Analysis Pipeline for Single Cell ATAC-seq

🎯 ChIP peak Annotation, Comparison and Visualization

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

Cell type specific enrichments using finemapped variants and quantitative epigenetic 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

Modelling DNA methylation profiles

Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.

Calculate DNA methylation age using Horvath 2013 method

Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Bacterial Epigenomics Analysis SuiTe

R/Bioconductor package for optimized functional annotation of ChIP-seq data

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.

Differential Epigenetic Correlation Test

Epi-Impute: single-cell RNA-seq imputation via integration with single-cell ATAC-seq data

Online version of tool is live

For inferring ancestry, gestational age, and cell type proportions from placental DNA methylation array data

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)

Scan input genomic regions with known DNA motifs

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.

An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).