ChAMP

Bismark — bisulfite-seq alignment and methylation calling toolkit. Maps bisulfite-treated reads to a reference genome using Bowtie 2, HISAT2, or minimap2, performs cytosine methylation calls in CpG/CH

1 shared topic

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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SeSAMe (SEnsible Step-wise Analysis of DNA MEthylation BeadChips) — R/Bioconductor package for processing Illumina Infinium DNA methylation arrays. Supports EPIC, EPICv2, HM450, HM27, MM285, and Mamma

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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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