Package Recipe 'bioconductor-chetah'

recipe bioconductor-chetah

Fast and accurate scRNA-seq cell type identification

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

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.9.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0,

1.26.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.9.0-0, 1.8.0-0, 1.6.0-1, 1.6.0-0, 1.4.0-0, 1.2.0-0, 1.0.4-0

Depends:

on bioconductor-biodist >=1.82.0,<1.83.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-singlecellexperiment >=1.32.0,<1.33.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on r-base >=4.5,<4.6.0a0
on r-corrplot
on r-cowplot
on r-dendextend
on r-ggplot2
on r-pheatmap
on r-plotly
on r-reshape2
on r-shiny

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-chetah

to add into an existing workspace instead, run:

pixi add bioconductor-chetah

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-chetah

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-chetah

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-chetah:<tag>

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