Science Score: 57.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓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: biorxiv.org, nature.com -
○Committers with academic emails
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✓Institutional organization owner
Organization cbg-ethz has institutional domain (www.bsse.ethz.ch) -
○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.9%) to scientific vocabulary
Repository
LongSom tool for long-reads
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- Language: Python
- Default Branch: main
- Size: 274 MB
Statistics
- Stars: 10
- Watchers: 4
- Forks: 1
- Open Issues: 4
- Releases: 2
Metadata Files
README.md
LongSom
A Snakemake workflow for calling somatic SNVs, fusions, and CNAs in high-quality long-read single-cell RNA-seq cancer samples, and infer subclonal structures based on those variants.
LongSom takes a bam file and a barcodes file as input. Before calling variants, it performs a cell types reannotation step for improved results. For more informations about the methods, please read our Genome Research publication Dondi et al. 2025.
For more information, including installation and usage, please visit our Wiki.
Workflow
Cite
If you use LongSom, please cite:
Arthur Dondi, Nico Borgsmüller, Pedro Ferreira, Brian Haas, Francis Jacob, Viola Heinzelmann-Schwarz, Tumor Profiler Consortium, Niko Beerenwinkel. De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data. Genome Research (2025)
In addition, please cite SComatic if you use LongSom for SNV detection, CTAT-LR-fusion for fusion detection, and BnpC for subclonal structure reconstruction.
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
- Issues event: 8
- Watch event: 6
- Issue comment event: 1
- Push event: 2
- Pull request event: 1
- Gollum event: 5
- Fork event: 1
Last Year
- Issues event: 8
- Watch event: 6
- Issue comment event: 1
- Push event: 2
- Pull request event: 1
- Gollum event: 5
- Fork event: 1
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| ArthurDondi | a****i@g****m | 14 |
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 1.5
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- HarrisonWismer (2)
- hwismer (2)
- modalaigh (1)
- xuxif (1)
Pull Request Authors
- rezabehboudi (2)