Alternatives and similar repositories for hic2cool:

Users that are interested in hic2cool are comparing it to the libraries listed below

• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆79Updated 4 months ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆108Updated last month
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆92Updated 3 months ago
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated 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
• ay-lab / fithic
  Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture…
  ☆82Updated 2 years ago
• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆62Updated last year
• XiaoTaoWang / HiCLift
  A fast and efficient tool for converting chromatin interaction data between genome assemblies
  ☆70Updated last year
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆67Updated last year
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆60Updated last year
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆64Updated 4 months ago
• hms-dbmi / 3d-genome-processing-tutorial
  A 3D genome data processing tutorial for ISMB/ECCB 2017
  ☆50Updated 7 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
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆46Updated 5 years ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated last year
• LabTranslationalArchitectomics / riboWaltz
  optimization of ribosome P-site positioning in ribosome profiling data
  ☆48Updated 3 weeks ago
• harbourlab / SparK
  Publication quality NGS track plotting
  ☆111Updated 2 years ago
• biocore-ntnu / epic2
  Ultraperformant reimplementation of SICER
  ☆56Updated 3 years ago
• aidenlab / straw
  Extract data quickly from Juicebox via straw
  ☆67Updated 11 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
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆40Updated 2 years ago
• YaqiangCao / cLoops2
  Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
  ☆45Updated last week
• VRam142 / combinatorialHiC
  Scripts + resources for analyzing combinatorial Hi-C data
  ☆29Updated 5 years ago
• open2c / quaich
  snakemake pipeline for Hi-C post-processing
  ☆22Updated 8 months 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
• mlbendall / telescope
  Quantification of transposable element expression using RNA-seq
  ☆64Updated last year
• GuttmanLab / sprite-pipeline
  A self-contained repository of all code needed for SPRITE analysis
  ☆20Updated 3 years ago
• ygidtu / trackplot
  trackplot is a tool for visualizing various next-generation sequencing (NGS) data, including DNA-seq, RNA-seq, single-cell RNA-seq and fu…
  ☆84Updated last week
• ucagenomix / sicelore
  Single Cell Long Read is a suite of tools dedicated to Cell barcode / UMI assignment and analysis of highly multiplexed single cell Nanop…
  ☆73Updated 2 years ago
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆59Updated 3 months ago