cytofkit

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last 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>

Citation (from within R, enter citation("cytofkit")):

Installation

To install this package, start R (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cytofkit")

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("cytofkit")
Analysis Pipeline HTML R Script
Quick Start HTML R Script
ShinyAPP tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, CellBiology, Clustering, DimensionReduction, FlowCytometry, GUI, Software
Version 1.12.0
In Bioconductor since BioC 3.1 (R-3.2) (9 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)
System Requirements
URL https://github.com/JinmiaoChenLab/cytofkit
Bug Reports https://github.com/JinmiaoChenLab/cytofkit/issues
See More
Suggests knitr, RUnit, testthat, BiocGenerics
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 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 https://bioconductor.org/packages/cytofkit/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive