README.md

flowPloidy

Caution!

The development version of flowPloidy is working well, and corrects a number of issues present in the stable version. However, the documentation is now (2017-03-03) out-dated! Work to update the help files and vignettes is ongoing.

Installation

Stable Version

flowPloidy is available in Bioconductor.

To install it, you need to install the bioconductor R package (more details on the Bioconductor site ):

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

Once that's installed, you can install flowPloidy using the Bioconductor tools:

biocLite("flowPloidy")
biocLite("flowPloidyData")   # (optional) data for the examples

This should pull in all the package dependencies for flowPloidy, after which you can load the package with the normal function library("flowPloidy").

Development Version

Bioconductor focuses on stable software, and consequently only releases updates once every 6 months. Development on flowPloidy is currently (March 2017) proceeding at a faster rate. You may install the development version directly from the GitHub repository if you wish to use the latest updates:

## Install Bioconductor tools first:
source("https://bioconductor.org/biocLite.R")
biocLite()

## Install flowCore from Bioconductor:
biocLite("flowCore")

## Install devtools so you can directly access GitHub
install.packages(devtools)
library(devtools)

## Install flowPloidy:
install_github("plantarum/flowPloidy", dependencies = TRUE, 
    build_vignettes = TRUE)

Getting Started

library("flowPloidy")

The flowPloidy workflow is documented in the vignette, which you can view from R:

fpVig <- vignette("flowPloidy-overview")
fpVig ## open vignette in a browser
edit(name = fpVig) ## open vignette source code in a text editor

Getting Help

For general help using the package, you can post questions on the Bioconductor Support Site. Use the tag flowploidy to ensure your question is brought to my attention.

The development repository for flowPloidy is on Github, and you can file bugs there using the issues tab. You are also welcome to contribute features or bug-fixes via pull requests!



Bioconductor-mirror/flowPloidy documentation built on June 1, 2017, 8:41 a.m.