Uncovering correlated variability in epigenomic datasets using the Karhunen-Loeve Transform

🔬 A replication of ChiP-Seq analysis from an experiment regarding gene induction and repression during terminal erythropoiesis that are mediated by distinct epigenetic changes

This R package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. Tested on ChIP-Seq peaks and nucleosome positions.

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

ChIP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.

This repository contains my own ChIP-seq analysis workflow, which I have been using so far during my PhD project.

Supplementary Materials for "Intragenomic conflict underlies extreme phenotypic plasticity in queen-worker caste determination in honey bees (Apis mellifera)"

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

Project for the Epigenomics course of Bioinformatics for Computational Genomics MSc

A comprehensive source for Stathopoulos lab code generated and used in data analysis.

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

This project explores the PBRM1-PIAS1 interaction in epithelial differentiation through ChIP-seq analysis, highlighting EZH2's role and implications for cholesterol biosynthesis in cellular processes.

ChIP-seq pipeline specific for the Zwart lab

Extraction of genomic background set of DNA sequences for a given foreground set of sequences for subsequent de novo motif discovery