Nanomotif - a tool for identifying methylated motifs in metagenomic samples

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

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

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

ForkedTF is an R-library that introduces Forked-PMW (FPMW) and Forked-Sequence Logos (F-Logos) to provide a more comprehensive depiction of the sequence affinity of a Transcription factor (TF) of interest, including its DNA sequence and DNA methylation level, along with a segregated list of partner TFs.

A multiomics approach reveals RNA dynamics promote cellular sensitivity to DNA hypomethylation

methylR: a single shiny solution from sequencer data to pathway analysis

DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types

Toolkit for single-cell DNA methylation analysis.

Msuite2: integrated DNA methylation data analysis toolkit with enhanced performance

TFregulomeR reveals transcription factors’ context-specific features and functions

R package for DNA Methylation Analysis (and Gene Expression Integration) for Illumina Infinium Array and BS-Seq Data

Python package with CLI for downstream analysis of single cell methylation data.

Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package

Predicts the age of a person using the methylation frequencies of CpG sites in human blood/saliva samples.

Regional Association of Methylation variability with the Exposome and geNome (RAMEN) is an R package whose goal is to identify Variable Methylated Regions (VMRs) in microarray DNA methylation data. Additionally, using Genotype (G) and Environmental (E) data, it can identify which G, E, G+E or GxE model better explains this variability.

NANOME pipeline (Nanopore long-read sequencing data consensus DNA methylation detection)

A chronological age predictor based on DNA methylation

Analysis of Single Molecule Footprinting (SMF) data for the analysis of DNA methylation, chromatin accessibility and TF binding. The repository contains all primary code to reproduce the main analyses for the publication "Single molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation" (Kreibich et al., 2023)

Code to estimate Tumor Content end Phenotype Evidence score from samples sequenced with the NEMO panel