sincell

DOI:10.18129/B9.bioc.sincell

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

Bioconductor版本:版本(3.15)

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

Maintainer: Miguel Julia , Antonio Rausell

Installation

To install this package, start R (version "4.2") and enter:

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

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

Documentation

查看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

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Version	1.28.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 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	//www.andersvercelli.com/
Depends On Me
Imports Me	ctgGEM
Suggests Me
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Build Report

Package Archives

Follow2021年欧洲杯比分预测 instructions to use this package in your R session.

Source Package	sincell_1.28.0.tar.gz
Windows Binary	sincell_1.28.0.zip(64-bit only)
macOS 10.13 (High Sierra)	sincell_1.28.0.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	//www.andersvercelli.com/packages/sincell/
Package Downloads Report	Download Stats