CytoTree

DOI: 10.18129/B9.bioc.CytoTree    

A Toolkit for Flow And Mass Cytometry Data

Bioconductor version: Release (3.12)

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 "4.0") 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")

 

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Details

biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
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_1.0.0.tar.gz
Windows Binary CytoTree_1.0.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) CytoTree_1.0.0.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/
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