| combine_methrix | Combine methrix objects | 
| convert_HDF5_methrix | Converts HDF5 methrix object to standard in-memory object. | 
| convert_methrix | Converts an in-memory object to an on-disk HDF5 object. | 
| coverage_filter | Filter matrices by coverage | 
| extract_CPGs | Extracts all CpGs from a genome | 
| get_matrix | Extract methylation or coverage matrices | 
| get_region_summary | Extract and summarize methylation or coverage info by regions of interest | 
| get_stats | Estimate descriptive statistics | 
| load_HDF5_methrix | Loads HDF5 methrix object | 
| mask_methrix | Masks too high or too low coverage | 
| methrix | Class methrix | 
| methrix-class | Class methrix | 
| methrix2bsseq | Convert 'methrix' to 'bsseq' object | 
| methrix_data | WGBS for colon cancer, chr21 and chr22 | 
| methrix_pca | Principal Component Analysis | 
| methrix_report | Creates a detailed interative html summary report from Methrix object | 
| order_by_sd | Order mathrix object by SD | 
| plot_coverage | Coverage QC Plots | 
| plot_density | Density Plot of beta-Values | 
| plot_pca | Plot PCA results | 
| plot_stats | Plot descriptive statistics | 
| plot_violin | Violin Plot for beta-Values | 
| read_bedgraphs | Versatile BedGraph reader. | 
| region_filter | Filter matrices by region | 
| remove_snps | Removes CpG sites from the object if they overlap with common SNPs | 
| remove_uncovered | Remove loci that are uncovered across all samples | 
| save_HDF5_methrix | Saves HDF5 methrix object | 
| subset_methrix | Subsets 'methrix' object based on given conditions. | 
| write_bedgraphs | Writes bedGraphs from methrix object | 
| write_bigwigs | Exports methrix object as bigWigs |