For help with your analysis contact. r.s.n.ferhmann@umcg.nl >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Precompiled version of unpublished tool AnalyzerTool v5 Tested on: macOS 11.1 Qt 5.15.1 Qt version is very important otherwise program will not run. Installing time: precompiled program that does not need installation. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>To run independent component analysis<<<<<< Open AnalyzerTool In upper menu: File > Import > Data matrix for a single file In window specify how to load your whitened matrix Loaded file will appear on left hand side In upper menu: Select the loaded dataset in the lelft hand side Analyses > Component analysis > independent component analysis In window specify parameters of ICA and output directory. Expected running time: Unknown due to nondeterministic algorithm. Not feasible to run on commodity hardware (laptop). We used: Intel Xeon Platinum 8160 CPU @ 2.10GHz x 96 (112 cores) 754.6 GiB RAM 64 bit Ubuntu 19.10 Our experience: Human affymetrix dataset 1 month. Human RNAseq dataset 3 weeks. >>>>>>>>To generate gene set predictions<<<<<<<<<<< Open AnalyzerTool In upper menu: File > Import > Data matrix for a single file In window specify how to load your mixing matrix Loaded file will appear on left hand side In upper menu: Tools > create Gene Network In window:select gene set definitions specify gene set files (GMT without header) See Supporting Data in genetica-network.com for example format Select whether to perform permutation test. Select output directory for output files and intermediates. Expected running time - no permutation test: less than one hour in commodity hardware for 1 small gene set collection (Hallmark). Expected running time - with permutation test: Not feasible in commodity hardware. Memory intensive (Permutations x Genes x Unique gene set sizes x 2). We used: Intel Xeon Platinum 8160 CPU @ 2.10GHz x 96 (112 cores) 754.6 GiB RAM 64 bit Ubuntu 19.10 Our experience: Human affymetrix dataset 3 days. Human RNAseq dataset 1 week. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The source code is available at: https://bitbucket.org/groupfehrmann/analyzertool/src/master/