sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

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 might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such 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.

Package details

AuthorMiguel Julia <>, Amalio Telenti <>, Antonio Rausell <>
Bioconductor views BiomedicalInformatics CellBiology Clustering FunctionalGenomics GeneExpression GeneSetEnrichment GraphAndNetwork ImmunoOncology RNASeq Sequencing SystemsBiology Visualization
MaintainerMiguel Julia <>, Antonio Rausell<>
LicenseGPL (>= 2)
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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sincell documentation built on Nov. 8, 2020, 5:58 p.m.