Alternatives and similar repositories for hicrep

Users that are interested in hicrep are comparing it to the libraries listed below

• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆18Updated 2 years ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆43Updated 2 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆28Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 11 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 3 years ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated 2 months ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆47Updated 6 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 3 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆65Updated last year
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆18Updated 4 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆35Updated 9 years ago
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆59Updated 6 months ago
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆41Updated last year
• CSOgroup / CALDER2
  CALDER is a Hi-C analysis tool that allows: (1) compute chromatin domains from whole chromosome contacts; (2) derive their non-linear hie…
  ☆22Updated last month
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated 10 months ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆32Updated 2 months ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆48Updated last month
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆59Updated last year
• ren-lab / hic-pipeline
  ☆24Updated 4 years ago
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆18Updated 7 months ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆25Updated last year
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆22Updated 3 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆73Updated last year
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• bernardo-de-almeida / motif-clustering
  Clustering TF motif models from multiple species (mostly focused on Drosophila and human) by similarity to remove redundancy
  ☆26Updated 2 years ago