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Bonsai analysis of scRNA-seq data


NimwegenLab

Data upload.

Email address (optional)
Project name (optional)  
Select mRNA count table (.tsv)
Select annotation file(s)
Email address (optional)
Project name (optional)  
Select MTX file
Select gene TSV file
Select cell TSV file
Select annotation file

Bonsai-Scout

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:

  1. The Bonsai-Scout webserver will be used by you and/or your institution solely for non-commercial purposes, except with express permission from the authors.
  2. You may provide us with feedback on the use of the Bonsai-Scout webserver in your research, and we are permitted to use any information you provide in making changes to Bonsai-Scout.
  3. Any risk associated with using the Bonsai-Scout webserver is with you and your institution.
  4. Any results produced with Bonsai-Scout are licenced under CC BY-NC 4.0 .

Commercial users should contact us for licensing arrangements.

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