,<1.33.0

• r-base >=4.1,<4.2.0a0

• r-igraph

• r-matrix

Required By:

Installation

With an activated Bioconda channel (see 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>)

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