Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq

Détails

Ressource 1Télécharger: BIB_6C5AA7247E78.P001.pdf (132.04 [Ko])
Etat: Public
Version: Final published version
ID Serval
serval:BIB_6C5AA7247E78
Type
Article: article d'un périodique ou d'un magazine.
Sous-type
Etude de cas (case report): rapporte une observation et la commente brièvement.
Collection
Publications
Institution
Titre
Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq
Périodique
Bioinformatics
Auteur⸱e⸱s
Juliá M., Telenti A., Rausell A.
ISSN
1367-4803 (Print)
1367-4811 (Electronic)
ISSN-L
1367-4803
Statut éditorial
Publié
Date de publication
2015
Volume
31
Numéro
20
Pages
3380-3382
Langue
anglais
Notes
Publication types: Applications Notes ; brief-report Identifiant PubMed Central: PMC4595899
Résumé
Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data can be formalized under a general framework composed of (i) a metric to assess cell-to-cell similarities (with or without a dimensionality reduction step) and (ii) a graph-building algorithm (optionally making use of a cell clustering step). The Sincell R package implements a methodological toolbox allowing flexible workflows under such a framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies. The functionalities of Sincell are illustrated in a real case study, which demonstrates its ability to discriminate noisy from stable cell-state hierarchies.
AVAILABILITY AND IMPLEMENTATION: Sincell is an open-source R/Bioconductor package available at http://bioconductor.org/packages/sincell. A detailed manual and a vignette are provided with the package.
CONTACT: antonio.rausell@isb-sib.ch
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Mots-clé
Cell Differentiation/genetics
Pubmed
Web of science
Open Access
Oui
Création de la notice
25/07/2016 8:19
Dernière modification de la notice
20/08/2019 14:26
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