Table 1 Comparisons of MethylC-analyzer with other methylation analysis tools
Features | MethylC-analyzer | BAT (2017) | Bicycle (2018) | RnBeads 2.0 (2019) | HOME (2019) | nf-core/methylseq (2020) |
|---|---|---|---|---|---|---|
Environment | CLI/GUI/ Docker | Docker | CLI | CLI/GUI | CLI | Docker |
Experimental approaches | WGBS, RRBS | WGBS, RRBS | WGBS and 5hmC seq | EPIC microarrays, WGBS and RRBS | WGBS, RRBS | WGBS, RRBS |
Alignment | − | + | + | − | − | + |
Sequence context of cytosine methylation | CG, CHG, CHH | CG | CG, CHG, CHH | CG | CG, CHG, CHH | CG, CHG, CHH |
Visualization of the general methylome | PCA, Hierarchical clustering heatmap | − | − | PCA, Hierarchical clustering heatmap | − | − |
Genome-wide visualization | + | + | − | + | − | − |
Visualization of methylation levels at specific regions | + | − | − | − | − | − |
Differential methylation analysis | DMRs and DMGs | DMRs | DMRs | DMRs | DMRs | - |
Visualization of DMR enrichment within specific genomic features | + | − | − | − | − | − |
Converting GTF gene annotation to .bed files with 7 genomic regions | + | − | − | − | − | − |
Generating files for loading into genome browsers (i.e., IgV) | + | − | + | − | − | − |
DMR testing method | Student's t test | 2D-KS with dynamic border | Likelihood ratio of beta-binomial models | Welch’s t test | Weighted logistic regression | − |