Side project to find jointly accessible regions in pairs of celltypes

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Analysis scripts for Metzis et. al. (2018)

MEGA ATAC-seq Workflow implementation

ATACseq workshop, Jachranka 2017

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

Functions used for ATAC-seq analysis using R

This is an automated workflow pipeline for analyzing bulk ATAC-seq data, implemented primarily in bash scripts, and wrapped in a NextFlow workflow.

Illumina BaseSpace ATACseq pipeline.

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

Chromatin analysis module

This pipeline has been superceeded. Please use >>>

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

A tool for replacing promoter accessibility with a gene activity score.

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

Preprocessing workflow for ATAC-seq and ChIP-seq data

Visualization Analysis of RNAseq,ATACseq,Chipseq and ScRNAseq