Alternatives and similar repositories for scHiCExplorer:

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

• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆37Updated 3 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆36Updated last year
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆26Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆36Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• XiaoTaoWang / Best-Labs-of-3D-Genome
  Data and the co-authored network I extracted for lab selection in 3D genome research field
  ☆14Updated 3 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆28Updated this week
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆20Updated 3 years 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
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆20Updated last year
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 7 months ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆31Updated 2 years ago
• kundajelab / idr
  IDR
  ☆31Updated last year
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆11Updated 3 years ago
• PSI-Lab / HiCSR
  HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
  ☆13Updated 2 years ago
• ma-compbio / Fast-Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
  ☆19Updated last year
• open2c / open2c_examples
  ☆17Updated 11 months ago
• comprna / MoSEA
  Motif Scan and Enrichment Analysis (MoSEA)
  ☆16Updated 4 years ago
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆16Updated 4 years ago
• liu-bioinfo-lab / scHiCTools
  a computational tool for analyzing single cell Hi-C data
  ☆24Updated 9 months ago
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆26Updated this week
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated last year
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆60Updated last year
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆40Updated 10 months ago
• huyustats / SCATS
  A statistical tool to detect differential alternative splicing events using single-cell RNA-seq
  ☆22Updated last year