We believe that high quality, reproducible data requires open software, and we make our software tools available on GitHub and ShinyApps.io. If you use these tools and have questions or comments, please feel free to contact me and I will do my best to help.
fpcountr: protein number from fluorescence
FPCountR is a simple and accurate method to (a) generate and use fluorescent protein calibrants and (b) to use these calibrations to enable the extraction of absolute protein units from plate reader experiments.
The method is described in detail in our paper, ‘Absolute protein quantification using fluorescence measurements with FPCountR’, which is available open access at Nature Communications. The most up-to-date version of the experimental protocol can be found in Supplementary Note 5 of the paper or on protocols.io. A complete mathematical description of the analytical workflow carried out by the software can also be found in Supplementary Note 6 of the paper.
We have developed a corresponding analytical software package, fpcountr, to enable the accurate analysis of calibration data to obtain conversion factors, as well as of experimental data to convert arbitrary fluorescence units to fluorescent protein units in copies per cell or molar concentrations.
The package code is available on GitHub, along with a guide on how to install and run the package in RStudio.
parsley: extract/tidy/combine data from any plate reader
Parsley is a web application designed to help users extract raw data from the wide variety of data formats produced by plate readers, and reformat the data into a format usable by existing analytical packages for eg. growth curve analysis, fluorescent protein expression analysis, phenotype (or drug) screening assays. Read more about Parsley here and the paper here.
Parsley is available as a free web application that does not require installing software or setting up an account. A complete Guide, as well as Youtube Demos are available via the application link above. Alternatively, the package may be installed from GitHub and run locally by following the instructions provided here.
