Alternatives and similar repositories for HiCMatrix

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

• dixonlab / hic_breakfinder
  ☆36Updated 6 years ago
• agalitsyna / avTAD
  Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).
  ☆10Updated 4 years ago
• ay-lab / HiCnv
  HiCnv is used to call copy number variations and breakpoints from Hi-C data
  ☆21Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆44Updated 3 years ago
• paulsengroup / hictk
  Blazing fast toolkit to work with .hic and .cool files
  ☆38Updated this week
• LappalainenLab / lorals
  ☆36Updated 2 years ago
• maxplanck-ie / HiCAssembler
  Software to assemble contigs/scaffolds into chromosomes using Hi-C data
  ☆28Updated 11 months ago
• CSOgroup / CALDER
  ☆22Updated 2 years ago
• scoutzxb / CscoreTool
  ☆21Updated 5 years ago
• josiegleeson / BamSlam
  Summarise and plot data from long-read ONT (direct RNA/cDNA) BAM files
  ☆14Updated last year
• vaquerizaslab / tadtool
  TADtool is an interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
  ☆48Updated 2 years ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆50Updated 4 months ago
• vierstralab / genome-tools
  Processing and plotting tools for genomics data
  ☆21Updated 2 weeks ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆50Updated 6 years ago
• parklab / HiNT
  HiC for copy Number variation and Translocation detection
  ☆39Updated 4 years ago
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆27Updated 2 years ago
• anlin00007 / OnTAD
  An Optimized Nested TAD caller for Hi-C data
  ☆22Updated 4 years ago
• XiaoTaoWang / domaincaller
  A Python implementation of the original DI domain caller
  ☆12Updated 5 years ago
• ay-lab / HiCtrans
  HiCtrans is a pipeline to call translocations from Hi-C data
  ☆15Updated 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
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• qunhualilab / hicrep
  R package to evaluate reproducibility of Hi-C data
  ☆10Updated 2 years ago
• adamewing / tebreak
  Find and characterise transposable element insertions
  ☆21Updated 2 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• rjdkmr / gcMapExplorer
  Genome Contact Map Explorer - gcMapExplorer. Visit:
  ☆21Updated 3 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆36Updated 10 years ago
• keleslab / FreeHiC
  FreeHi-C pipeline for high fidelity Hi-C data simulation.
  ☆11Updated 4 years ago
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• agalitsyna / RedClib
  Red-C data processing
  ☆15Updated 2 years ago
• BlanchetteLab / HIFI
  Hi-C Interaction Frequency Inference (HIFI): High-resolution estimation of DNA-DNA interaction frequency from Hi-C data
  ☆24Updated 2 years ago