Scan input genomic regions with known DNA motifs

Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

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

🎯 ChIP peak Annotation, Comparison and Visualization

DecoFlex deconvolution method for Omic data implemented as DecoFlexR

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)

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

Identification of epigenetic sites in MealyBugs using ONT Nanopore Sequencing

This pipeline is designed for the analysis of DNA methylation data generated from the Illumina HumanMethylation450 BeadChip platform.

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Code for SCLC cfMeDIP-seq PRIME as described in the following paper: doi: 10.1016/j.isci.2022.105487

Code for the crb2a multi omics manuscript

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

This repository contains the code used in the following publication: doi.org/10.1016/j.isci.2022.105487

After getting the bed file from the Peak calling, we can annotate and create all downstream analysis of two sets of data

GAMLSS code for modeling PFAS DNA methylation relationship.

Differential Epigenetic Correlation Test

Analysis Pipeline for Single Cell ATAC-seq

Provides easy to use, objective oriented functions for preprocessing methylation data produced by an Illumina Infinium BeadChip and detecting differentially methylated positions and regions within the DNA.