Package: sincell
Type: Package
Title: R package for the statistical assessment of cell state
        hierarchies from single-cell RNA-seq data
Version: 1.0.0
Date: 2014-12-04
Author: Miguel Juliá <migueljuliamolina@gmail.com>, Amalio Telenti
        <atelenti@jcvi.org>, Antonio
        Rausell<antonio.rausell@isb-sib.ch>
Maintainer: Miguel Juliá <migueljuliamolina@gmail.com>, Antonio
 Rausell<antonio.rausell@isb-sib.ch>
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
LinkingTo: Rcpp
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, biomaRt, stringr, monocle
biocViews: Sequencing, RNASeq, Clustering, GraphAndNetwork,
        Visualization, GeneExpression, GeneSetEnrichment,
        BiomedicalInformatics, CellBiology, FunctionalGenomics,
        SystemsBiology
NeedsCompilation: yes
Packaged: 2015-04-17 06:04:08 UTC; biocbuild
Built: R 3.2.0; i386-w64-mingw32; 2015-04-17 13:21:45 UTC; windows
Archs: i386, x64
