PuSH - Publikationsserver des Helmholtz Zentrums München

Export: TXT Text RIS Endnote (RIS) BIB BibTeX
Danese, A. ; Richter, M. ; Chaichoompu, K. ; Fischer, D.S. ; Theis, F.J. ; Colomé-Tatché, M.

EpiScanpy: Integrated single-cell epigenomic analysis.

Nat. Commun. 12:5228 (2021)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
EpiScanpy is a toolkit for the analysis of single-cell epigenomic data, namely single-cell DNA methylation and single-cell ATAC-seq data. To address the modality specific challenges from epigenomics data, epiScanpy quantifies the epigenome using multiple feature space constructions and builds a nearest neighbour graph using epigenomic distance between cells. EpiScanpy makes the many existing scRNA-seq workflows from scanpy available to large-scale single-cell data from other -omics modalities, including methods for common clustering, dimension reduction, cell type identification and trajectory learning techniques, as well as an atlas integration tool for scATAC-seq datasets. The toolkit also features numerous useful downstream functions, such as differential methylation and differential openness calling, mapping epigenomic features of interest to their nearest gene, or constructing gene activity matrices using chromatin openness. We successfully benchmark epiScanpy against other scATAC-seq analysis tools and show its outperformance at discriminating cell types.
Impact Factor
Scopus SNIP
Web of Science
Times Cited
Scopus
Cited By
Altmetric
14.919
3.055
1
11
Tags
Anmerkungen
Besondere Publikation
Auf Hompepage verbergern

Zusatzinfos bearbeiten
Eigene Tags bearbeiten
Privat
Eigene Anmerkung bearbeiten
Privat
Auf Publikationslisten für
Homepage nicht anzeigen
Als besondere Publikation
markieren
Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Accessibility
Sprache englisch
Veröffentlichungsjahr 2021
HGF-Berichtsjahr 2021
ISSN (print) / ISBN 2041-1723
e-ISSN 2041-1723
Zeitschrift Nature Communications
Quellenangaben Band: 12, Heft: 1, Seiten: , Artikelnummer: 5228 Supplement: ,
Verlag Nature Publishing Group
Verlagsort London
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-554200-001
G-503800-001
Förderungen Joachim Herz Stiftung
German research foundation (DFG) fellowship through the Graduate School of Quantitative Biosciences Munich (QBM)
Incubator grant sparse2big
Federal Ministry of Education and Research (Single Cell Genomics Network Germany)
Graduate School QBM)
German Science Foundation
Impulsund Vernetzungsfonds of the Helmholtz-Gemeinschaft
DOI 10.1038/s41467-021-25131-3
WOS ID WOS:000692406100023
Scopus ID 85114164805
PubMed ID 34471111
Erfassungsdatum 2021-10-08
[➜Korrektur melden]