sincell

DOI: 10.18129/B9.bioc.sincell    

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

Bioconductor version: Release (3.13)

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

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sincell")

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")

 

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

Details

biocViews	BiomedicalInformatics, CellBiology, Clustering, FunctionalGenomics, GeneExpression, GeneSetEnrichment, GraphAndNetwork, ImmunoOncology, RNASeq, Sequencing, Software, SystemsBiology, Visualization
Version	1.24.0
In Bioconductor since	BioC 3.1 (R-3.2) (6.5 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
LinkingTo	Rcpp
Suggests	BiocStyle, knitr, biomaRt, stringr, monocle
SystemRequirements
Enhances
URL	http://bioconductor.org/
Depends On Me
Imports Me	ctgGEM
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	sincell_1.24.0.tar.gz
Windows Binary	sincell_1.24.0.zip
macOS 10.13 (High Sierra)	sincell_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/sincell
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/sincell
Package Short Url	https://bioconductor.org/packages/sincell/
Package Downloads Report	Download Stats