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This is the development version of CytoTree; for the stable release version, see CytoTree.
Bioconductor version: Development (3.16)
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")
):
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") # The following initializes usage of Bioc devel BiocManager::install(version='devel') BiocManager::install("CytoTree")
For older versions of R, please refer to the appropriate Bioconductor release.
Reference Manual |
biocViews | CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization |
Version | 1.7.0 |
In Bioconductor since | BioC 3.12 (R-4.0) (1.5 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 |
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 |
Follow Installation instructions to use this package in your R session.
Source Package | |
Windows Binary | |
macOS 10.13 (High Sierra) | |
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 |
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