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 copyTags: 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
Tags: 3DGenome, Browser, explore, chromatin, interaction, data, Hi-C, ChIA-PET, Capture, Hi-C, PLAC-Seq
1161 days ago