CytoTree

DOI: 10.18129/B9.bioc.CytoTree    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see CytoTree.

A Toolkit for Flow And Mass Cytometry Data

Bioconductor version: 3.13

A trajectory inference toolkit for flow and mass cytometry data. CytoTree is a valuable tool to build a tree-shaped trajectory using flow and mass cytometry data. The application of CytoTree ranges from clustering and dimensionality reduction to trajectory reconstruction and pseudotime estimation. It offers complete analyzing workflow for flow and mass cytometry data.

Author: Yuting Dai [aut, cre]

Maintainer: Yuting Dai <forlynna at sjtu.edu.cn>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("CytoTree")

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("CytoTree")

 

HTML	R Script	Quick_start
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.12 (R-4.0) (1 year)
License	GPL-3
Depends	R (>= 4.0), igraph
Imports	FlowSOM, Rtsne, ggplot2, destiny, gmodels, flowUtils, Biobase, Matrix, flowCore, sva, matrixStats, methods, mclust, prettydoc, RANN (>= 2.5), Rcpp (>= 0.12.0), BiocNeighbors, cluster, pheatmap, scatterpie, umap, scatterplot3d, limma, stringr, grDevices, grid, stats
LinkingTo	Rcpp
Suggests	BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL	http://www.r-project.org https://github.com/JhuangLab/CytoTree
BugReports	https://github.com/JhuangLab/CytoTree/issues
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	CytoTree_1.2.0.tar.gz
Windows Binary	CytoTree_1.2.0.zip
macOS 10.13 (High Sierra)	CytoTree_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CytoTree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CytoTree
Package Short Url	https://bioconductor.org/packages/CytoTree/
Package Downloads Report	Download Stats