https://github.com/cbg-ethz/scicone

Single-cell copy number calling and event history reconstruction.
https://github.com/cbg-ethz/scicone

bayesian-inference cancer-genomics copy-number-variation mcmc single-cell

Last synced: 6 months ago
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Single-cell copy number calling and event history reconstruction.

• Host: GitHub
• URL: https://github.com/cbg-ethz/scicone
• Owner: cbg-ethz
• License: gpl-3.0
• Created: 2018-05-29T08:33:12.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2024-12-21T17:05:22.000Z (10 months ago)
• Last Synced: 2025-04-28T13:14:15.891Z (6 months ago)
• Topics: bayesian-inference, cancer-genomics, copy-number-variation, mcmc, single-cell
• Language: C++
• Homepage: https://www.biorxiv.org/content/10.1101/2020.04.28.065755v1
• Size: 47 MB
• Stars: 23
• Watchers: 6
• Forks: 8
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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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](https://github.com/cbg-ethz/SCICoNE/blob/master/docs/tutorial.md)

* [Python package tutorial](https://github.com/cbg-ethz/SCICoNE/blob/master/docs/notebooks/tutorial.ipynb)

* [Example run on 10X Genomics data using the Python package](https://github.com/cbg-ethz/SCICoNE/blob/master/docs/notebooks/10x_example.ipynb)

## 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/