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CellTrails

Reconstruction, visualization and analysis of branching trajectories


Bioconductor version: Release (3.18)

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.

Author: Daniel Ellwanger [aut, cre, cph]

Maintainer: Daniel Ellwanger <dc.ellwanger.dev at gmail.com>

Citation (from within R, enter citation("CellTrails")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CellTrails")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CellTrails")
CellTrails: Reconstruction, visualization, and analysis of branching trajectories from single-cell expression data PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, TimeCourse
Version 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
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
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Suggests AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CellTrails_1.20.0.tar.gz
Windows Binary CellTrails_1.20.0.zip (64-bit only)
macOS Binary (x86_64) CellTrails_1.20.0.tgz
macOS Binary (arm64) CellTrails_1.20.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CellTrails
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellTrails
Bioc Package Browser https://code.bioconductor.org/browse/CellTrails/
Package Short Url https://bioconductor.org/packages/CellTrails/
Package Downloads Report Download Stats