3. CpGtools Release History

3.1. Version 3.0.0

Version 3.0.0 is a major release that expands CpGtools with epigenetic-clock analysis, missing-value imputation, cell-type deconvolution, and a modernized command-line and packaging structure.

3.1.1. New features

  • Added epical, a unified command-line interface for calculating DNA methylation age and related aging measures using multiple published epigenetic clocks.

  • Added beta_impute, a unified framework for DNA methylation missing-value analysis and imputation.

  • Added beta_deconvolution for estimating cell-type proportions from DNA methylation profiles.

  • Added imputation methods including:

    • constant, mean, median, minimum, maximum, and random-value imputation;

    • moving-window and K-nearest-neighbor (KNN) imputation;

    • reference-based KNN;

    • iterative Buck regression and Random Forest regression;

    • SoftImpute matrix completion;

    • MOREL block-wise imputation; and

    • genomic nearest-neighbor (GNN) imputation.

  • Added utilities for generating synthetic methylation matrices, inserting missing values, summarizing missingness, and evaluating imputation accuracy against a truth matrix using MAE, RMSE, and \(R^2\).

3.1.2. Command-line and packaging changes

  • Standardized command-line programs as installed console commands.

  • Reorganized command-line modules under cpgmodule.cli.

  • Refactored epical into a registry-based CLI architecture.

  • Added automated tests for epical and beta_impute.

  • Modernized package configuration using pyproject.toml and the src package layout.

  • Updated dependency and license metadata for modern Python packaging.

3.1.3. Documentation

  • Expanded documentation for epical, beta_impute, and beta_deconvolution.

  • Clarified input-file conventions, including the default methylation-matrix orientation of CpGs in rows and samples in columns.

  • Updated installation and command-line usage documentation.

3.2. Version 2.0.4

3.2.1. New features

  • Added beta_combat for batch-effect correction.

3.3. Version 2.0.3

3.3.1. Bug fixes

  • Fixed an issue in the ANOVA workflow where p-values and adjusted p-values were reported as missing for all CpGs.

3.4. Version 2.0.1

3.4.1. New features

  • Added predict_sex.

  • Added beta_selectNBest.

3.5. Version 1.10.0

3.5.1. New features

  • Added beta_UMAP.

3.6. Version 1.0.8

3.6.1. Bug fixes

  • Fixed an issue in beta_tSNE and beta_PCA when sample identifiers were numeric.

3.7. Version 1.0.7

3.7.1. New features

  • Added CpG_density_gene_centered.

3.8. Version 1.0.2

3.8.1. New features

  • Added beta_tSNE for t-distributed stochastic neighbor embedding (t-SNE) analysis of DNA methylation samples.

3.9. Version 1.0.1

3.9.1. New features

  • Added CpG_anno_position for annotating CpGs using pre-built or user-supplied genomic annotation files.

3.10. Version 1.0.0

Initial public release.