Alternatives and similar repositories for scHiCExplorer:

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

• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆41Updated 2 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆38Updated 3 years ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆31Updated 2 weeks ago
• 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
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 6 years ago
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆42Updated last year
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆17Updated 4 years ago
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆25Updated 11 months ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 9 months ago
• tjs23 / nuc_dynamics
  Particle dynamics and simulated annealing for chromosome structure calculation
  ☆29Updated last year
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated 2 weeks ago
• open2c / open2c_examples
  ☆17Updated last year
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆30Updated this week
• agalitsyna / fontanka
  Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling …
  ☆11Updated last year
• CraigIDent / SpliSER
  Bioinformatic tool for Splice site Strength Estimation using RNA-seq
  ☆15Updated 2 years ago
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆41Updated last year
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated last year
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆26Updated 2 months ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 4 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆68Updated last year
• kundajelab / idr
  IDR
  ☆31Updated 2 years ago
• ma-compbio / Fast-Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
  ☆19Updated last year
• cboix / EPIMAP_ANALYSIS
  Epimap processing and analysis code repository
  ☆33Updated 2 years ago
• XiaoTaoWang / StripeCaller
  A toolkit for analyzing architectural stripes
  ☆19Updated 4 months ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago