FREDIS (FRAP Reaction Diffusion Solver) is a Java program written for the analysis of Fluorescence Recovery After Photobleaching (FRAP) experiments. FREDIS features the calculation of the corrected recovery curve as well as the fitting with three different models. Details on FREDIS can be found in the following publication:
Müller KP, Erdel F, Caudron M, Marth C, Fodor BD, Richter M, Scaranaro M, Beaudouin J, Wachsmuth M & Rippe K (2009). A multi-scale analysis of dynamics and interactions of heterochromatin protein 1 in the nucleus by fluorescence fluctuation microscopy. Biophys J 97, 2876-2885. Abstract | Reprint (3.3 MB pdf file)
Further details on the FREDIS software are available at http://malone.bioquant.uni-heidelberg.de/software/fredis
MCORE (Multi-scale CORrelation Evaluation) is a software for analyzing deep sequencing data sets. It uses the fluctuation spectrum of mapped sequencing reads to quantify and compare spatial patterns on multiple length scales in a model-independent manner. MCORE can be used to dissect the chromatin domain topology by integrating sequencing data from chromatin immunoprecipitation, RNA expression, DNA methylation and chromosome interaction experiments. Furthemore, it can be applied to construct network models that reflect the relationships among these features on different genomic scales. Details on MCORE can be foundin the following publication:
Molitor J, Mallm JP, Rippe K & Erdel F (2017). Retrieving chromatin patterns from deep sequencing data with correlation functions. Biophys J 112, 473-490. doi: 10.1016/j.bpj.2017.01.001 | Abstract | Reprint (10.3 MB) | Article metrics.
Further details on the MCORE software are available at http://malone.bioquant.uni-heidelberg.de/software/mcore