Alternatives and similar repositories for cLoops2

Users that are interested in cLoops2 are comparing it to the libraries listed below

• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆65Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆43Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆73Updated last year
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆22Updated 3 years 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
• ren-lab / hic-pipeline
  ☆24Updated 4 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated last year
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆65Updated last year
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated 10 months ago
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆59Updated last year
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆43Updated last year
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆67Updated 6 months ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆66Updated 5 years ago
• AmpliconSuite / AmpliconClassifier
  Classify output of AmpliconArchitect to detect types of focal amplifications present
  ☆19Updated this week
• XiaoTaoWang / Best-Labs-of-3D-Genome
  Data and the co-authored network I extracted for lab selection in 3D genome research field
  ☆15Updated 3 years ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆80Updated 7 months ago
• nerettilab / RepEnrich2
  RepEnrich2 is an updated method to estimate repetitive element enrichment using high-throughput sequencing data.
  ☆39Updated 3 years ago
• LuyiTian / FLAMES
  Full-length transcriptome splicing and mutation analysis
  ☆83Updated 11 months ago
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆109Updated 4 years ago
• dovetail-genomics / Micro-C
  Micro-C QC and data analysis
  ☆16Updated last year
• stjude / ROSE
  ROSE: RANK ORDERING OF SUPER-ENHANCERS
  ☆47Updated 10 months ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 7 years ago
• shawnzhangyx / cvdc_scripts
  scripts for analyzing the CVDC data.
  ☆18Updated 5 years ago
• jlab-code / MethylStar
  A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing (WGBS) data.
  ☆35Updated 3 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆35Updated 9 years ago
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 3 years ago
• 3UTR / DaPars2
  Dynamics analysis of Alternative PolyAdenylation from RNA-seq
  ☆59Updated last year