cytofkit

DOI: 10.18129/B9.bioc.cytofkit    

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 3.8 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: 3.8

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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("cytofkit")

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

Documentation

PDF		Reference Manual

Details

biocViews	BiomedicalInformatics, CellBiology, Clustering, DimensionReduction, FlowCytometry, GUI, Software
Version	1.14.0
In Bioconductor since	BioC 3.1 (R-3.2) (4 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
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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