CytoTree

DOI: 10.18129/B9.bioc.CytoTree    

A Toolkit for Flow And Mass Cytometry Data

Bioconductor version: Release (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")

 

HTML R Script Quick_start
PDF   Reference Manual
Text   NEWS

Details

biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version 1.6.0
In Bioconductor since BioC 3.12 (R-4.0) (2 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
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_1.6.0.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
Package Short Url https://bioconductor.org/packages/CytoTree/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: