CytoTree

This package is for version 3.15 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see CytoTree.

A Toolkit for Flow And Mass Cytometry Data


Bioconductor version: 3.15

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>

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

Installation

To install this package, start R (version "4.2") and enter:


if (!require("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")
Quick_start HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
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
System Requirements
URL http://www.r-project.org https://github.com/JhuangLab/CytoTree
Bug Reports https://github.com/JhuangLab/CytoTree/issues
See More
Suggests BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle
Linking To Rcpp
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 CytoTree_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) CytoTree_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/CytoTree
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CytoTree
Bioc Package Browser https://code.bioconductor.org/browse/CytoTree/
Package Short Url https://bioconductor.org/packages/CytoTree/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.15 Source Archive