https://github.com/cbg-ethz/scicone
Single-cell copy number calling and event history reconstruction.
Science Score: 36.0%
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
-
○Academic publication links
-
✓Committers with academic emails
3 of 6 committers (50.0%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary
Keywords
Repository
Single-cell copy number calling and event history reconstruction.
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: gpl-3.0
- Language: C++
- Default Branch: master
- Homepage: https://www.biorxiv.org/content/10.1101/2020.04.28.065755v1
- Size: 47 MB
Statistics
- Stars: 24
- Watchers: 6
- Forks: 8
- Open Issues: 7
- Releases: 0
Topics
Metadata Files
README.md
Single-cell copy number calling and event history reconstruction.
A statistical model and MCMC algorithm tailored to single-cell copy number profiling from shallow whole-genome DNA sequencing data. SCICoNE reconstructs the history of copy number events in the tumour and uses these evolutionary relationships to identify the copy number profiles of the individual cells.
Quick start
SCICoNE takes a read counts matrix of cells by genomic bins and outputs the copy number profile of each cell and the underlying event history. * Command line interface tutorial * Python package tutorial * Example run on 10X Genomics data using the Python package
Requirements
- C++ compiler that supports C++14 standards (e.g.
gcc>=5.2.0,clang>=5.0.0)) - CMake >= 3.9
- Boost >= 1.6.x
- OpenMP >= 4.5
- NLopt >= 2.6.2
Installation
Once the requirements are in place, downloading and installing SCICoNE takes about 5 minutes.
bash
git clone https://github.com/cbg-ethz/SCICoNE.git # Clone the repository
cd SCICoNE
mkdir build && cd build # Create and enter the build directory
cmake ../scicone/ # Compile the program with cmake
make # Build the executables
cd .. # Return to root directory
Python package
We also provide a Python 3 package to facilitate plotting and easily integrate SCICoNE with other data analysis tools. This interface runs the C++ binaries and reads the outputs into numpy arrays. Even if you don't want to use the complete package, we recommend you install it to facilitate usage of the C++ command line interface.
```bash
pip install pyscicone/
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
- Watch event: 6
- Delete event: 2
- Push event: 4
- Pull request event: 4
- Fork event: 1
- Create event: 2
Last Year
- Watch event: 6
- Delete event: 2
- Push event: 4
- Pull request event: 4
- Fork event: 1
- Create event: 2
Committers
Last synced: 10 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| anilbey | t****l@g****m | 886 |
| pedrofale | p****a@b****h | 321 |
| FridljDa | d****d@g****m | 5 |
| pedrofale | p****f@e****h | 2 |
| Nicholas D. Socci | s****n@m****g | 1 |
| Pedro F. Ferreira | p****f@s****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 107
- Total pull requests: 73
- Average time to close issues: 4 months
- Average time to close pull requests: 4 days
- Total issue authors: 4
- Total pull request authors: 2
- Average comments per issue: 1.07
- Average comments per pull request: 0.15
- Merged pull requests: 67
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 2
- Average time to close issues: N/A
- Average time to close pull requests: 3 minutes
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- anilbey (54)
- pedrofale (6)
- ljwharbers (1)
- ingenumich (1)
Pull Request Authors
- anilbey (32)
- pedrofale (10)
- FridljDa (2)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- Phenograph *
- graphviz *
- h5py *
- numpy *
- pybiomart *
- scipy *
- seaborn *
- tqdm *
- actions/checkout v2 composite
- actions/setup-python v2 composite
- scicone master