A tutorial overview of flowPloidy is available on
the
Bioconductor website.
This vignette is provided with the package, so once you have flowPloidy
installed you can access it from with R (see below).
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 on flowPloidy is currently (June 2017) in a reasonably stable
state, and no major new features are in the works. However, if you'd like
to install the latest version from the development branch, you can get it
directly from the GitHub repository.
## 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)
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
It is also available online.
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!