recipe bioconductor-chetah

Fast and accurate scRNA-seq cell type identification

Homepage

https://bioconductor.org/packages/3.10/bioc/html/CHETAH.html

License

file LICENSE

Recipe

/bioconductor-chetah/meta.yaml

CHETAH (CHaracterization of cEll Types Aided by Hierarchical classification) is an accurate, selective and fast scRNA-seq classifier. Classification is guided by a reference dataset, preferentially also a scRNA-seq dataset. By hierarchical clustering of the reference data, CHETAH creates a classification tree that enables a step-wise, top-to-bottom classification. Using a novel stopping rule, CHETAH classifies the input cells to the cell types of the references and to “intermediate types”: more general classifications that ended in an intermediate node of the tree.

package bioconductor-chetah

Versions

1.2.0-0, 1.0.4-0

Depends

• bioconductor-biodist >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.24.0,<0.25.0

• bioconductor-singlecellexperiment >=1.8.0,<1.9.0

• bioconductor-summarizedexperiment >=1.16.0,<1.17.0

• r-base >=3.6,<3.7.0a0

• r-corrplot

• r-cowplot

• r-dendextend

• r-ggplot2

• r-gplots

• r-pheatmap

• r-plotly

• r-reshape2

• r-shiny

Required By

Installation

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

conda install bioconductor-chetah

and update with:

conda update bioconductor-chetah

or use the docker container:

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

(see bioconductor-chetah/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-chetah/README.html)