Analysis and reproducibility repository for the RECOMB 2027 manuscript:
Quantifying Chromatin Heterogeneity from Population-Conditioned Structural Divergence and Regulatory Programme Diversity
This repository contains the analysis scripts, prepared datasets, numerical results, and Jupyter notebooks used to reproduce the figures and analyses presented in the manuscript.
The scCHART Python package is available at LupienLab/scCHART. The reference software version is v0.1.0.
scCHART_analysis/
├── scripts/
│ ├── 01_benchmarks/
│ ├── 02_granja/
│ ├── 03_catlas/
│ ├── 04_hsc/
│ └── 05_method_comparisons/
├── data/
├── results/
├── notebooks/
├── environment/
├── README.md
└── LICENSE
scripts/— Scripts used to perform the computational analyses.data/— Prepared input datasets required by the scripts.results/— Numerical results generated by the analysis scripts.notebooks/— Notebooks that load the results and reproduce manuscript figures.environment/— Software dependencies and environment specifications.
The workflow separates computation from visualization:
- Analysis scripts use the prepared datasets to generate numerical results.
- Results are saved in
results/. - Jupyter notebooks load these outputs to reproduce the manuscript figures.
The repository uses scCHART v0.1.0. Some scCHART analyses involve stochastic sampling, including the estimation of sampling-based null distributions. Consequently, independent executions may produce slightly different numerical estimates depending on the random seed and random-number generation procedure.
The epiCHAOS comparisons use an independent Python reimplementation of epiCHAOS (Kelly et al., 2024), maintained under tools/epichaos_py/.
The analyses use publicly available single-cell chromatin accessibility and multiome datasets, including the Granja and Buenrostro datasets.
Prepared datasets and additional required inputs will be made available through Zenodo where redistribution is permitted. Download instructions and accession information will be added as the files are deposited.
Iyer A, Lupien M. Quantifying Chromatin Heterogeneity from Population-Conditioned Structural Divergence and Regulatory Programme Diversity. Manuscript in preparation.
See LICENSE.