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 (from within R, enter 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 PDF
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