flowSpy

DOI: 10.18129/B9.bioc.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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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")

 

HTML	R Script	Quick_start
HTML		Quick_start_of_flowSpy.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version	1.4.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 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
LinkingTo	Rcpp
Suggests	BiocGenerics, knitr, RColorBrewer, rmarkdown, testthat, BiocStyle
SystemRequirements
Enhances
URL	http://www.r-project.org https://github.com/JhuangLab/flowSpy
BugReports	https://github.com/JhuangLab/flowSpy/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	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