hanjunlee21/StructuralSimilarity

Identification of dynamic changes in chromatin conformation is a fundamental task in genetics. In 2020, Galan et al. presented CHESS (Comparison of Hi-C Experiments using Structural Similarity), a novel computational algorithm designed for systematic identification of structural differences in chromatin-contact maps. Using CHESS, the same group recently reported that chromatin organization is largely maintained across tissues during dorsoventral patterning of fruit fly embryos despite tissue-specific chromatin states and gene expression. However, here we show that the primary outputs of CHESS–namely, the structural similarity index (SSIM) profiles–are nearly identical regardless of the input matrices, even when query and reference reads were shuffled to destroy any significant differences. This issue stems from the dominance of the regional counting noise arising from stochastic sampling in chromatin-contact maps, reflecting a fundamentally incorrect assumption of the CHESS algorithm. Therefore, biological interpretation of SSIM profiles generated by CHESS requires considerable caution.

Language: Python - Size: 94 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

hugp-ri/hicup-plus

Hi-C data processing pipeline (with Dragen, HiSAT2, or STAR aligner)

Language: Perl - Size: 2.34 MB - Last synced at: 2 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 2

4dn-dcic/Rpairix

R binder for pairix - 2D/1D genomic indexing and querying on bgzipped text file

Language: C - Size: 78.3 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 7 - Forks: 4

3DGenomes/binless

Resolution-independent normalization of Hi-C data

Language: C++ - Size: 558 MB - Last synced at: about 1 year ago - Pushed at: almost 6 years ago - Stars: 7 - Forks: 2

YaqiangCao/cLoops

Accurate and flexible loops calling tool for 3D genomic data.

Language: Python - Size: 464 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 103 - Forks: 48

yezhengSTAT/mHiC

Language: Python - Size: 22.4 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 20 - Forks: 10

magnitov/pentad

A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.

Language: Python - Size: 3.81 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 9 - Forks: 1

koustav-pal/HiCBricks

HiCBricks offers user-friendly and efficient solutions for handling large high-resolution Hi-C datasets. The package provides a R/Bioconductor framework with the bricks to build more complex data analysis pipelines and algorithms.

Language: R - Size: 10.3 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 4

gavinf97/groupnextflow

Hi-C Nextflow script and Singularity container for a collaborative group MSc project.

Language: Nextflow - Size: 422 KB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1

magnitov/prokaryotic_cids

The code from the paper "Benchmark of software tools for prokaryotic chromosomal interaction domain identification"

Language: Python - Size: 106 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 1

HiC-inspector/HiC-inspector

HiC-inspector, a bioinformatics pipeline to facilitate the analysis of HiC dataset.

Language: JavaScript - Size: 341 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 9 - Forks: 5

flekschas/hipiler

Visual exploration of large genome interaction matrices with interactive small multiples.

Language: JavaScript - Size: 11.9 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 13 - Forks: 0

3DGenomes/MethodsMolBiol

Language: Jupyter Notebook - Size: 43.3 MB - Last synced at: 11 months ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 1

billgreenwald/pgltools

Paired Genomic Loci Tool Suite

Language: Python - Size: 1.03 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 27 - Forks: 5

Genome3d/alcohol-dependence

Analysis of tissue-specific regulatory impacts of alcohol dependence-associated SNPs.

Language: HTML - Size: 3.91 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 2

skkap/mdsga

Tool for chromatin 3D structure reconstruction from 3C experimental data. Improvement of ShRec3D.

Language: Python - Size: 23.7 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 1

JesperGrud/PCHiC_3T3L1

Size: 120 KB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 5 - Forks: 9

koszullab/3C_tutorial Fork of axelcournac/3C_tutorial

Step by step command-line tutorial to process Hi-C data

Language: Python - Size: 17.6 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 4 - Forks: 1

Genome3d/psychiatric_and_cognitive_multimorbidities

Analysis of regulatory impacts of GWAS SNPs associated with psychiatric disorders and cognitive functioning.

Language: HTML - Size: 35.3 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

dhslab/nf-core-hic

Pipeline for Hi-C data analysis

Language: Nextflow - Size: 3.13 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1

takaho/TADtree Fork of raphael-group/TADtree

JIT-accelerated HiC analysis tool

Language: Python - Size: 4.6 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

antoneri/hicparser

Python decoder for the HiC genome contact format

Language: Python - Size: 14.6 KB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

4dn-dcic/GiniQC

Tool for single-cell Hi-C quality control

Language: Python - Size: 52.7 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1

dawnmy/HAPPY

Hi-C data Analysis and Processing PIpeline

Language: Python - Size: 38.1 KB - Last synced at: almost 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

OluwadareLab/HiCARN

HiCARN: Resolution Enhancement of Hi-C Data Using Cascading Residual Networks

Language: Python - Size: 276 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 4 - Forks: 2

NuriddinovMA/C-InterSecture

Language: Python - Size: 540 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 4 - Forks: 1

kundajelab/genomedisco

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

Language: Jupyter Notebook - Size: 431 MB - Last synced at: 8 months ago - Pushed at: about 7 years ago - Stars: 25 - Forks: 10

flekschas/higlass-fancy

A collection of fancy HiGlass view configs

Size: 1.37 MB - Last synced at: 4 months ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0

koszullab/serpentine

Local, normalization-free contact map binning

Language: Python - Size: 9.65 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 3

dohlee/snakemake-hic-processing

Hi-C processing pipeline in snakemake.

Language: Python - Size: 6.84 KB - Last synced at: 16 days ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

kevinbdsouza/Hi-C-LSTM

Hi-C-LSTM is a framework to form Hi-C representations that are useful for tasks such as element identification and in-silico modification.

Language: Python - Size: 218 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0

LTLA/archive-InteractionSet 📦

An archived version of the InteractionSet repository, see https://github.com/LTLA/InteractionSet for the active version.

Language: R - Size: 455 KB - Last synced at: 12 months ago - Pushed at: about 8 years ago - Stars: 2 - Forks: 2

higlass/higlass-website 📦

HiGlass Project Website

Language: HTML - Size: 12.7 MB - Last synced at: about 1 year ago - Pushed at: about 6 years ago - Stars: 3 - Forks: 4

OluwadareLab/HiC-GNN

A Generalizable Model for 3D Chromosome Reconstruction Using Graph Convolutional Neural Networks

Language: Python - Size: 112 KB - Last synced at: over 2 years ago - Pushed at: almost 4 years ago - Stars: 4 - Forks: 1

CSOgroup/WGD

Analysis code for "Whole genome doubling drives oncogenic loss of chromatin segregation"

Language: Python - Size: 49.8 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Irenexzwen/3D-genome-gitbook

An ebook- introduction of Genome Interaction

Size: 55.3 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 5 - Forks: 2

OluwadareLab/CBCR

CBCR: A Curriculum Based Strategy For Chromosome Reconstruction

Language: MATLAB - Size: 1010 KB - Last synced at: over 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

wangyibin/collapse_rescue

Method for rescuing collapsed contigs.

Language: Python - Size: 10.7 KB - Last synced at: over 2 years ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

Genome3d/multimorbidity-atlas

Pipeline to investigate multimorbidity of complex traits/phenotypes by integrating chromatin interaction and expression quantitative trait loci data.

Language: HTML - Size: 25.5 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

JohnnyChen1113/3d-dna_pipeline_for_4_enzyme_arima

Adapted 3d-dna pipeline for 4 enzyme cocktail arima Hi-C toolkit

Language: Shell - Size: 17.6 KB - Last synced at: 11 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

XiaoTaoWang/Best-Labs-of-3D-Genome

Data and the co-authored network I extracted for lab selection in 3D genome research field

Language: Python - Size: 39.2 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 10 - Forks: 3

conchoecia/hormiphora

Hormiphora californensis genome annotation and supplemental materials related to the genome assembly.

Language: HTML - Size: 433 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

MaheshChandrra/Hi-C-Analysis

Hi-C Sequence Mapping using FANC

Language: Jupyter Notebook - Size: 226 KB - Last synced at: over 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

dmitrymyl/TADselect

Comparison of TAD callers with strategies for parameter selection.

Language: Python - Size: 88.9 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

kuzobuta/hic_paper_NG_2019

Processed data set of Miura et al., Nature Genetics, 2019

Language: R - Size: 193 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 2 - Forks: 3

kevinbdsouza/graph_embed_hic

SCI and LINE to form Hi-C graph embeddings. Comparison with Hi-C-LSTM. Modification of original repository.

Language: Python - Size: 5.71 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

DamienLegros/compartments-project

Projet MEET-U master 2 BIM : 2022 - 2023 Projet de bio-informatique sur les compartiments codé en Python

Language: Python - Size: 192 MB - Last synced at: over 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

Lan-lab/Chrom-Lasso

Chrom-Lasso is Hi-C cis interaction calling tool

Language: C++ - Size: 14.2 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 2

phicks22/HiCARN

Super enhancement of Hi-C contact map resolutions

Language: Python - Size: 179 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

4dn-dcic/4dn-policies

Policies for the NIH Common Fund 4D Nucleome Network.

Size: 12.7 KB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 6 - Forks: 0

UtkarshVerma/LineFollower

:zap: Repository dedicated to hosting files related to a Line Follower Robot based on PIC16F84A.

Language: C - Size: 86.3 MB - Last synced at: over 2 years ago - Pushed at: over 7 years ago - Stars: 2 - Forks: 0

cmdoret/vapormap

Cloud based pipeline for parallelized iterative alignment of Hi-C data

Language: Nextflow - Size: 74.4 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

Genome3d/ACE2-regulatory-network

Analysis of host regulatory networks that could be impacted upon infection with the Covid-19 virus

Language: HTML - Size: 778 KB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

gersteinlab/MrTADFinder

a method to identify TADs in Hi-C data

Language: Julia - Size: 394 KB - Last synced at: 25 days ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 3

liuyifang/disease

Language: HTML - Size: 1.73 MB - Last synced at: 2 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

GoodBoy962/Dictyostelium-loops

Dictyostelium loops recognizer

Language: Jupyter Notebook - Size: 458 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

Genome3d/blood-metabolites-regulation

Language: Python - Size: 14.2 MB - Last synced at: over 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

baudrly/yahcp

Yet Another Hi-C Pipeline

Language: Python - Size: 38.1 KB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

LTLA/BiocISet2016

Technical note for the InteractionSet package

Language: TeX - Size: 39.1 KB - Last synced at: 3 months ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0

4dn-dcic/docker-dedup-hic

Language: Shell - Size: 1.95 KB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

4dn-dcic/hicfilters

Language: Python - Size: 43.6 MB - Last synced at: about 1 year ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 0

4dn-dcic/docker-hicfilters

Language: Shell - Size: 4.22 MB - Last synced at: over 1 year ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0