# ROCCO: [R]obust [O]pen [C]hromatin Detection via [C]onvex [O]ptimization
<p align="center">
<img width="400" alt="logo" src="docs/logo.png">
ROCCO is an optimal consensus peak calling algorithm for open chromatin data that is scalable to large sample sizes.
**Features**
1. **Consideration of enrichment and spatial characteristics** of open chromatin signals to capture the full extent of peaks;
2. **Mathematically tractable model** that permits performance and efficiency guarantees.
3. **Efficient for large numbers of samples** with an asymptotic time complexity independent of sample size;
4. **No arbitrary thresholds** on the minimum number of supporting samples/replicates;
5. **No required training data** or a heuristically determined set of initial candidate peak regions;
# Paper/Citation
If using ROCCO in your research, please cite the [original paper](https://doi.org/10.1093/bioinformatics/btad725) in *Bioinformatics*
```
Nolan H Hamilton, Terrence S Furey, ROCCO: a robust method for detection of open chromatin via convex optimization,
Bioinformatics, Volume 39, Issue 12, December 2023
```
**DOI**: [10.1093/bioinformatics/btad725](`10.1093/bioinformatics/btad725`)
# Documentation
Documentation and example usage are available at https://nolan-h-hamilton.github.io/ROCCO/
# Installation
```
pip install rocco
```
# Demo
https://github.com/nolan-h-hamilton/ROCCO/tree/main/docs/demo/demo.ipynb
# Input
ROCCO accepts **BAM** alignments and a genome sizes file as input.
```
rocco -i sample1.bam sample2.bam sample3.bam [...] -g hg38.sizes --params hg38
```
or with a wildcard:
```
rocco -i *.bam -g hg38.sizes --params hg38
```
See `rocco --help` for more details.
# Output
A **BED** file containing peak regions and scores.
# Testing ROCCO
```
cd tests
pytest -v -rPA -l -k "regular" test_rocco.py
```
# Version History
Previous releases can be found at https://github.com/nolan-h-hamilton/ROCCO/tags
Additional dependencies for optional features:
- 'ortools': includes the first-order solver, PDLP.
- 'pytest': allows local execution of the Tests workflow.
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