Biocview "HiC"

R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

sirusb/R3CPET

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

steveped/chipExtra

Additional functions for working with ChIP-Seq data

steveped/extraChIPs

Additional functions for working with ChIP-Seq data

js2264/coolerr

Analysing cool files in R with HiContacts

js2264/cooleR

Analysing cool files in R with HiContacts

jianhong/interactionHub

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

jianhong/GenomicInteractionHub

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

jianhong/GenomicInteractionNodes

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

bioinfo-lab/TADBD

A sensitive and fast tool for detection of TAD boundaries

bnbc

Bandwise normalization and batch correction of Hi-C data

hansenlab/bnbc

Bandwise normalization and batch correction of Hi-C data

InteractionSet

Base Classes for Storing Genomic Interaction Data

LTLA/InteractionSet

Base Classes for Storing Genomic Interaction Data

GOTHiC

Binomial test for Hi-C data analysis

borimifsud/GOTHiC

Binomial test for Hi-C data analysis

Chicago

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

LTLA/GenomicInteractions

Classes and Methods for Handling Genomic Interaction Data

EricSDavis/Bioc2021

Collection of BioC2021 resources

ibn-salem/sevenC

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

ibn-salem/chromloop

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

sevenC

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

PhanstielLab/BentoBox

Coordinate-Based Genomic Visualization Package for R

PhanstielLab/plotgardener

Coordinate-Based Genomic Visualization Package for R

diffHic

Differential Analyis of Hi-C Data

LTLA/diffHic

Differential Analyis of Hi-C Data

HiCBricks

Framework for Storing and Accessing Hi-C Data Through HDF Files

koustav-pal/HiCBricks

Framework for Storing and Accessing Hi-C Data Through HDF Files

koustav-pal/HiCLegos

Framework for Storing and Accessing Hi-C Data Through HDF Files

koustav-pal/HiCBlocks

Framework for Storing and Accessing Hi-C Data Through HDF Files

LTLA/fugi

Further Utilities for Genomic Interactions

jrboyd/dthic

HiC analysis using data.table

mworkman13/HiCAGE

Hi-C Annotation and Graphics Ensemble

HiCcompare

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

dozmorovlab/HiCcompare

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

dozmorovlab/HiCdiff

HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

mervesa/HiCDCPlus

Hi-C Direct Caller Plus

bioinfo-pf-curie/HiTC

High Throughput Chromosome Conformation Capture analysis

HiTC

High Throughput Chromosome Conformation Capture analysis

jhammelman/spatzie

Identification of enriched motif pairs from chromatin interaction data

kkrismer/idr2d

Irreproducible Discovery Rate for Genomic Interactions Data

idr2d

Irreproducible Discovery Rate for Genomic Interactions Data

Pi

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

Pi

Leveraging Genetic Evidence to Prioritise Drug Targets at the Gene and Pathway Level

qunhualilab/hicrep

Measuring the reproducibility of Hi-C data

MonkeyLB/hicrep

Measuring the reproducibility of Hi-C data

hicrep

Measuring the reproducibility of Hi-C data

MACPET

Model based analysis for paired-end data

IoannisVardaxis/MACPET

Model based analysis for paired-end data

dozmorovlab/multHiCcompare

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

dozmorovlab/multiHiCcompare

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

multiHiCcompare

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

jstansfield0/multiHiCcompare

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

jstansfield0/HiCcompare2

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

dozmorovlab/preciseTAD

preciseTAD: A machine learning framework for precise TAD boundary prediction

preciseTAD

preciseTAD: A machine learning framework for precise TAD boundary prediction

stilianoudakis/preciseTAD

preciseTAD: A machine learning framework for precise TAD boundary prediction

InTAD

Search for correlation between epigenetic signals and gene expression in TADs

kokonech/InTAD

Search for correlation between epigenetic signals and gene expression in TADs

SpectralTAD

SpectralTAD: Hierarchical TAD detection using spectral clustering

cresswellkg/SpectralTAD

SpectralTAD: Hierarchical TAD detection using spectral clustering

dozmorovlab/SpectralTAD

SpectralTAD: Hierarchical TAD detection using spectral clustering

cresswellkg/TADCompare

TADCompare: Identification and characterization of differential TADs

TADCompare

TADCompare: Identification and characterization of differential TADs

dozmorovlab/TADCompare

TADCompare: Identification and characterization of differential TADs

Sushi

Tools for visualizing genomics data

PhanstielLab/Sushi

Tools for visualizing genomics data

dphansti/Sushi

Tools for visualizing genomics data

GenomicInteractions

Utilities for handling genomic interaction data

ComputationalRegulatoryGenomicsICL/GenomicInteractions-new

Utilities for handling genomic interaction data

ComputationalRegulatoryGenomicsICL/GenomicInteractions

Utilities for handling genomic interaction data