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("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 | ||
| 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 |