Alternatives and similar repositories for HiCLift:

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

• XiaoTaoWang / NeoLoopFinder
  A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
  ☆64Updated last year
• tariks / peakachu
  Genome-wide contact analysis using sklearn
  ☆64Updated last year
• tanlongzhi / dip-c
  Tools to analyze Dip-C (or other 3C/Hi-C) data
  ☆63Updated 5 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
• ay-lab / dcHiC
  dcHiC: Differential compartment analysis for Hi-C datasets
  ☆68Updated last year
• lh3 / hickit
  TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C
  ☆107Updated 4 years ago
• open2c / pairtools
  Extract 3D contacts (.pairs) from sequencing alignments
  ☆112Updated 3 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
• 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…
  ☆22Updated 2 weeks ago
• ren-lab / hic-pipeline
  ☆24Updated 3 years ago
• dovetail-genomics / Micro-C
  Micro-C QC and data analysis
  ☆16Updated last year
• ay-lab / mustache
  Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
  ☆70Updated 3 months ago
• open2c / coolpuppy
  A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
  ☆79Updated 6 months ago
• XiaoTaoWang / HiCPeaks
  A Python implementation for BH-FDR and HiCCUPS
  ☆48Updated 2 weeks ago
• FelixKrueger / SNPsplit
  Allele-specific alignment sorting
  ☆55Updated 2 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…
  ☆85Updated 2 years ago
• 4dn-dcic / hic2cool
  Lightweight converter between hic and cool contact matrices.
  ☆71Updated 9 months ago
• magnitov / pentad
  A simple tool to perform the calculation and visualization of the average chromatin A/B compartment.
  ☆14Updated 2 years ago
• kundajelab / 3DChromatin_ReplicateQC
  Software to compute reproducibility and quality scores for Hi-C data
  ☆47Updated 6 years ago
• JinLabBioinfo / HiCorr
  HiCorr: a Hi-C data bias-correction pipeline
  ☆28Updated last month
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆94Updated 5 months ago
• ENCODE-DCC / hic-pipeline
  HiC uniform processing pipeline
  ☆59Updated last year
• yezhengSTAT / CUTTag_tutorial
  Tutorial Website
  ☆59Updated 4 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…
  ☆89Updated last month
• 4dn-dcic / docker-4dn-hic
  Docker for 4DN Hi-C processing pipeline
  ☆59Updated 5 months ago
• GuttmanLab / sprite-pipeline
  A self-contained repository of all code needed for SPRITE analysis
  ☆20Updated 3 years ago
• dekkerlab / crane-nature-2015
  code associated with crane-nature-2015, 10.1038/nature14450
  ☆34Updated 9 years ago
• ysora / stripenn
  Architectural stripe detection from 3D genome conformation data
  ☆17Updated last year
• XiaoTaoWang / TADLib
  A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
  ☆42Updated 2 years ago
• 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