Alternatives and similar repositories for pentad

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

• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆52Updated 6 months ago
• 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…
  ☆24Updated 6 months ago
• ahansenlab / RCMC_analysis_code
  Code associated with with the 2023 Nature Genetics Paper "Region Capture Micro-C reveals coalescence of enhancers and promoters into nest…
  ☆12Updated 2 years ago
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆75Updated 3 months ago
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆61Updated last month
• zhongmicai / Hic_tools_collection
  ☆12Updated 6 years ago
• 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 …
  ☆12Updated 2 years ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆52Updated 4 months ago
• deLaatLab / pipe4C
  4C-seq processing pipeline
  ☆26Updated 7 months ago
• ChenFengling / HiCpipe
  an efficient Hi-C data processing pipeline
  ☆17Updated last year
• Tian-Dechao / diffDomain
  DiffDomain is a statistically sound method for detecting differential TADs between conditions
  ☆18Updated 4 months ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆72Updated last year
• open2c / cooler-binder
  Cooler demo using a Jupyter notebook Binder
  ☆18Updated 5 years ago
• mirnylab / hiclib-legacy
  A legacy repository. Was replaced by distiller, cooler, and cooltools.
  ☆21Updated 5 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆73Updated 2 years ago
• dixonlab / hic_breakfinder
  ☆37Updated 6 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆24Updated 4 years ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated 11 months ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆69Updated last year
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• ZhaiLab-SUSTech / snuupy
  single-nucleus nanopore reads processing pipeline
  ☆16Updated 2 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• agalitsyna / avTAD
  Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
  ☆10Updated 4 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆19Updated 5 years ago
• wyang17 / SQuIRE
  Software for Quantifying Interspersed Repeat Expression
  ☆63Updated 3 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago