Side project to find jointly accessible regions in pairs of celltypes

Analysis scripts for Metzis et. al. (2018)

ATAC-Seq Transcription Factor Footprint Discovery and Analysis

ATACseq workshop, Jachranka 2017

Functions used for ATAC-seq analysis using R

Transcriptional and epigenetic signature of muscle tissue cells linked to atrophy

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

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

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.

Snakemake pipeline for ATAC-Seq

Nazzari, et al. (2023) 'Investigation of the effects of phthalates on in vitro thyroid models with RNA-Seq and ATAC-Seq'

Lab data processing pipelines

Computational Suite For Bioinformaticians and Biologists (CSBB) provides 18 modules focused on analytical tasks like performing upper-quantile normalization, interactive visualization and next generation sequencing pipelines. CSBB now also has capability to process public data. Providing User with End to End pipeline experience

Code for Karakaslar, Katiyar et al., Aging Cell 2023

Code and data for the bulk RNA-seq and bulk ATAC-seq data of tumor-infiltrating CD8 T cells (and controls) as published in Scott et al., Nature (2019).

ATAC-seq Quality Control

NGS analysis pipeline for ATAC-seq experiments.