Chromosight
WebChromosight is a user-friendly python package, with minimal installation requirements. It can be applied to any contact map, independently of species, protocol or genome size. … WebMar 24, 2024 · Another relevant method is Chromosight, which was developed to detect specific patterns such as loop and hairpin structures using computer vision 21. …
Chromosight
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WebChromosight is a command line tool that uses computer vision to detect patterns on Hi-C chromosomal contact maps. It also exposes a python API for interoperability with other … WebFeb 1, 2024 · Results Therefore, we propose a novel deep learning-based framework for Hi-C chromatin loop detection (HiC-LDNet) and provide corresponding downstream analysis. HiC-LDNet can give relatively more accurate predictions in multiple tissue types and contact technologies. Compared to other loop calling algorithms, such as HiCCUPS, Peakachu, …
WebDec 29, 2024 · Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps - Issues · koszullab/chromosight WebQuaich also makes use of chromosight and mustache to call Hi-C peaks (peaks, dots) as well as coolpuppy to generate lots of pileups. Snakemake is a workflow manager for reproducible and scalable data analyses, …
WebMar 8, 2024 · We developed Chromosight, an algorithm based on computer vision approaches that automatically detect and quantify any type of pattern in contact data. … WebMay 29, 2024 · We developed Chromosight, an algorithm based on computer vision approaches that automatically detect and quantify any type of pattern in contact data. Chromosight detects 3 times as many patterns as existing programs, while being faster and fit to any genome, including small, compact ones.
WebChromosight workflow and benchmark a Examples of distinct patterns visible on contact maps (loop, border and hairpin) and the corresponding chromosight kernels. b Matrix preprocessing involves...
Webchromosight detect takes input in the form of Hi-C matrices in cool format. This command allows to detect patterns on Hi-C maps, such as chromatin loops or domain (e.g. TADS) … oversized solid navy blue bean bag chairWebOptions. ‘coo’ refers to a tab-delimited sparse triplet file (bin1, bin2, count). ‘bg2’ refers to a 2D bedGraph-like file (chrom1, start1, end1, chrom2, start2, end2, count). [required] Path to JSON file containing user metadata. Add supplemental value fields or override default field numbers for the specified format. oversized spark plug repair threadWebWe found that chromosight demonstrates a positive version release cadence with at least one new version released in the past 12 months. In the past month we didn't find any pull … ranch masters keith reedWebChromosight is designed to run on UNIX-like environments (e.g. Linux, OS X, Windows Subsystems for Linux, etc.) and has been tested on Ubuntu >= 14.10. It is entirely written in Python 3.6 with no planned … oversized spatulaWebChromosight: A computer vision program for pattern detection in chromosome contact maps Preprint Full-text available Mar 2024 Cyril Matthey-Doret Lyam Baudry Axel Breuer [...] Axel Cournac... oversized spark plug repair kitWebJan 26, 2024 · Converter between hic files (from juicer) and single-resolution or multi-resolution cool files (for cooler). Both hic and cool files describe Hi-C contact matrices. Intended to be lightweight, this can be used as an imported package or a stand-alone Python tool for command line conversion oversized spatula for nonstick cookwareWebNov 16, 2024 · Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including … oversized soup bowls