https://github.com/cbg-ethz/ctc-scite
Computational method and analyses to study the clonality of circulating tumor cell clusters
Science Score: 67.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: nature.com, zenodo.org -
✓Committers with academic emails
1 of 1 committers (100.0%) from academic institutions -
✓Institutional organization owner
Organization cbg-ethz has institutional domain (www.bsse.ethz.ch) -
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (5.2%) to scientific vocabulary
Repository
Computational method and analyses to study the clonality of circulating tumor cell clusters
Basic Info
Statistics
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 2
- Releases: 4
Metadata Files
README.md
Interrogating the clonality of circulating tumor cell (CTC) clusters
This repository accompanies the publication: Gremmelspacher, D. and Gawron, J. et al. Phylogenetic inference reveals clonal heterogeneity in circulating tumor cell clusters. Nat. Genetics (2025) (doi:10.1038/s41588-025-02205-2).
Synopsis
The clonal diversity of cells within individual CTC clusters in human malignancies is poorly defined. In this study, we provide substantial evidence for the presence and quantification of the prevalence of oligoclonal CTC clusters in human cancer.
Contents
CTC_SCITE: It contains the CTC-SCITE algorithm, a bayesian phylogenetic tree inference algorithm which takes the genomic profiles of circulating tumor cells and ciculating tumor cell clusters and infers a phylogenetic tree on all cells, jointly calling the genotypes of each cell
Experiments: Analyses of CTCs and CTC clusters from breast, prostate, lung, and ovarian cancer patients, as well as from mouse cancer models. We infer the clonality of CTC clusters, and quantitatively study the prevalence of oligoclonal CTC clusters as a function of the clonal complexity of primary tumors, based on a injection of genetically barcoded xenografts into mice.
Availability
All software is freely available under a GPL3 license. If you are using CTC-SCITE in a publication, please cite 10.1038/s41588-025-02205-2.
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
Total
- Release event: 2
- Watch event: 2
- Member event: 1
- Push event: 26
- Pull request event: 8
- Create event: 2
Last Year
- Release event: 2
- Watch event: 2
- Member event: 1
- Push event: 26
- Pull request event: 8
- Create event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| JohannesGawron | j****n@b****h | 94 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 3
- Total pull requests: 9
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 9
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 6
- Average time to close issues: N/A
- Average time to close pull requests: less than a minute
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- JohannesGawron (3)
Pull Request Authors
- JohannesGawron (13)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- actions/checkout v4 composite
- super-linter/super-linter v6.4.1 composite