sincell

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

Bioconductor version: 3.1

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 Juliá <migueljuliamolina at gmail.com>, Amalio Telenti <atelenti at jcvi.org>, Antonio Rausell<antonio.rausell at isb-sib.ch>

Maintainer: Miguel Juliá <migueljuliamolina at gmail.com>, Antonio Rausell<antonio.rausell at isb-sib.ch>

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("sincell")

Documentation

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

browseVignettes("sincell")

Details

Package Archives

Follow Installation instructions to use this package in your R session.