Metadata-Version: 2.4
Name: consenrich
Version: 0.11.2a0
Summary: Genome-wide estimation of signals hidden in noisy multi-sample HTS datasets
Author-email: "Nolan H. Hamilton" <nolan.hamilton@unc.edu>
License-Expression: MIT
Project-URL: Documentation, https://nolan-h-hamilton.github.io/Consenrich/
Project-URL: Source, https://github.com/nolan-h-hamilton/Consenrich
Project-URL: Issues, https://github.com/nolan-h-hamilton/Consenrich/issues
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: THIRD_PARTY_LICENSES.md
License-File: HTSLIB_LICENSE.txt
License-File: HTSCODECS_LICENSE.md
Requires-Dist: numpy>=2.1
Requires-Dist: scipy>=1.15
Requires-Dist: pandas>=2.3.0
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Requires-Dist: PyWavelets>=1.9.0
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Requires-Dist: itrigamma>=0.2.0a1
Provides-Extra: bigwig
Requires-Dist: pyBigWig>=0.3.24; extra == "bigwig"
Provides-Extra: plots
Requires-Dist: matplotlib>=3.8; extra == "plots"
Provides-Extra: memory
Requires-Dist: psutil>=5.9; extra == "memory"
Provides-Extra: all
Requires-Dist: pyBigWig>=0.3.24; extra == "all"
Requires-Dist: matplotlib>=3.8; extra == "all"
Requires-Dist: psutil>=5.9; extra == "all"
Dynamic: license-file

# Consenrich

Consenrich estimates regulatory signals from multi-sample functional genomics datasets.

![Consenrich overview](docs/images/fig.png)

**Input:** Sequencing data (BAM files, fragments, etc.) from ATAC-seq, DNase-seq, ChIP-seq, CUT&RUN, and other functional genomics assays where multiple samples or replicates measure a shared regulatory signal but differ in local noise, artifacts, sequencing depth, assay quality, or biological heterogeneity.

**Output:** Consensus signal estimate tracks (bedGraph, bigWig), associated uncertainty/background tracks (bedGraph, bigWig), and optional consensus peak calls (narrowPeak, gappedPeak, BED).


[**See the Documentation**](https://nolan-h-hamilton.github.io/Consenrich/).


## Manuscript Preprint and Citation

**BibTeX Citation**

```bibtex
@article {Hamilton2025,
	author = {Hamilton, Nolan H and Huang, Yu-Chen E and McMichael, Benjamin D and Love, Michael I and Furey, Terrence S},
	title = {Genome-Wide Uncertainty-Moderated Extraction of Signal Annotations from Multi-Sample Functional Genomics Data},
	year = {2025},
	doi = {10.1101/2025.02.05.636702},
	publisher = {Cold Spring Harbor Laboratory},
	journal = {bioRxiv}
}
```
