

# Author: William M. Old & Steve Guard, University of Colorado Boulder
# Date: 6/13/2019
# Guard, S. et al. JOVE manuscript
# License:  GPL-2 (GNU General Public License Version 2)

To perform CRAPome differential analysis and empirical Bayes differential statistical analysis on the MaxQuant proteinGroups.txt IP-MS data, ensure you have the following files. Start with "export_CRAPomeSAINT_Input_File.R", upload the output file that is generated to CRAPome.org (see script and paper for details), and then see "main_differential_analysis.R" for details on visualization and reproducing figures in the paper.

Required files:

1. DYRK1A_Interactome_MaxQuantAnalysis.txt 			: MaxQuant proteinGroups.txt file with perseus
                                                                        imputed LFQ intensities
2. export_CRAPomeSAINT_Input_File.R                                   : Script to generate the input file provided to CRAPome.org
                                                                        tool for generating the analysis results file

3. targets_for_crapome.txt                                            : Contains sample name information for subsetting analysis files

4. Nuclear_Subcell_CRAPome.txt                                        : CRAPome analysis results file (obtained by running export_CRAPomeSAINT_Input_File.R)

5. genes2plot_JOVEPaper.txt                                           : put gene symbols you want to annotate in plots in a
                                                                        file genes2plot_JOVEPaper.txt in working directory

6. ggmaplot_functions.R                                               : R file with functions for plotting MA plots and
                                                                        other accessory tasks
7. main_differential_analysis.R  (main file)


