Analysis scripts for Metzis et. al. (2018)

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

Functions used for ATAC-seq analysis using R

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

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

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

R package for QC of enrichment based NGS assays. ChIP-seq, cut&run, ATAC-seq, etc.

ATAC-seq Quality Control

summarising outputs of samtools stats with ATAC-seq qc in mind

Analysing Capture Seq Count Data

A tool to call CNV (Copy Number Variation) from bulk ATAC-Seq data

Locus Overlap Analysis: Enrichment of Genomic Ranges

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

Chromatin accessibility analysis of spaceflight (NASA) mouse brains using ArchR (Master's Thesis Project)

scRNA-seq and scATAC-seq utilities

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

Functions for QC and analysis of ATAC-seq data

ATAC-Seq Transcription Factor Footprint Discovery and Analysis