Orchestrating chromosome conformation capture analysis with Bioconductor
Abstract Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-44761-x |
| _version_ | 1797274034423988224 |
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| author | Jacques Serizay Cyril Matthey-Doret Amaury Bignaud Lyam Baudry Romain Koszul |
| author_facet | Jacques Serizay Cyril Matthey-Doret Amaury Bignaud Lyam Baudry Romain Koszul |
| author_sort | Jacques Serizay |
| collection | DOAJ |
| description | Abstract Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data. |
| first_indexed | 2024-03-07T14:52:37Z |
| format | Article |
| id | doaj.art-784cfdce3e7a42eebf731e94e75d445b |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-07T14:52:37Z |
| publishDate | 2024-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-784cfdce3e7a42eebf731e94e75d445b2024-03-05T19:35:36ZengNature PortfolioNature Communications2041-17232024-02-011511910.1038/s41467-024-44761-xOrchestrating chromosome conformation capture analysis with BioconductorJacques Serizay0Cyril Matthey-Doret1Amaury Bignaud2Lyam Baudry3Romain Koszul4Institut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des GénomesInstitut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des GénomesInstitut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des GénomesInstitut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des GénomesInstitut Pasteur, CNRS UMR3525, Université Paris Cité, Unité Régulation Spatiale des GénomesAbstract Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, computational methods and visualization tools available in Bioconductor to investigate Hi-C, micro-C and other 3C-related data, in R. An online book ( https://bioconductor.org/books/OHCA/ ) further provides prospective end users with a number of workflows to process, import, analyze and visualize any type of chromosome conformation capture data.https://doi.org/10.1038/s41467-024-44761-x |
| spellingShingle | Jacques Serizay Cyril Matthey-Doret Amaury Bignaud Lyam Baudry Romain Koszul Orchestrating chromosome conformation capture analysis with Bioconductor Nature Communications |
| title | Orchestrating chromosome conformation capture analysis with Bioconductor |
| title_full | Orchestrating chromosome conformation capture analysis with Bioconductor |
| title_fullStr | Orchestrating chromosome conformation capture analysis with Bioconductor |
| title_full_unstemmed | Orchestrating chromosome conformation capture analysis with Bioconductor |
| title_short | Orchestrating chromosome conformation capture analysis with Bioconductor |
| title_sort | orchestrating chromosome conformation capture analysis with bioconductor |
| url | https://doi.org/10.1038/s41467-024-44761-x |
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