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: over 7 years ago - Stars: 3 - Forks: 1

zwang-bioinformatics/scHiGex

This repository includes code and a pre-trained model of scHiGex for single-cell gene expression prediction.

Language: Python - Size: 40 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

sa501428/clear-tools

Chromatin Landscape Exploration, Analysis, and Research Tools

Language: Java - Size: 80.9 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 2 - Forks: 2

roybarkan2020/AbsGenome

Genome assembly steps (Haliotis asinina)

Size: 2.6 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

insilicoconsulting/snake-chic

Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow

Language: Python - Size: 8.79 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0

OluwadareLab/TADMaster

TADMaster: A Comprehensive Web-based Tool For Analysis of Topologically Associated Domains

Language: Python - Size: 81.4 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 2 - 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

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

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: about 2 years ago - Pushed at: about 7 years ago - Stars: 2 - 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An archived version of the InteractionSet repository, see https://github.com/LTLA/InteractionSet for the active version.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: 10 months ago - Pushed at: almost 8 years ago - Stars: 2 - Forks: 2

SLUR-m-Py/SLURPY

SLUR(M)-py: A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

Language: Python - Size: 421 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 1 - Forks: 0

sebgra/hicberg

Statistical profiling based program for contact (Hi-C) and pair ended genomic data reconstruction

Language: Python - Size: 110 MB - Last synced at: 4 days ago - Pushed at: 4 months ago - Stars: 1 - Forks: 1

hanjunlee21/Lee-et-al-2023

RB represses cohesin-dependent loop formation and safeguards E2F-independent transcription

Language: Jupyter Notebook - Size: 70.4 MB - Last synced at: about 2 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

yufanzhouonline/HiSIF

HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops

Language: C++ - Size: 140 MB - Last synced at: 2 months ago - Pushed at: 7 months ago - Stars: 1 - Forks: 0

robomics/call_tad_cliques

Nextflow workflow to call TAD cliques

Language: Python - Size: 194 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

lanl/SLUR-M-py

SLUR(M)-py (pronounced slurpy): A SLURM Powered Pythonic Pipeline for Parallel Processing of 3D (Epi)genomic Profiles

Language: Python - Size: 203 KB - Last synced at: about 1 month ago - Pushed at: 10 months ago - Stars: 1 - Forks: 0

dyxstat/ImputeCC

ImputeCC enhances integrative Hi-C-based metagenomic binning through constrained random-walk-based imputation

Language: Python - Size: 4.9 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 1

sshen82/BandNorm

Simple Normalization Method for single-cell Hi-C

Language: R - Size: 17.8 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 2

dhslab/nf-core-hic

Pipeline for Hi-C data analysis

Language: Nextflow - Size: 3.13 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 1

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

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: 9 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

wangyibin/collapse_rescue

Method for rescuing collapsed contigs.

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

phicks22/HiCARN

Super enhancement of Hi-C contact map resolutions

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

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: about 2 years ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 0

4DNucleome/tad_compare

Compare different sets of TADs inferred from Hi-C data (or other 3C technique) using different methods.

Language: Python - Size: 97.7 KB - Last synced at: 11 months ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 2

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

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

nlawlor/Multiomic_Browser

An R shiny application for visualization of EndoC-bH1 and human islet genomic data

Language: R - Size: 18 MB - Last synced at: about 1 year ago - Pushed at: over 6 years ago - Stars: 1 - Forks: 1

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

flekschas/hipiler-server 📦

[OUTDATED: Use HiGlass Server instead] The HiPiler Server

Language: Python - Size: 46.9 KB - Last synced at: about 1 year ago - Pushed at: almost 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: about 8 years ago - Stars: 1 - Forks: 0

4dn-dcic/docker-dedup-hic

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

Ashley-Milton/OAN-epigenetic-profiling

Language: R - Size: 41 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

OpenOmics/HiIP

An awesome Hi-C + ChIP (HiChIP) sequencing pipeline.

Language: Python - Size: 577 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

Siegel-Lab/libBioSmoother

On-the-fly processing and visualization of interactome data.

Language: C++ - Size: 32.7 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 1

mderakh3/IBD_variants-to-gene-mapping

Source code for uncovering IBD risk-driving regulatory mechanisms within different immune cell types

Language: R - Size: 181 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

ytanaka-bio/cisMultiDeep

Workflow to identify functional cis-regulatory regions for each annotated cell type

Language: Python - Size: 830 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

jlchen5/Hi-C-Data-analysis

Language: Shell - Size: 7.81 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

CSOgroup/WGD

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

Language: Python - Size: 49.8 KB - Last synced at: about 2 years ago - Pushed at: over 2 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: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

Genome3d/blood-metabolites-regulation

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

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: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

foerstner-lab/HiCsuntdracones

HiC sunt dracones - or HiCDS in short - Your little helper for the HiC analysis

Language: Python - Size: 273 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 1

dohlee/snakemake-hic-processing

Hi-C processing pipeline in snakemake.

Language: Python - Size: 6.84 KB - Last synced at: 2 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

MaheshChandrra/Hi-C-Analysis

Hi-C Sequence Mapping using FANC

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

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: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

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: over 3 years ago - Stars: 0 - Forks: 1

kevinbdsouza/GraphTransHiC

A Graph Transformer that creates hierarchal representations for HiC data.

Language: Python - Size: 7.22 MB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

OluwadareLab/CBCR

CBCR: A Curriculum Based Strategy For Chromosome Reconstruction

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

cmdoret/vapormap

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

Language: Nextflow - Size: 74.4 MB - Last synced at: 3 months ago - Pushed at: over 4 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: over 5 years ago - Stars: 0 - Forks: 0

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

baudrly/yahcp

Yet Another Hi-C Pipeline

Language: Python - Size: 38.1 KB - Last synced at: 3 months ago - Pushed at: over 6 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

liuyifang/disease

Language: HTML - Size: 1.73 MB - Last synced at: 28 days ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

takaho/TADtree Fork of raphael-group/TADtree

JIT-accelerated HiC analysis tool

Language: Python - Size: 4.6 MB - Last synced at: over 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

SmythLab/diffHicUsersGuide

Source code and comments for the diffHic user's guide.

Language: TeX - Size: 414 KB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

LTLA/BiocISet2016

Technical note for the InteractionSet package

Language: TeX - Size: 39.1 KB - Last synced at: about 1 month ago - Pushed at: almost 9 years ago - Stars: 0 - Forks: 0