Results for "Hi-C"

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  • ShRec3D

    ShRec3D is a program that aims at reconstructing a genome 3D structure (b) from the sole knowledge of the contacts between different genomic regions (a) as determined by Hi-C (http://www.ncbi.nlm.nih.gov/pubmed/19815776). There are two options to run ShRec3D (on linuX only so far): the first one...

    Tags: Bioinformatics, Computational Biology, ShRec3D, 3D genome, Genome, Hi-C, Chromosome

    3381 days ago

  • HiC-Pro: an optimized and flexible pipeline for Hi-C data processing

    HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzyme such as DNase Hi-C. I...

    Tags: HiC-Pro, pipeline, Hi-C, processing

    2305 days ago

  • LACHESIS: Genome Assembly with Hi-C-based Contact Probability Maps (LACHESIS)

    LACHESIS is method that exploits contact probability map data (e.g. from Hi-C) for chromosome-scale de novo genome assembly. Further information about LACHESIS, including source code, documentation and a user's guide are available at: http://shendurelab.github.io/LACHESIS. Manusc...

    Tags: LACHESIS, Genome, Assembly, Hi-C, Contact, Probability, Maps, Genome, Assembly

    2146 days ago

  • SALSA: A tool to scaffold long read assemblies with Hi-C

    This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch. To use the latest version, first run the following commands: cd SALSA m...

    Tags: SALSA, tool, scaffold, long, read, assemblies, Hi-C, Genome

    2114 days ago

  • What are the difference between 3C, 4C and Hi-C methods ?

    3C: chromosome conformation capture 4C:chromosome conformation capture-on-chip 5C : chromosome conformation capture carbon copy

    Tags: 3C, 4C, Hi-C, chromosome, conformation, capture

    2014 days ago

  • ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data

    The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline, called ALLHIC,...

    Tags: ALLHiC, Phasing, scaffolding, polyploid, genomes, Hi-C, data, assembly

    1926 days ago

  • Juicebox: Visualization and analysis software for Hi-C data

    Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is available on the wiki. Instructions below pertain pri...

    Tags: Juicebox, Visualization, analysis, software, Hi-C, data

    1498 days ago

  • DeepHiC: A Generative Adversarial Network for Enhancing Hi-C Data Resolution

    DeepHiC is a GAN-based model for enhancing Hi-C data resolution. We developed this server for helping researchers to enhance their own low-resolution data by a few steps of clicks. Ab initio training could be performed according to our published code. We provided trained models for various depth ...

    Tags: DeepHiC, Generative, Adversarial, Network, Enhancing, Hi-C, Data, Resolution

    1487 days ago

  • chromosight: Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

    Python package to detect chromatin loops (and other patterns) in Hi-C contact maps. Stable version with pip: pip3 install --user chromosight Stable version with conda: conda install -c bioconda -c conda-forge chromosight or, if you want to get the latest development version: pip3 in...

    Tags: chromosight, Computer, vision, program, pattern, recognition, chromosome, Hi-C, contact, maps

    1467 days ago

  • 3D Genome Browser: explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C, PLAC-Seq, and more

    Beside visualizing chromatin interaction data, you can also seamlessly browse other omics data such as ChIP-Seq or RNA-Seq for the same genomic region, and gain a complete view of both regulatory landscape and 3D genome structure for any given gene. You can also check the expression of any querie...

    Tags: 3DGenome, Browser, explore, chromatin, interaction, data, Hi-C, ChIA-PET, Capture, Hi-C, PLAC-Seq

    1161 days ago