methylation

Signal-level algorithms for MinION data

R package for DNA methylation analysis

Deep neural networks for predicting CpG methylation

A (mostly) universal methylation extractor for BS-seq experiments.

Detecting methylation using signal-level features from Nanopore sequencing reads

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

Arioc: GPU-accelerated DNA short-read alignment

Methylation/modified base calling separated from basecalling.

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

An information-theoretic pipeline for methylation analysis of WGBS data

Bioinformatics library in Kotlin

A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.

Differential methylation: Easy, Fast, Identification and ANnoTation

Python package to analyze DNA methylation data

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes

Suite of tools to conduct methylation data analysis. Methods from this workspace can be used for alignment and quality control analysis for various protocols including Whole Genom Bisulfite Sequencing (WGBS), Reduced Representation Bisulfite Sequencing (RRBS) and Hybrid Selection Bisulfite Sequencing (HSBS).

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

Bayesian Clustering and Imputation of Single Cell Methylomes

JBrowse plugin for methylation related things

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies

BiSulfite Bolt - A Bisulfite Sequencing Alignment and Processing Tool

Important papers relating to the biology of cell free DNA

Targeted Amplicon Bisulfite Sequencing Analysis Tool

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

Get methylation-based age estimates.

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

A computational toolkit of fast and automatical identification of back-splice junctions of potential circular RNAs (circRNAs) from RNA-seq data.

Bacterial Epigenomics Analysis SuiTe

bicycle (bisulfite-based methylcytosine caller) is a next-generation sequencing bioinformatics pipeline able to perform a full DNA methylation level analysis