CHOIR (clustering hierachy optimization by iterative random forests) is a clustering algorithm for single-cell sequencing data. CHOIR applies a framework of permutation tests and random forest classifiers across a hierarchical clustering tree to statistically identify clusters that represent distinct populations.

Installation

To install the package, please use the following:

remotes::install_github("corceslab/CHOIR", ref="main", repos = BiocManager::repositories(), upgrade = "never")

Usage

Please follow the vignette. Alternately, install the package with build_vignettes = TRUE, as follows:

remotes::install_github("corceslab/CHOIR", ref="main", repos = BiocManager::repositories(), upgrade = "never", build_vignettes = TRUE)

And access the vignette by running:

vignette("CHOIR")