hic

There are 1 repository under hic topic.

• deeptools / HiCExplorer

  HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

  hicgenomicschromosome-conformation-capturegalaxypythonbioinformatics
  Language:Python 221

• marbl / SALSA

  SALSA: A tool to scaffold long read assemblies with Hi-C data

  scaffoldassemblyhiclong-read
  Language:Python 171

• omegahh / DeepHiC

  A GAN-based method for Enhancing Hi-C data

  ganhic
  Language:Python 28

• junjunlab / BioSeqUtils

  Extract Sequence from Genome According to Annotation File

  gtfgenometranscriptatac-seqchip-seqhicmerip-seqcoverage-plot
  Language:R 26

• kundajelab / genomedisco

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

  bioinformaticsbioinformatics-pipelinehi-chiccontact-matrix3d-genome3ccapture-c
  Language:Jupyter Notebook 25

• ren-lab / hic-pipeline

  hic
  Language:C 23

• sanger-tol / genomenote

  This Nextflow DSL2 pipeline takes aligned HiC reads, creates contact maps and a table of statistics.

  hicnextflowpublicationsstatisticsgenomicspipeline
  Language:Groovy 19

• HenrikBengtsson / TopDom

  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes

  rpackagehicgenomicscrantopological-domains
  Language:R 18

• dozmorovlab / HiCcompare

  Joint normalization of two Hi-C matrices, visualization and detection of differential chromatin interactions. See multiHiCcompare for the analysis of multiple Hi-C matrices

  hichi-cdifference-detectionvisualizationnormalization
  Language:R 16

• paulsengroup / modle

  High-performance stochastic modeling of DNA loop extrusion interactions

  bioinformaticsbiologycppcpp17dnahigh-performanceloop-extrusionstochastic-modeltadtopologically-associated-domainshic
  Language:C++ 16

• paulsengroup / hictk

  Blazing fast toolkit to work with .hic and .cool files

  bioinformaticscli-applicationconversioncoolercxxcxx-librarycxx17hichictk
  Language:C++ 15

• zhqu1148980644 / hictools

  Tools for processing HIC data.

  hicnextflow-pipelines
  Language:Python 11

• data-fun / 3d-genome-builder

  3DGB is a workflow to build 3D models of genomes from HiC data

  hic3d-genomevizualization
  Language:Python 9

• ViriatoII / Hi-C-scaffolding-pipelines

  I'm sharing my automation of the 3D_DNA and SALSA Hi-C scaffolding pipelines.

  3d-dnajuicerhicscaffoldinggenome
  Language:Shell 7

• paulsengroup / hictkpy

  Python bindings for hictk: read and write .cool and .hic files directly from Python

  bindingsbioinformaticscoolerhichictkpython3
  Language:C++ 6

• nf-core / hicar

  Pipeline for HiCAR data, a robust and sensitive multi-omic co-assay for simultaneous measurement of transcriptome, chromatin accessibility and cis-regulatory chromatin contacts.

  nf-corenextflowworkflowpipelinehicarhicatacatac-seqtranscriptomemulti-omics
  Language:Nextflow 5

• cellular-genomics / python-FIREcaller

  FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

  genomicshicgenomic-data-analysis3d-genomecooler
  Language:Python 4

• lux563624348 / HiC_Hubs

  hicclustersnetwork-analysispython
  Language:Python 4

• 4DGB / hic-converter

  A few tools for converting contact maps to .hic format compatible with the 4D Genome Browser.

  h5hic
  Language:Python 3

• insilicoconsulting / snake-chic

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

  bioinformaticsgenomicshi-chicsnakemakesnakemake-workflowworkflow
  Language:Python 3

• kkrismer / idr2d

  Irreproducible discovery rate for genomic interaction data

  chia-pethichiphicr-packagebioinformatics
  Language:R 3

• sebastian-gregoricchio / snHiC

  Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

  hi-chichicexplorersnakemakesnakemake-pipelinedchicselfishgenovastripenncompartmentslooptad
  Language:Python 3

• dekkerlab / Topo-II-Inhibition-Manuscript

  Github Repo for Hi-C and MC-3C analysis scripts for the Topo II Inhibition Manuscript

  hicmc3c
  Language:Jupyter Notebook 2

• jhammelman / spatzie

  Identification of enriched motif pairs from chromatin interaction data

  transcription-factorsbioinformaticsr-packagehicchia-pethichip
  Language:R 2
• ChrVis

  orionpax00 / ChrVis

  [Research Intern work] HiC Data Analysis Suite

  network-graphfeature-extractiondjangodockerhicmachine-learningdeep-learning
  Language:Jupyter Notebook 2

• paulsengroup / hictkR

  R bindings for hictk: read .cool and .hic files directly from R

  bindingsbioinformaticscoolerhichictkr
  Language:C++ 2

• sanger-tol / curationpretext

  A Nextflow DSL2 pipeline for pretext generation in curation

  nextflowpipelinegenomicshic
  Language:Nextflow 2

• Yin-Shen / CharID

  A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.

  deep-learningchromatin-accessibiityhicloopsinteractionde-novo-prediction
  Language:Python 2

• YoussefAyachii / HiCDataAnalysis

  Using chromatin-chromatin interaction scores generated by the Capture Hi-C technology, I developed this R code during my six week internship in the Spicuglia lab, part of the INSERM institute (TAGC) related to the Aix-Marseille University, France, in order to identify the DNA interactions happening between different regions, specifically the interaction of the OAS3 Epromoter with its target promoters OAS1 and OAS2, before and after IFN alpha stress stimulation and then to figure out the changes of the 3D chromatin organization upon this stress stimulation.

  hicrnarna-seqoasoas3chromatin3cgenetics
  2

• cresswellkg / SpectralTAD

  TAD Calling using spectral clustering in R

  topologicallyassociatingdomainstadstadcallerspectralclusteringspectraltadmachinelearningdatamininghic3dgenomicsrpackage
  Language:R 1

• ctlab / HiCT_JVM

  Interactive visualizer ad manual scaffolder of Hi-C contact maps. All-in-one Java-based implementation.

  all-in-onegenomegenome-assemblygradlehdf5hdf5-fileshdf5-formathdf5-libraryhi-chicitmoitmo-universityjavaopenlayersscaffoldingscaffolding-toolvisualizationvisualization-tooljhdf5manual-scaffolding
  Language:Java 1

• epigen-UCSD / HiC_scripts

  HiC processing scripts used in the center.

  hicpipeline
  Language:Jupyter Notebook 1

• fkarg / HiC-rs

  This part is the python-rust interface for the iterative matrix correction

  rustrust-langpython3bioinformaticshic
  Language:Rust 1

• gifford-lab / spatzie

  Identification of enriched motif pairs from chromatin interaction data

  r-packagechia-pethichiphicbioinformatics
  Language:R 1

• TrEE-TIMC / circhic

  A python library to display HiC data on a circular strip and to integrate genomic data

  visualizationhicgenomicspython
  Language:Python 1

• wtsi-hpag / AncesBin

  Pipeline to bin 10X, HiC, PacBio and ONT reads based on ancestry assemblies

  genome-assemblygenome-ancestryreads-binning10xhicpacbioont
  Language:C 1