Bonsai is a data representation method that
reconstructs the tree that best captures the
structure in high-dimensional data. Its accompanying
exploration tool, Bonsai-scout, can be used
to explore the data by browsing through the
tree. Although Bonsai can be used on any
high-dimensional data, this server was built for
analyzing scRNA-seq data. Users can upload mRNA
count tables, after which the pipeline first
runs Cellstates to group statistically
indistinguishable cells, and Sanity to
normalize the data by inferring log-transcription
quotients. Bonsai will use the output of these
methods, and reconstruct a tree that best represents
the scRNA-seq data, which can then be browsed using
Bonsai-scout.
These computations will take some time. Therefore,
users can upload their data and will get an email
once the results are done. The email will contain a
link to all computed results, and a link to an
online instance of Bonsai-scout at which the data
can be explored.
The Bonsai-Scout source code is avaliable on github:
https://github.com/dhdegroot/Bonsai-data-representation
Please cite Bonsai server as:
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data.
Daan Hugo de Groot, Sarah X Morillo Leonardo, Mikhail Pachkov, Erik van Nimwegen, bioRxiv, 2025
doi: 10.1101/2025.05.08.652944
The developers of Bonsai-Scout give permission to you and your institution to use the Bonsai-Scout webserver for internal, research purposes, on the following conditions:
Commercial users should contact us for licensing arrangements.