Changes in version 0.99.6 (2025-08-11):
- Updated the Description file
- Accepted and made changes based on the reviewer's feedback.
- Initial release of HiCPotts.
- Added core functions: get_data(), process_data(), run_chain_betas(), compute_HMRFHiC_probabilities().
- Supported distributions: Poisson, Zero-Inflated Poisson, Negative Binomial, Zero-Inflated Negative Binomial.
- Implemented C++ optimizations using Rcpp and RcppArmadillo for performance.
- Integrated covariates: genomic distance, GC content, accessibility, and transposable element counts.
- Addressed BiocCheck requirements: added runnable examples, replaced sapply with vapply, moved large data files to ExperimentHub.