# Quantitative visual exploration of scRNA-seq data

## Documentation for package ‘scBubbletree’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

scBubbletree-package | The R package scBubbletree
d_500 | Dataset: 500 PBMCs
d_ccl | Dataset: scRNA-seq data of 3,918 cells from 5 adenocarcinoma cell lines
get_bubbletree_dummy | Build bubbletree given matrix A and vector cs of externally generated cluster IDs
get_bubbletree_graph | Louvain clustering and hierarchical grouping of k' clusters (bubbles)
get_bubbletree_kmeans | k-means clustering and hierarchical grouping of k clusters (bubbles)
get_cat_tiles | Visualization of categorical cell features using tile plots
get_gini | Gini impurity index computed for a clustering solution and a vector of categorical cell feature labels
get_gini_k | Gini impurity index computed for a list of clustering solutions obtained by functions get_k or get_r and a vector of categorical cell feature labels
get_k | Finding optimal number k of clusters
get_num_tiles | Visualization of numeric cell features using tile plots
get_num_violins | Visualization of numeric cell features using violin plots
get_r | Finding optimal clustering resulution r and number of communities k'
scBubbletree | The R package scBubbletree