chip-seq-analysis

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

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

ChIP-seq pipeline specific for the Zwart lab

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.

Reproducing ChIPDiff’s hidden Markov model to identify changes in H3K27me3 during the differentiation of mouse embryonic stem cells into neural progenitor cells

Project for the Epigenomics course of Bioinformatics for Computational Genomics MSc

Simulation based analysis of ChIP-seq peak calling methods

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

Analysis pipelines for multi-omics study of chromatin dynamics in Arabidopsis pollen - ChIP-seq, ATAC-seq, RNA-seq, and scRNA-seq workflows.

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

Analysis of Existing ChIP-seq data to identify NANOG and SOX2 binding targets

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

Assessment of transcription factor binding sites motifs similarity for any motif models due to motif recognition at different thresholds in the test sample of DNA sequences and estimation of motif co-occurrence

This repository contains the analysis of the Plasmodium falciparum U-DNA-Seq results for the article from Izrael et al.

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

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

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.

This package is designed to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.