CpGtools Documentation

• 1. Overview
  • 1.1. CpG Position Analysis
  • 1.2. CpG Signal Analysis
  • 1.3. Differential Methylation Analysis
  • 1.4. Missing-value Imputation
  • 1.5. Cell-type Deconvolution
  • 1.6. Epigenetic Aging Analysis
  • 1.7. Command-line Usage
• 2. Installation
  • 2.1. Install in a Virtual Environment
  • 2.2. Install from PyPI
  • 2.3. Install from GitHub
  • 2.4. Install from Source
  • 2.5. Python Dependencies
  • 2.6. Optional Dependencies
  • 2.7. Verify the Installation
  • 2.8. Troubleshooting
• 3. CpGtools Release History
  • 3.1. Version 3.0.0
  • 3.2. Version 2.0.4
  • 3.3. Version 2.0.3
  • 3.4. Version 2.0.1
  • 3.5. Version 1.10.0
  • 3.6. Version 1.0.8
  • 3.7. Version 1.0.7
  • 3.8. Version 1.0.2
  • 3.9. Version 1.0.1
  • 3.10. Version 1.0.0

Data Format

• 1. Input Files and Data Formats
  • 1.1. Matrix Orientation
  • 1.2. Beta Values
  • 1.3. M Values
  • 1.4. Converting Between Beta-values and M-values
  • 1.5. Proportion Values
  • 1.6. BED Files
  • 1.7. Command-Specific Formats

Test and Demo Datasets

• 1. Pre-compiled datasets
  • 1.1. Test datasets
  • 1.2. Reference gene models
  • 1.3. Annotation datasets

Usage Information

• 1. CpG_aggregation
  • 1.1. Overview
  • 1.2. Input Files
  • 1.3. Count-mode Outlier Filtering
  • 1.4. Usage
  • 1.5. Output
  • 1.6. Header and Missing Values
  • 1.7. Example Data
• 2. CpG_anno_position
  • 2.1. Overview
  • 2.2. Input Files
  • 2.3. Centered Annotation Window
  • 2.4. Usage
  • 2.5. Output
  • 2.6. Pre-computed Annotation Datasets
  • 2.7. Example Data
• 3. CpG_anno_probe
  • 3.1. Overview
  • 3.2. Input Files
  • 3.3. Duplicate Probe IDs
  • 3.4. Usage
  • 3.5. Output
  • 3.6. Example Data
  • 3.7. Annotation Content
• 4. CpG_density_gene_centered
  • 4.1. Overview
  • 4.2. Input Files
  • 4.3. Usage
  • 4.4. Output
  • 4.5. Example Data
  • 4.6. Example Figure
• 5. CpG_distrb_chrom
  • 5.1. Overview
  • 5.2. Input Files
  • 5.3. Sample Names
  • 5.4. Usage
  • 5.5. Chromosomes Not in the Size File
  • 5.6. Output
  • 5.7. Plots
  • 5.8. Example Data
  • 5.9. Example Figures
• 6. CpG_distrb_gene_centered
  • 6.1. Overview
  • 6.2. Input Files
  • 6.3. Usage
  • 6.4. Output
  • 6.5. Example Data
  • 6.6. Example Figure
• 7. CpG_distrb_region
  • 7.1. Overview
  • 7.2. Input Files
  • 7.3. Region Names
  • 7.4. Usage
  • 7.5. Output
  • 7.6. Example Data
  • 7.7. Example Figure
• 8. CpG_logo
  • 8.1. Overview
  • 8.2. Input Files
  • 8.3. Sequence Window
  • 8.4. Requirements
  • 8.5. Usage
  • 8.6. Output
  • 8.7. Example Data
  • 8.8. Example Figure
• 9. CpG_to_gene
  • 9.1. Overview
  • 9.2. Input Files
  • 9.3. Usage
  • 9.4. Output
  • 9.5. Assignment Behavior
  • 9.6. Example Data
• 10. beta_PCA
  • 10.1. Overview
  • 10.2. Input Files
  • 10.3. Usage
  • 10.4. Output
  • 10.5. Example Data
  • 10.6. Example Figure
• 11. beta_UMAP
  • 11.1. Overview
  • 11.2. Input Files
  • 11.3. Missing Values and Preprocessing
  • 11.4. Usage
  • 11.5. Output
  • 11.6. Example Data
  • 11.7. Example Figure
• 12. beta_combat
  • 12.1. Overview
  • 12.2. Input Files
  • 12.3. Usage
  • 12.4. Output
  • 12.5. Figures
  • 12.6. Example Data
  • 12.7. Notes
  • 12.8. Reference
• 13. beta_deconvolution
  • 13.1. Overview
  • 13.2. Input
  • 13.3. Cell Types
  • 13.4. Fitting Methods
  • 13.5. Usage
  • 13.6. Output
  • 13.7. Fit Metrics
  • 13.8. Plot
• 14. beta_impute
  • 14.1. Overview
  • 14.2. Commands
  • 14.3. General Usage
  • 14.4. Examples
  • 14.5. Evaluating Imputation
  • 14.6. Missing-value Utilities
  • 14.7. MOREL
  • 14.8. Genomic Nearest-neighbor Imputation
• 15. beta_jitter_plot
  • 15.1. Overview
  • 15.2. Requirements
  • 15.3. Input
  • 15.4. Usage
  • 15.5. Output
  • 15.6. Example Figure
• 16. beta_m_conversion
  • 16.1. Overview
  • 16.2. Conversion
  • 16.3. Input
  • 16.4. Usage
  • 16.5. Output
• 17. beta_profile_gene_centered
  • 17.1. Overview
  • 17.2. Input Files
  • 17.3. Usage
  • 17.4. Output
  • 17.5. Example Data
  • 17.6. Example Figure
• 18. beta_profile_region
  • 18.1. Overview
  • 18.2. Input Files
  • 18.3. Usage
  • 18.4. Output
  • 18.5. Example Data
  • 18.6. Example Figure
• 19. beta_selectNBest
  • 19.1. Overview
  • 19.2. Scoring Methods
  • 19.3. Input Files
  • 19.4. Usage
  • 19.5. Output
  • 19.6. Example Data
• 20. beta_stacked_barplot
  • 20.1. Overview
  • 20.2. Input
  • 20.3. Usage
  • 20.4. Output
  • 20.5. Example Data
  • 20.6. Example Figure
• 21. beta_stats
  • 21.1. Overview
  • 21.2. Input Files
  • 21.3. Usage
  • 21.4. Output
  • 21.5. Example Data
• 22. beta_tSNE
  • 22.1. Overview
  • 22.2. Input Files
  • 22.3. Missing Values and Preprocessing
  • 22.4. Usage
  • 22.5. Output
  • 22.6. Example Data
  • 22.7. Example Figure
• 23. beta_topN
  • 23.1. Overview
  • 23.2. Ranking Scores
  • 23.3. Input
  • 23.4. Usage
  • 23.5. Output
  • 23.6. Example Data
• 24. beta_trichotmize
  • 24.1. Overview
  • 24.2. Algorithm
  • 24.3. Input
  • 24.4. Missing Values
  • 24.5. Usage
  • 24.6. Output
  • 24.7. Example Data
  • 24.8. Example Figure
• 25. dmc_Bayes
  • 25.1. Overview
  • 25.2. Input Files
  • 25.3. Usage
  • 25.4. Output
  • 25.5. Interpretation
  • 25.6. Reproducibility
  • 25.7. Example Data
• 26. dmc_bb
  • 26.1. Overview
  • 26.2. Requirements
  • 26.3. Input Files
  • 26.4. Model
  • 26.5. Usage
  • 26.6. Output
  • 26.7. Notes
  • 26.8. Example Data
• 27. dmc_fisher
  • 27.1. Overview
  • 27.2. Input Files
  • 27.3. Method
  • 27.4. Usage
  • 27.5. Output
  • 27.6. Notes
  • 27.7. Example Data
• 28. dmc_glm
  • 28.1. Overview
  • 28.2. Requirements
  • 28.3. Input Files
  • 28.4. Usage
  • 28.5. Output
  • 28.6. Important Behavior
  • 28.7. Example Data
• 29. dmc_logit
  • 29.1. Overview
  • 29.2. Statistical Model
  • 29.3. Requirements
  • 29.4. Input Files
  • 29.5. Usage
  • 29.6. Output
  • 29.7. Important Behavior
  • 29.8. Example Data
• 30. dmc_nonparametric
  • 30.1. Overview
  • 30.2. Input Files
  • 30.3. Method
  • 30.4. Usage
  • 30.5. Output
  • 30.6. Input-row Handling
  • 30.7. Example Data
• 31. dmc_ttest
  • 31.1. Overview
  • 31.2. Input Files
  • 31.3. Two-group Tests
  • 31.4. Multi-group ANOVA
  • 31.5. Delta Beta
  • 31.6. Usage
  • 31.7. Output
  • 31.8. Input-row Handling
  • 31.9. Example Data
• 32. epical
  • 32.1. Overview
  • 32.2. Supported Clocks
  • 32.3. Input
  • 32.4. Common Options
  • 32.5. Example
  • 32.6. Mouse-clock Example
  • 32.7. Mammalian-clock Example
  • 32.8. EPM Options
  • 32.9. Version
  • 32.10. Command-specific Help
• 33. predict_sex
  • 33.1. Overview
  • 33.2. Prediction Rule
  • 33.3. Input Files
  • 33.4. Usage
  • 33.5. Output
  • 33.6. Example Data
  • 33.7. Evaluation

Compare Differential Analysis Tools

• 1. Compare Differential CpG Analysis Tools
• 2. P-value distributions

Liscense

• MIT License

Reference

• Reference