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| MethTargetedNGS-package | Methylation Analysis of Next Generation Sequencing data. |
| bconv | Convert non-bisulfite sequences to bisulfite sequences. |
| compare_samples | Complete Methylation Analysis of Next Generation Sequencing Data |
| fishertest_cpg | Perform Fisher Exact Test on Methylation Data. |
| hmmbuild | Create Profile Hidden Markov Model of given aligned sequences |
| methAlign | Align sequences with the reference sequence using pairwiseAlignment function from BioStrings |
| methAvg | Calculate Methylation Average of given methylation matrix |
| methEntropy | Calculate Methylation Entropy |
| methHeatmap | Generate Heatmap of the given methylation data. |
| MethTargetedNGS | Methylation Analysis of Next Generation Sequencing data. |
| nhmmer | Calculate likelihood of the given profile hidden markov model against group of sequences |
| odd_ratio | Calculate log odd ratio of the given samples (healthy/tumor) |