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

Data analysis of DNA methylation EPIC array data in post-mortem brain tissue from DLB and control subjects.

🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips

R package to represent the differences in DNA methylation at CpG level across 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.

R package for DNA methylation analysis

An R 📦 for fast and flexible DNA methylation analysis

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.

TFregulomeR reveals transcription factors’ context-specific features and functions

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

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

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

R-based DNA methylation array data analysis workflow.

Code accompanying the findings in Duran-Ferrer 2020, Nat Cancer. The epiCMIT mitotic clock calculator and a Pan B-cell tumor classifier algorithm are provided.

Blood-derived DNA methylation-based prediction of midlife dementia risk

Identification of epigenetic sites in MealyBugs using ONT Nanopore Sequencing

Annotating epigenetic variation among samples with region sets in R

An R package for weighted region comethylation network analysis