cytofkit

DOI: 10.18129/B9.bioc.cytofkit    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see cytofkit.

cytofkit: an integrated mass cytometry data analysis pipeline

Bioconductor version: 3.7

An integrated mass cytometry data analysis pipeline that enables simultaneous illustration of cellular diversity and progression.

Author: Jinmiao Chen, Hao Chen, Matthew Myint

Maintainer: Jinmiao Chen <Chen_Jinmiao at immunol.a-star.edu.sg>, Matthew Myint <a0124008 at u.nus.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("cytofkit")

Documentation

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

browseVignettes("cytofkit")

 

HTML	R Script	Analysis Pipeline
HTML	R Script	Quick Start
HTML	R Script	ShinyAPP tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, CellBiology, Clustering, DimensionReduction, FlowCytometry, GUI, Software
Version	1.12.0
In Bioconductor since	BioC 3.1 (R-3.2) (3.5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0), ggplot2, plyr
Imports	tcltk, grDevices, graphics, utils, stats, Rtsne, e1071, flowCore, gplots, colourpicker, VGAM, reshape2, ggrepel, shiny, shinyFiles, vegan, Biobase, doParallel, parallel, pdist, methods, destiny, FlowSOM(>= 1.4.0), igraph (>= 1.1.2), RANN (>= 2.5), Rcpp (>= 0.12.0)
LinkingTo	Rcpp
Suggests	knitr, RUnit, testthat, BiocGenerics
SystemRequirements
Enhances
URL	https://github.com/JinmiaoChenLab/cytofkit
BugReports	https://github.com/JinmiaoChenLab/cytofkit/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	cytofkit_1.12.0.tar.gz
Windows Binary	cytofkit_1.12.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	cytofkit_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/cytofkit
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/cytofkit
Package Short Url	http://bioconductor.org/packages/cytofkit/
Package Downloads Report	Download Stats