nucim R package

nucim (Nucleome Imaging Toolbox) is an R package for quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

Installation

The stable version is available on CRAN:

setRepositories(ind=c(1,2))
install.packages(c("nucim"))

Installation will take about 5 to 10 seconds. Tested platforms can be found here.

The development version is available on github. The development version probably depends on the development version of bioimagetools:

setRepositories(ind=c(1,2))
install.packages(c("devtools","tiff","EBImage"))
devtools::install_github("bioimaginggroup/bioimagetools")
devtools::install_github("bioimaginggroup/nucim")

You may need to install additional libraries on your OS before you can install nucim. E.g. on Ubuntu/Debian systems, please execute:

sudo apt install libssl-dev libcurl4-openssl-dev libtiff5-dev libfftw3-dev

in the terminal before installing nucim.

More information

Description of the package and basic instructions can be found in:

• Volker J. Schmid, Marion Cremer, Thomas Cremer: Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy. Methods 123 (2017), p. 33–46. [DOI]

Contributors

This package is developed at the BioImaging group at the Department of Statistics, in cooperation with the Biocenter, Department of Biology II, both at LMU Munich.

• Main development and implementation: Volker J Schmid
• Developement of workflow: Marion and Thomas Cremer
• Input on specific parts: Barbara Hübner, Yolanda Markaki, Jens Popken, Lothar Schermelleh, Daniel Smeets