README.md

In mingchen-lab/cytosee: automatic computation and evaluation of cytometry data

CytoSEE: A Web-based toolkit for automatic computation and evaluation of cytometry data

Workflow of CytoSEE

Installation

Currently, A docker version is available at dockerhub cytosee, you can also edit and build your own image with cytosee Dockerfile

Linux

install.package("devtools")
source("http://bioconductor.org/biocLite.R")
biocLite(c('FlowSOM','flowMeans','SamSPECTRAL'),ask=FALSE)
devtools::install_github('madlogos/recharts')
devtools::install_github('mingchen-lab/cytosee')

Windows

Rtool34 or higher version is needed depended on the R version. Download address: https://www.r-project.org/

install.package("devtools")
source("http://bioconductor.org/biocLite.R")
biocLite(c('FlowSOM','flowMeans','SamSPECTRAL'),ask=FALSE)
devtools::install_github('madlogos/recharts')
devtools::install_github('mingchen-lab/cytosee')

Usage

# CytoSEE start with one command in your IDE(R/Rstudio)
library("cytosee")
cytosee_gui()

NEWS

We have integrate FIt-SNE into CytoSEE to deal with dimention reduction of large cell counts. To enable this function, FIt-SNE should be avaliable in your environment.

mingchen-lab/cytosee documentation built on May 6, 2019, 8:34 p.m.