Package: sincell
Type: Package
Title: R package for the statistical assessment of cell state
        hierarchies from single-cell RNA-seq data
Version: 1.45.0
Date: 2015-05-28
Author: Miguel Julia <migueljuliamolina@gmail.com>, Amalio Telenti
        <atelenti@jcvi.org>, Antonio Rausell
        <antonio.rausell@institutimagine.org>
Maintainer: Miguel Julia <migueljuliamolina@gmail.com>, Antonio
 Rausell<antonio.rausell@institutimagine.org>
Depends: R (>= 3.0.2), igraph
Description: 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.
License: GPL (>= 2)
Encoding: UTF-8
URL: http://bioconductor.org/
Imports: Rcpp (>= 0.11.2), entropy, scatterplot3d, MASS, TSP, ggplot2,
        reshape2, fields, proxy, parallel, Rtsne, fastICA, cluster,
        statmod
LinkingTo: Rcpp
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, biomaRt, stringr, monocle
biocViews: ImmunoOncology, Sequencing, RNASeq, Clustering,
        GraphAndNetwork, Visualization, GeneExpression,
        GeneSetEnrichment, BiomedicalInformatics, CellBiology,
        FunctionalGenomics, SystemsBiology
Packaged: 2026-07-12 09:13:44 UTC; root
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:40:32 UTC
RemoteUrl: https://github.com/bioc/sincell
RemoteRef: HEAD
RemoteSha: 99d31de7915953ff4c85bd5bb4c8d985be494c57
NeedsCompilation: yes
Built: R 4.6.1; x86_64-w64-mingw32; 2026-07-12 09:15:43 UTC; windows
Archs: x64
