CellTrails

DOI: 10.18129/B9.bioc.CellTrails    

Reconstruction, visualization and analysis of branching trajectories

Bioconductor version: Release (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("CellTrails", version = "3.8")

Documentation

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

browseVignettes("CellTrails")

 

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

Details

biocViews Clustering, DataRepresentation, DifferentialExpression, DimensionReduction, GeneExpression, Sequencing, SingleCell, Software, TimeCourse
Version 1.0.0
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
LinkingTo
Suggests AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package CellTrails_1.0.0.tar.gz
Windows Binary CellTrails_1.0.0.zip
Mac OS X 10.11 (El Capitan) CellTrails_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CellTrails
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CellTrails
Package Short Url http://bioconductor.org/packages/CellTrails/
Package Downloads Report Download Stats

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