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Bioconductor - sincell (development version)

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 (3.22)

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 "4.5") 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 1.41.0 In Bioconductor since BioC 3.1 (R-3.2) (10 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 Package Archives

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

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