Alternatives and similar repositories for chromunity

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

• dovetail-genomics / HiChiP
  HiChiP QC and data analysis
  ☆13Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆43Updated 2 years ago
• nanoporetech / Pore-C-Snakemake
  ☆33Updated 2 years ago
• Zhong-Lab-UCSD / HiCtool
  Python library for processing and visualizing Hi-C data
  ☆20Updated 5 years ago
• zhengdafangyuan / HiPore-C
  We developed a protocol of in situ high throughput multi-way contact long read Pore-C sequencing (in situ HiPore-C), a strategy that inte…
  ☆19Updated last year
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆47Updated last week
• epi2me-labs / wf-pore-c
  ☆41Updated 4 months ago
• dejunlin / hicrep
  Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support
  ☆38Updated last year
• cmdoret / hicreppy
  Python reimplementation of hicrep with compatibility for sparse matrices
  ☆18Updated 2 years ago
• wangjr03 / FLAMINGO
  ☆17Updated last year
• joachimwolff / scHiCExplorer
  Single-cell Hi-C data analysis toolbox
  ☆27Updated 3 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆65Updated last year
• TaoYang-dev / hicrep
  R package to evaluate the reproducibility of Hi-C data
  ☆26Updated 2 years ago
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆69Updated last year
• vaquerizaslab / chess
  Comparison of Hi-C Experiments using Structural Similarity.
  ☆28Updated last year
• HenrikBengtsson / TopDom
  R package: TopDom - An efficient and Deterministic Method for identifying Topological Domains in Genomes
  ☆21Updated 2 years 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…
  ☆23Updated 2 months ago
• liu-bioinfo-lab / caesar
  An accurate and interpretable computational model for predicting nucleosome resolution chromatin contact maps
  ☆10Updated last year
• dixonlab / hic_breakfinder
  ☆37Updated 5 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆48Updated 6 years ago
• ay-lab / FitHiChIP
  Statistically Significant loops from HiChIP data
  ☆43Updated last year
• XiaoTaoWang / EagleC
  A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
  ☆59Updated last year
• StatBiomed / CamoTSS
  Detection and couting alternative TSS in single cells
  ☆14Updated last year
• XueyiDong / LongReadBenchmark
  Benchmarking long-read RNA-seq analysis tools
  ☆27Updated 4 months ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆73Updated 11 months ago
• dekkerlab / cworld-dekker
  perl cworld module and collection of utility/analysis scripts for C data (3C, 4C, 5C, Hi-C)
  ☆65Updated 6 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated last year
• fansalon / TEspeX
  TEspeX - pipeline for Transposable Elements expression quantification
  ☆21Updated last year
• epi2me-labs / pore-c-py
  ☆14Updated 10 months ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆68Updated last year