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sincell

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 gmail.com>, Amalio Telenti <atelenti at jcvi.org>, Antonio Rausell <antonio.rausell at institutimagine.org>

Maintainer: Miguel Julia <migueljuliamolina at gmail.com>, Antonio Rausell<antonio.rausell at institutimagine.org>

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

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 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
System Requirements
URL http://bioconductor.org/
See More
Suggests BiocStyle, knitr, biomaRt, stringr, monocle
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package sincell_1.37.0.tar.gz
Windows Binary sincell_1.37.0.zip
macOS Binary (x86_64) sincell_1.37.0.tgz
macOS Binary (arm64) sincell_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/sincell
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/sincell
Bioc Package Browser https://code.bioconductor.org/browse/sincell/
Package Short Url https://bioconductor.org/packages/sincell/
Package Downloads Report Download Stats