Package: sincell
Type: Package
Title: R package for the statistical assessment of cell state
        hierarchies from single-cell RNA-seq data
Version: 1.38.0
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: 2024-10-30 01:46:55 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/sincell
git_branch: RELEASE_3_20
git_last_commit: 892a15e
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: yes
Built: R 4.4.1; x86_64-apple-darwin20; 2024-10-30 11:38:00 UTC; unix
