Replication dataset for "A comprehensive review and benchmark of differential analysis tools for Hi-C data"

DOI

Processed Hi-C matrices with 3D chromatine conformation data obtained by high-throughput sequencing, corresponding to the experiments used in http://dx.doi.org/10.1093/bib/bbaf074 to benchmark differential analysis tools for Hi-C data.

R, 4.1.2

bash, 4.2.46

nf-core/hic, 1.2.2

ENCODE data : The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414):57–74, 2012. https://doi.org/10.1038/nature11247 CTCF depletion data : Haoyue Zhang, Jessica Lam, Di Zhang, Yemin Lan, Marit W. Vermunt, Cheryl A. Keller, Belinda Giardine, Ross C. Hardison, and Gerd A. Blobel. CTCF and transcription influence chromatin structure re-configuration after mitosis. Nature Communications, 12:5157, 2021. https://doi.org/10.1038/s41467-021-25418-5

Identifier
DOI https://doi.org/10.57745/LR0W9R
Related Identifier IsCitedBy https://doi.org/10.1093/bib/bbaf074
Metadata Access https://entrepot.recherche.data.gouv.fr/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.57745/LR0W9R
Provenance
Creator Vialaneix, Nathalie ORCID logo; Foissac, Sylvain ORCID logo
Publisher Recherche Data Gouv
Contributor Vialaneix, Nathalie; Foissac, Sylvain; Institut national de recherche pour l'agriculture, l'alimentation et l'environnement; Entrepôt-Catalogue Recherche Data Gouv
Publication Year 2024
Rights etalab 2.0; info:eu-repo/semantics/openAccess; https://spdx.org/licenses/etalab-2.0.html
OpenAccess true
Contact Vialaneix, Nathalie (MIAT ; Université Fédérale de Toulouse, INRAE); Foissac, Sylvain (GenPhySE ; Université de Toulouse, INRAE, ENVT)
Representation
Resource Type Dataset
Format application/x-shellscript; text/x-r-markdown; text/html; application/octet-stream; text/x-r-source; application/vnd.realvnc.bed; text/markdown; text/plain; application/gzip
Size 7099; 2600; 1848; 823808; 827808; 825296; 822495; 822840; 823711; 825532; 826416; 284350; 281602; 285044; 278342; 280195; 6142; 11877; 11745; 11843; 11660; 11717; 1197; 177214; 176257; 177426; 174541; 175619; 4096; 83050; 6293003; 6125962; 6322081; 5879090; 6035918; 31396; 244202; 239991; 244665; 233214; 236896; 6205; 3743437; 3687070; 3754196; 3605606; 3657872; 20407; 408288; 1106204; 1096474; 1108030; 1082359; 1090855; 12394; 41609; 41225; 41785; 40554; 40922; 2397; 660475; 656316; 661286; 651199; 654315; 8167; 162843; 2976; 805546; 35129; 3608; 181938667
Version 2.2
Discipline Mathematics; Life Sciences; Medicine