Signal-level algorithms for MinION data

Deep neural networks for predicting CpG methylation

R package for DNA methylation analysis

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

An information-theoretic pipeline for methylation analysis of WGBS data

Differential methylation: Easy, Fast, Identification and ANnoTation

Bayesian Clustering and Imputation of Single Cell Methylomes

JBrowse plugin for methylation related things

Important papers relating to the biology of cell free DNA

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

Targeted Amplicon Bisulfite Sequencing Analysis Tool

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).

Bioinformatics library in Kotlin

Python package to analyze DNA methylation data

SCREW: A Reproducible Workflow for Single-Cell Epigenomics

METHYLSTAR Project

Get methylation-based age estimates.

Python-based Illumina methylation array analysis software

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

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

💹 The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.

ENCODE whole-genome bisulfite sequencing (WGBS) pipeline

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data

Gaussian mixture modelling - Unsupervised learning

Toolkit for concretely describing non-canonical DNA, RNA, and proteins