ROCCO: [R]obust [O]pen [C]hromatin Detection via [C]onvex [O]ptimization

Tests PyPI - Version

What

ROCCO is an efficient algorithm for detection of "consensus peaks" in large datasets with multiple HTS data samples, where an enrichment in read counts/densities is observed in a nontrivial subset of samples.

Input/Output

  • Input: Samples' BAM alignments (-i) or a bigWig file, and a reference genome assembly (-g) for chromosome sizes and annotation of blacklisted regions (if available)
  • Output: BED file of consensus peak regions (Default format is BED3: chrom,start,end). Use --peak_mode both to obtain both narrow and broad peak calls.

How

ROCCO models consensus peak calling as a constrained optimization problem with constraints/penalties for the total proportion of the genome selected as enriched and a fragmentation penalty (TV) to promote spatial consistency in active regions and sparsity elsewhere.

Why

  1. Consideration of enrichment magnitude and spatial characteristics of open chromatin signals
  2. Scaling to large sample sizes (100+)
  3. Unsupervised Does not require training data or a heuristically determined set of initial candidate peak regions
  4. Less rigid thresholds with respect to the minimum number/width of supporting samples/replicates.
  5. Mathematically tractable model permitting worst-case analysis of runtime and performance

Usage

rocco -i <bam files, or a single aggregate bigWig file> -g <hg38, hg19, mm10, mm39, dm6, ...> -o <output_file.bed> [--peak_mode both]

for example:

rocco -i sample1.bam sample2.bam sample3.bam -g hg38 -o consensus_peaks.bed --peak_mode both

See rocco --help for more options and details.

Paper/Citation

If using ROCCO in your research, please cite the original paper in Bioinformatics (DOI: btad725)

 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

Installation

PyPI (pip)

python -m pip install rocco --upgrade

If lacking administrative control, you may need to append --user to the above.

Build from Source

If preferred, ROCCO can easily be built from source:

  • Clone or download this repository

    git clone https://github.com/nolan-h-hamilton/ROCCO.
cd ROCCO
python setup.py sdist bdist_wheel
python -m pip install -e .

Project links

Data verified by PyPI on Jul 9, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (1.14.0)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for nolan-h-hamilton from gravatar.com nolan-h-hamilton

Credits

Author: Nolan Holt Hamilton

GitHub Statistics

Data verified by PyPI on Jul 9, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

MIT

Requires

Python <4, >=3.10

Provides Extra

pytest bigwig

Tags

genomics functional genomics epigenomics epigenetics peak calling chromatin accessibility chromatin consensus peak DNase ATAC ChIP-seq

Classifiers

Report project as malware

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Release history Release notifications | RSS feed

1.14.0

31 files

1.13.0

31 files

This release

1.12.0 This release

31 files

1.11.0

31 files

1.10

31 files

1.7.0

2 files

1.6.3

2 files

1.6.1

2 files

1.6.0.post1

2 files

1.6.0

2 files

1.4.1

2 files

1.3.4

2 files

1.2.0

2 files

1.1.1

2 files

1.1.0

2 files

1.0.3

2 files

1.0.2

2 files

1.0.1

2 files

Pre-release

1.0.0rc1

2 files

0.13.0

2 files

0.12.1

2 files

0.12.0

2 files

0.11.8

2 files

0.11.7

2 files

0.11.6.1

2 files

0.11.6

2 files

0.11.4

2 files

0.11.1

2 files

0.11.0

2 files

0.9.5

2 files

0.9.4

2 files

0.9.3

2 files

0.9.1

2 files

0.9.0

2 files

0.8.4

2 files

0.8.3.1

2 files

0.8.3

2 files

0.8.2

2 files

0.8.0

2 files

0.6.15

2 files

0.6.14

2 files

0.6.13

2 files

0.6.12

2 files

0.6.10

2 files

0.6.7.1

2 files

0.6.7

2 files

0.6.5.1

2 files

0.6.5

2 files

0.6.4

2 files

0.6.3

2 files

0.6.0

2 files

0.5.2.2

2 files

0.5.2.1

2 files

0.5.2

2 files

0.5.1

2 files

0.4.6.1

2 files

0.4.5

2 files

0.4.4

2 files

0.4.3

2 files

0.4.2

2 files

0.4.1

2 files

0.4.0

2 files

0.3.12

2 files

0.3.11

2 files

0.3.10

2 files

0.3.9

2 files

0.3.8

2 files

0.3.7

2 files

0.3.6

2 files

0.3.4

2 files

0.3.3

2 files

0.3.2

2 files

0.3.1

2 files

0.3.0

2 files

0.2.0

2 files

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