CellTrails

This is the development version of CellTrails; for the stable release version, see CellTrails.

Reconstruction, visualization and analysis of branching trajectories

Bioconductor version: Development (3.21)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, ImmunoOncology, Sequencing, SingleCell, Software, TimeCourse
Version	1.25.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 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
System Requirements
URL

Suggests	AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CellTrails_1.25.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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