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DESCRIPTION
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DESCRIPTION
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Package: CellTrails
Type: Package
Title: Reconstruction, visualization and analysis of branching trajectories
Version: 1.7.1
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'