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("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 | ||
| 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 |