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Quality control software tools | Hi-C data analysis

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Juicer
Desktop

Juicer

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a…

Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file…

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HiC-Pro
Desktop

HiC-Pro

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data)…

Designs to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. The pipeline is flexible, scalable and optimized. It can operate either on a single…

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QuASAR
Desktop

QuASAR Quality Assessment of Spatial Arrangement Reproducibility

Allows users to evaluate Hi-C data quality inside a single sample and between…

Allows users to evaluate Hi-C data quality inside a single sample and between multiple ones. QuASAR intends to help in making choices in Hi-C data production or performing data comparisons. The…

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GenomeDISCO
Desktop

GenomeDISCO Genome DIfferences between Smoothed COntact maps

Assesses the similarity of a pair of contact maps obtained from chromosome…

Assesses the similarity of a pair of contact maps obtained from chromosome capture experiments. GenomeDISCO is designed for evaluating concordance and reproducibility of chromatin contact maps…

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HiCRep
Desktop

HiCRep

Measures the Hi-C data reproducibility. HiCRep evaluates the reproducibility of…

Measures the Hi-C data reproducibility. HiCRep evaluates the reproducibility of Hi-C intra-chromosome Hi-C data. It can infer confidence intervals for stratum-adjusted correlation coefficient (SCC),…

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HIPPIE
Desktop
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HiC-Spector
Desktop

HiC-Spector

A collection of matrix-related functions for analysing Hi-C contact maps. A…

A collection of matrix-related functions for analysing Hi-C contact maps. A contact map is a matrix whose elements store the population-averaged co-location frequencies between pairs of loci.…

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HiC-inspector
Desktop

HiC-inspector

A bioinformatics pipeline for the automated analysis of data generated by…

A bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome…

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HiCUP
Desktop

HiCUP Hi-C User Pipeline

A tool for mapping and performing quality control on Hi-C data. HiCUP is…

A tool for mapping and performing quality control on Hi-C data. HiCUP is designed to take the raw sequence output from a HiC experiment and produce a filtered set of mapped interaction pairs,…

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