flowSpy
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see flowSpy.
A Toolkit for Flow And Mass Cytometry Data
Bioconductor version: 3.12
A trajectory inference and visualization toolkit for flow and mass cytometry data. flowSpy offers complete analyzing workflow for flow and mass cytometry data. flowSpy can be a valuable tool for application ranging from clustering and dimensionality reduction to trajectory reconstruction and pseudotime estimation for flow and mass cytometry data.
Author: Yuting Dai [aut, cre]
Maintainer: Yuting Dai <forlynna at sjtu.edu.cn>
citation("flowSpy")
):
Installation
To install this package, start R (version "4.0") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("flowSpy")
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("flowSpy")
Quick_start | HTML | R Script |
Quick_start_of_flowSpy.html | HTML | |
Reference Manual | ||
NEWS | Text |
Details
biocViews | CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization |
Version | 1.4.0 |
In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
License | GPL-3 |
Depends | R (>= 3.6), 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/flowSpy |
Bug Reports | https://github.com/JhuangLab/flowSpy/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 | flowSpy_1.4.0.tar.gz |
Windows Binary | flowSpy_1.4.0.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | flowSpy_1.4.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/flowSpy |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/flowSpy |
Package Short Url | https://bioconductor.org/packages/flowSpy/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.12 | Source Archive |