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This is the development version of sincell; for the stable release version, see sincell.

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

Bioconductor version: Development (3.20)

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.

Author: Miguel Julia <migueljuliamolina at>, Amalio Telenti <atelenti at>, Antonio Rausell <antonio.rausell at>

Maintainer: Miguel Julia <migueljuliamolina at>, Antonio Rausell<antonio.rausell at>

Citation (from within R, enter citation("sincell")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Sincell: Analysis of cell state hierarchies from single-cell RNA-seq PDF R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version 1.37.0
In Bioconductor since BioC 3.1 (R-3.2) (9.5 years)
License GPL (>= 2)
Depends R (>= 3.0.2), igraph
Imports Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2, reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster, statmod
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Suggests BiocStyle, knitr, biomaRt, stringr, monocle
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Source Package sincell_1.37.0.tar.gz
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