Results 11 to 20 of about 20,056,738 (185)
Puzzle Hi-C: An accurate scaffolding software.
PLoS ONEHigh-quality, chromosome-scale genomes are essential for genomic analyses. Analyses, including 3D genomics, epigenetics, and comparative genomics rely on a high-quality genome assembly, which is often accomplished with the assistance of Hi-C data ...
Guoliang Lin +12 more
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Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization [PDF]
Nucleic Acids Research, 2020 AbstractThe Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize Hi-C, Capture Hi-C (cHi-C) and single-cell Hi-C (scHi-C) data.
Joachim Wolff +6 more
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DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis [PDF]
Genes, 2019 Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation ...
Hong, Ping +6 more
openaire +4 more sources
Comparison of normalization methods for Hi-C data [PDF]
BioTechniques, 2020 Hi-C has been predominately used to study the genome-wide interactions of genomes. In Hi-C experiments, it is believed that biases originating from different systematic deviations lead to extraneous variability among raw samples, and affect the ...
Hongqiang Lyu, Erhu Liu, Zhifang Wu
doaj +3 more sources
Measuring the reproducibility and quality of Hi-C data
Genome Biology, 2019 Background Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease.
Galip Gürkan Yardımcı +18 more
doaj +4 more sources
Cold Spring Harbor Protocols, 2015 Hi-C enables simultaneous detection of interaction frequencies between all possible pairs of restriction fragments in the genome. The Hi-C method is based on chromosome conformation capture (3C), which uses formaldehyde cross-linking to fix chromatin regions that interact in three-dimensional space, irrespective of their genomic locations.
Belton, Jon-Matthew, Dekker, Job
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Computational Processing and Quality Control of Hi-C, Capture Hi-C and Capture-C Data [PDF]
Genes, 2019 Hi-C, capture Hi-C (CHC) and Capture-C have contributed greatly to our present understanding of the three-dimensional organization of genomes in the context of transcriptional regulation by characterizing the roles of topological associated domains, enhancer promoter loops and other three-dimensional genomic interactions.
Peter Hansen +6 more
openaire +4 more sources
Hi-C read-pair classifications.
, 2021 A reference-based classification scheme for read-pairs generated by the Hi-C protocol has previously been devised [11, 13]. Regardless of orientation, read-pairs are considered valid if two or more intervening enzymatic cut-site exist between them ...
Matthew Z. DeMaere (6404834) +1 more
core +1 more source
Motif-Hi-C: A motif-based framework for rapid quality control of Hi-C data. [PDF]
aBIOTECHKong D +7 more
europepmc +2 more sources
, 2022 As the table shows, the average read count of significant interactions identified by MaxHiC are much higher than those identified by CHiCAGO, GOTHiC, Fit-Hi-C, Fit-HiC2 and HiCDC+. (XLSX)
Hamid Alinejad-Rokny (518381) +6 more
core +1 more source