Sincell

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

Bioconductor version: Release (3.8)

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 , Amalio Telenti , Antonio Rausell <antonio.rausell at isb-sib.ch>

Maintainer: Miguel Julia , Antonio Rausell <antonio.rausell at isb-sib.ch>

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

Juliá M, Telenti A, Rausell A (2014). “Sincell: R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data.” bioRxiv. http://dx.doi.org/.

Installation

To install this package, start R (version “3.5”) and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("sincell", version = "3.8")

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

Documentation

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

browseVignettes("sincell")

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

Download stats