Alternatives and similar repositories for scHiCTools:

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

• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated last year
• zhoujt1994 / scHiCluster
  ☆63Updated 2 months ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆26Updated 3 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆37Updated last year
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆29Updated 5 years ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated last year
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• ma-compbio / Fast-Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
  ☆19Updated last year
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆17Updated 4 years ago
• JinLabBioinfo / DeepLoop
  DeepLoop robustly identifies enhancer-promoter interactions from low-depth and single-cell Hi-C data
  ☆31Updated 2 years ago
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆63Updated 4 months ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆70Updated 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
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆68Updated 8 months ago
• lhqing / ALLCools
  Toolkit for single-cell DNA methylation analysis.
  ☆41Updated 2 weeks ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆63Updated last year
• HuMingLab / SnapHiC
  SnapHiC: Single Nucleus Analysis Pipeline for Hi-C Data
  ☆40Updated last year
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆37Updated 3 years ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆58Updated last year
• ay-lab / selfish
  SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.
  ☆17Updated last year
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆17Updated 5 months ago
• JiaqiLiZju / Nvwa
  ☆34Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆67Updated last year
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆17Updated 2 years ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 7 years ago
• mdozmorov / scHiC_notes
  Notes on single-cell Hi-C technologies, tools, and data
  ☆76Updated 5 months ago
• ren-lab / hic-pipeline
  ☆24Updated 3 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• StatBiomed / CamoTSS
  Detection and couting alternative TSS in single cells
  ☆14Updated 11 months ago