DOI: 10.18129/B9.bioc.flowSpy    

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see flowSpy.

A Toolkit for Flow And Mass Cytometry Data

Bioconductor version: 3.10

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")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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


biocViews CellBasedAssays, CellBiology, Clustering, FlowCytometry, Network, NetworkInference, Software, Visualization
Version 1.0.4
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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
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_1.0.4.tar.gz
Windows Binary flowSpy_1.0.4.zip
Mac OS X 10.11 (El Capitan) flowSpy_1.0.4.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

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: