Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
An efficient, documented, reproducible Snakemake methylation analysis pipeline for BS-seq and EM-seq samples, including cfDNA.
Pipeline for BS-Seq data based on snakemake
A flexible and sensitive method for capturing and integrating multimodal epigenetic information from cell-free DNA (cfDNA) using a single experimental assay.
Snakemake workflow for EM-seq / bisulfite sequencing (WGBS) DNA methylation analysis
An integrated deconvolution approach to cfDNA methylation data.
Convert methylation data to sparse objects for machine learning.
Figure and analysis code for the blood–saliva DNA methylation pilot study in a single Korean individual (KOREF1, EM-seq), analysed against hg38 and a personal telomere-to-telomere assembly (KOREF-TTAGGA). Choi et al. 2026.
Pipeline for differential DNA methylation analysis
Code for the plasma cfDNA methylation analyses (36-DMR score) in the BRAND study manuscript: Multimodal genomic features in exhaled breath and plasma in advanced non-small cell lung cancer.
To associate your repository with the em-seq topic, visit your repo's landing page and select "manage topics."