Package: CellTrails
Type: Package
Title: Reconstruction, visualization and analysis of branching
        trajectories
Version: 1.28.0
Authors@R: person(given="Daniel", family="Ellwanger", 
  role=c("aut", "cre", "cph"), email="dc.ellwanger.dev@gmail.com")
Description: CellTrails is an unsupervised algorithm for the de novo
        chronological ordering, visualization and analysis of
        single-cell expression data. CellTrails makes use of a
        geometrically motivated concept of lower-dimensional manifold
        learning, which exhibits a multitude of virtues that counteract
        intrinsic noise of single cell data caused by drop-outs,
        technical variance, and redundancy of predictive variables.
        CellTrails enables the reconstruction of branching trajectories
        and provides an intuitive graphical representation of
        expression patterns along all branches simultaneously. It
        allows the user to define and infer the expression dynamics of
        individual and multiple pathways towards distinct phenotypes.
License: Artistic-2.0
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R (>= 3.5), SingleCellExperiment
Imports: BiocGenerics, Biobase, cba, dendextend, dtw, EnvStats,
        ggplot2, ggrepel, grDevices, igraph, maptree, methods, mgcv,
        reshape2, Rtsne, stats, splines, SummarizedExperiment, utils
Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr,
        org.Mm.eg.db, rmarkdown
RoxygenNote: 7.1.0
biocViews: ImmunoOncology, Clustering, DataRepresentation,
        DifferentialExpression, DimensionReduction, GeneExpression,
        Sequencing, SingleCell, Software, TimeCourse
Collate: 'AllClasses.R' 'AllGenerics.R' 'accessor-methods.R'
        'cluster-methods.R' 'data-sets.R' 'diffexp-methods.R'
        'dimred-methods.R' 'export-methods.R' 'filter-methods.R'
        'fitting-methods.R' 'import-methods.R' 'imputation-methods.R'
        'layout-methods.R' 'plot-methods.R' 'show-methods.R'
        'simulation-methods.R' 'test-methods.R' 'trajectory-methods.R'
        'utility-methods.R'
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:46:02 UTC
RemoteUrl: https://github.com/bioc/CellTrails
RemoteRef: RELEASE_3_22
RemoteSha: 0fc34ed1c78643b68548786fbac194016e718c10
NeedsCompilation: no
Packaged: 2025-11-11 14:23:03 UTC; root
Author: Daniel Ellwanger [aut, cre, cph]
Maintainer: Daniel Ellwanger <dc.ellwanger.dev@gmail.com>
Built: R 4.5.2; ; 2025-11-11 14:31:24 UTC; windows
