Computational Methods for 3D Genome Analysis

Methods for Genome-Wide Chromatin Interaction Analysis.- Structural Maintenance of Chromosomes Complexes.- Read Mapping for Hi-C Analysis.- Micro-C Analysis Workflow using Pairtools and Juicer.- HOMER for Analysis of Hi-C Data and Assessment of Composite Structure of the X Chromosome.- CWL-Based Analysis Pipeline for Hi-C Data: From FASTQ Files to Matrices.- Acquisition and Analysis Methods for Hi-C Data from Medaka Early Embryos.- Step-by-Step Protocol to Generate Hi-C Contact Maps Using the rfy_hic2 Pipeline.- Hi-C/3C-seq Data Analysis for Prokaryotic Genomes with HiC-Pro.- Exploring Contact Distance Distributions with Google Colaboratory.- Supervised Chromatin Loop Detection using Peakachu Version 2.- Systematic Inference of Multi-Scale Chromatin Sub-Compartments using Calder2.- Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy.- Single-Cell Hi-C Analysis Workflow with Pairtools.- Reconstruction of 3D Chromosome Structure from Single Cell Hi-C Data via Recurrence Plots.- 4D Genome Analysis using PHi-C2.- Construction of Coarse-Grained Molecular Dynamics Model of Nuclear Global Chromosomes Dynamics in Mammalian Cells.- Three-Dimensional Simulation of Whole-Genome Structuring through the Transition from Anaphase to Interphase.- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.- Prediction of Enhancer-Gene Interactions using Chromatin-Conformation Capture and Epigenome Data using STARE.- Learning Enhancer-Gene Associations from Bulk Transcriptomic and Epigenetic Sequencing Data with STITCHIT.- Machine and Deep Learning Methods for Predicting 3D Genome Organization.- Processing and Visualization of Protec-Seq Data for the Generation of Calibrated, Genome-Wide Double DSB (Double Strand Break) Maps.- Image Analysis Protocol for DNA/RNA/Immunofluorescence (IF)-seqFISH Data.- Extracting Chromosome Structural Information as One-Dimensional Metrics and Integrating Them with Epigenomics.- Exploring Cohesin-Related Multiomics Information in the Web Browser.