Juicer provides a one-click system for analyzing loop-resolution Hi-C experiments
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Summary
This work introduces Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets, which allows users without a computational background to transform raw sequence data into normalized contact maps with one click.
- Type
- article
- Published
- 2016-07-01
- Cited by
- 3,423
- References
- 9
- Access
- Open access
- OpenAlex
- https://openalex.org/W2481029670
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3893657
Keywords
Computer science, Visualization, Software, Open source, Loop (graph theory)
References
- Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
- HiFive: a tool suite for easy and efficient HiC and 5C data analysis
- A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping
- Comprehensive mapping of long range interactions reveals folding principles of the human genome
- A Fast Algorithm for Matrix Balancing
- HiCdat: a fast and easy-to-use Hi-C data analysis tool
- HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
- Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
Cited by
- Storage, visualization, and navigation of 3D genomics data.
- Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome
- De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
- Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
- HiChIP: Efficient and sensitive analysis of protein-directed genome architecture
- Minute-made data analysis: tools for rapid interrogation of Hi-C contacts
- Genetic determinants of co-accessible chromatin regions in T cell activation across humans
- Capturing genomic relationships that matter
- How best to identify chromosomal interactions: a comparison of approaches
- Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map
- Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data
- The Cohesin Release Factor WAPL Restricts Chromatin Loop Extension
- Cohesin loss eliminates all loop domains, leading to links among superenhancers and downregulation of nearby genes
- Static and dynamic DNA loops form AP-1 bound activation hubs during macrophage development
- HiCcompare: a method for joint normalization of Hi-C datasets and differential chromatin interaction detection
- Comparison of computational methods for Hi-C data analysis
- GEM: A manifold learning based framework for reconstructing spatial organizations of chromosomes
- Genome Organization Drives Chromosome Fragility
- 4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities
- Computational tools for Hi-C data analysis
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