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 , Amalio Telenti , Antonio Rausell Maintainer: Miguel Julia , Antonio Rausell 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