ctriermaansson / scbubbletree

scBubbletree: quantitative tool for visual exploration of scRNA-seq data

scBubbletree

Overview

Single cell RNA sequencing has revolutionized biological research by allowing us to interrogate the expression of thousands of genes at single cell resolution. The rapid growth of scRNA-seq data has also created an unique set of challenges, for instance, how can we perform visual exploration of this massive data in order to extract useful biological information from our scRNA-seq samples.

scBubbletree was designed to overcome challenges associated with the rapid growth of the scale of scRNA-seq datasets, such as overplotting, and to accurately preserve the local and global structure of the data. The workflow of scBubbletree is easy-to-use and allows seamless integration with popular approaches for scRNA- seq data analysis.

How to use scBubbletree

scBubbletree is an R-package available from Bioconductor:

https://bioconductor.org/packages/scBubbletree/ (coming soon)

To install this package, start R and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scBubbletree")

Multiple case studies are provided in the directory /vignettes

Workflow & output