methylation-analysis

A collection of resources to filter 'bad' probes from the Illumina 450k and EPIC methylation arrays

Bayesian modelling of DNA methylation heterogeneity at single-cell resolution

ATaRVa - Analysis of Tandem Repeat Variation

MultiNano is a deep learning framework designed for predicting m6A RNA modifications using raw electrical signals from Oxford Nanopore sequencing. It provides high accuracy across species and conditions, offering a user-friendly pipeline for researchers. MultiNano supports both training from scratch and direct prediction modes.

Python toolkit for parsing, processing, and analysis of Illumina methylation array IDAT files

Comprehensive tool for visualizing genome-wide cytosine data.

Regional Association of DNA Methylome variability with the Exposome and geNome (RAMEN) is an R package which goal is to identify Variable Methylated Loci (VML) in microarray DNA methylation data. Then, using genome (G) and exposome (E) data, it can identify which individual (G or E) or joint (G+E or GxE) model better explains the VML variability.

A methylation array analysis pipeline tailored for discovering rare methylation events with interactive data visualization

This package provides Illumina Mouse Methylation Array Annotation (12.v1, Genome Build mm10) compatible with minfi.

This package provides Illumina Mouse Methylation Array Manifest (12.v1, Genome Build mm10) compatible with minfi.

Visualizer for Motifs/Methylation in Tandem-Repeat Alleles

adaptable and intrepretable,multi-task learning based gene-level methylation estimations

The transferase system for retrieving methylome data from methbase

Re-implementation of J. Beaulaurier et al's SMSN strategy, using the default PacBio tools

DNA methylation analysis pipeline for reduced representation bissulfite sequencing data

Fast and efficient conversion of Nanopore modBAM from guppy basecaller to BED files for differential methylation and machine learning predictions

Impact of lossy compression of nanopore raw signal data on basecall and consensus accuracy

Differentially methylated regions analysis

DNA methylation (DNAm) Bioconductor package for Illumina Methylation arrays (EPICv2, EPIC and 450K). DOI: 10.18129/B9.bioc.dnaEPICO

The following repository contains code to analyse MeD-seq data and detect statistically significant genomic bins.