A cool place to store your Hi-C
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Updated
Sep 16, 2024 - Python
A cool place to store your Hi-C
TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…
C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
Chromosome polymer simulations and in silico capture experiments
Methods for summarizing and visualizing multi-biosample functional genomic annotations
A Python implementation for BH-FDR and HiCCUPS
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
Comparison of Hi-C Experiments using Structural Similarity.
Scripts to create cartoons of 3D genomes
Processing, quality control and analysis of GAM datsets
Step-by-step instructions and Snakemake pipeline for processing Cut&Run data
Chromatin loop caller using Topological Data Analysis based on Hi-C data
This is the code for the chromatin packing model in macrogenomics engineering study
Workflow for processing single-cell sortChIC data
ChIPseq pipeline for Pasini's lab written in snakemake
Make a phylogeny using the chromatin structure information extracted from Hi-C experiments (mirror of the original repo)
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