Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq.
- Juliá M Vital-IT group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, University of Lausanne, 1015 Lausanne, Switzerland and.
- Telenti A J. Craig Venter Institute, La Jolla, CA 92037.
- Rausell A Vital-IT group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, University of Lausanne, 1015 Lausanne, Switzerland and.
- 2015-06-24
Published in:
- Bioinformatics (Oxford, England). - 2015
Algorithms
Cell Differentiation
Data Interpretation, Statistical
Gene Expression Profiling
Sequence Analysis, RNA
Single-Cell Analysis
Software
English
UNLABELLED
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.
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.
- Language
-
- English
- Open access status
- hybrid
- Identifiers
-
- DOI 10.1093/bioinformatics/btv368
- PMID 26099264
- Persistent URL
- https://sonar.ch/global/documents/20431
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