Quantitative visual exploration of scRNA-seq data

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Documentation for package ‘scBubbletree’ version 1.9.0

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

Help Pages

scBubbletree-package	The R package scBubbletree
compare_bubbletrees	Comparison of two bubbletrees generated from the same scRNA-seq data
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 from matrix A of low-dimensional projections 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_cell_tiles	Visualization of numeric features of individual cells using tile plots
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