ATAC-Seq Transcription Factor Footprint Discovery and Analysis

Analysis scripts for Metzis et. al. (2018)

Batch annotation and visualization of the peaks identified from ChIP-seq, ChIP-chip, ATAC-seq experiments or any experiments resulted in large number of chromosome ranges

Functions used for ATAC-seq analysis using R

Peak calling optimization via real time results assessment and interactive parameter adjustment.

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

scRNA-seq and scATAC-seq utilities

ATAC-seq Quality Control

Definitive endoderm differentiation of human ESCs in G1 phase of the cell cycle

Low coverage accessibility and transcriptomics

Code to reproduce Ponroy, et. al, 2020 in Human Molecular Gentetics

Locus Overlap Analysis: Enrichment of Genomic Ranges

Cell shape‐based chemical screening reveals an epigenetic network mediated by focal adhesions

Functions for QC and analysis of ATAC-seq data

Analyses combining ATAC-seq, RRBS, and RNA-seq data for purple urchins

Scripts to run footprinting and motif-flanking accessibility analysis in DNase-seq/ ATAC-seq data

Michida, H. et al. The number of transcription factors at an enhancer determines switch-like gene expression.

An R shiny application for visualization of EndoC-bH1 and human islet genomic data