Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
02 07 2020
02 07 2020
Historique:
accepted:
24
03
2020
revised:
11
03
2020
received:
04
02
2020
pubmed:
18
4
2020
medline:
2
10
2020
entrez:
18
4
2020
Statut:
ppublish
Résumé
The 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. Since the last publication, Galaxy HiCExplorer has been expanded considerably with new tools to facilitate the analysis of cHi-C and to provide an in-depth analysis of Hi-C data. Moreover, it supports the analysis of scHi-C data by offering a broad range of tools. With the help of the standard graphical user interface of Galaxy, presented workflows, extensive documentation and tutorials, novices as well as Hi-C experts are supported in their Hi-C data analysis with Galaxy HiCExplorer.
Identifiants
pubmed: 32301980
pii: 5821269
doi: 10.1093/nar/gkaa220
pmc: PMC7319437
doi:
Substances chimiques
Chromatin
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
W177-W184Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Science. 2009 Oct 9;326(5950):289-93
pubmed: 19815776
Nat Genet. 2006 Nov;38(11):1348-54
pubmed: 17033623
Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10
pubmed: 27137889
Nucleic Acids Res. 2018 Jul 2;46(W1):W11-W16
pubmed: 29901812
F1000Res. 2015 Nov 20;4:1310
pubmed: 26835000
Nature. 2017 Nov 2;551(7678):51-56
pubmed: 29094699
Genome Res. 2017 Feb;27(2):223-233
pubmed: 27923844
Nat Commun. 2018 Jan 15;9(1):189
pubmed: 29335486
Nat Rev Genet. 2020 Apr;21(4):207-226
pubmed: 31848476
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Nat Rev Genet. 2016 Oct 14;17(11):661-678
pubmed: 27739532
Nat Methods. 2016 Nov;13(11):919-922
pubmed: 27643841
Mol Cell. 2020 Feb 20;77(4):688-708
pubmed: 32001106
Nature. 2017 Jul 5;547(7661):61-67
pubmed: 28682332
Nature. 2012 Apr 11;485(7398):381-5
pubmed: 22495304
Cell Syst. 2018 Jun 27;6(6):752-758.e1
pubmed: 29953864
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Bioinformatics. 2018 Mar 15;34(6):1046-1047
pubmed: 29186290
Genome Biol. 2015 Oct 24;16:237
pubmed: 26498826
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Genome Res. 2006 Oct;16(10):1299-309
pubmed: 16954542
Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14011-14018
pubmed: 31235599
Nat Methods. 2018 Jul;15(7):475-476
pubmed: 29967506
Front Genet. 2019 Nov 04;10:1079
pubmed: 31749839
Nature. 2009 Nov 5;462(7269):58-64
pubmed: 19890323
Genome Res. 2014 Nov;24(11):1854-68
pubmed: 25122612
Nature. 2013 Oct 3;502(7469):59-64
pubmed: 24067610
Bioinformatics. 2020 Jan 1;36(1):311-316
pubmed: 31290943
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
Science. 2002 Feb 15;295(5558):1306-11
pubmed: 11847345
Nat Genet. 2006 Nov;38(11):1341-7
pubmed: 17033624
Genome Biol. 2015 Dec 01;16:259
pubmed: 26619908
Genome Biol. 2018 Aug 24;19(1):125
pubmed: 30143029
F1000Res. 2016 May 20;5:950
pubmed: 27303634
Nat Methods. 2012 Oct;9(10):999-1003
pubmed: 22941365
Nat Commun. 2019 Sep 26;10(1):4376
pubmed: 31558714