SeSAMe

RnBeads — comprehensive R/Bioconductor package for DNA methylation analysis. Supports Illumina Infinium arrays (450K, EPIC/850K), WGBS, RRBS, and other bisulfite sequencing platforms. Key capabilities

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deepTools — suite of Python tools for efficient analysis and visualization of high-throughput sequencing data including ChIP-seq, ATAC-seq, MNase-seq, and RNA-seq. BAM-to-bigWig conversion with normal

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dmrseq is an R/Bioconductor package for detecting differentially methylated regions (DMRs) from whole-genome bisulfite sequencing (WGBS) data. It fits a generalized least squares model with a smooth c

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MOFA+ (Multi-Omics Factor Analysis) — Bayesian group factor analysis framework for unsupervised integration of multiple omics data modalities. Discovers shared and modality-specific latent factors fro

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wateRmelon v2.16.0 — Bioconductor R package for Illumina 450K and EPIC DNA methylation array normalization and performance metrics. Provides 15 normalization methods (dasen, nasen, naten, danes, swan,

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