01 Input tab
If you just want to try out the software select the 'Load in example' option and press 'Upload'. After the upload the QC -, Diff. abundance - and Compare amica data sets - tabs open in the main tab bar.
If you want to (re-)inspect previously analyzed amica output you can just upload the amica_protein_groups.tsv file together with the experimental design and after pressing the 'Upload' button you can also inspect the aforementioned tabs.
Automatically recognized input files are MaxQuant's 'proteinGroups.txt' file and FragPipe's 'combined_proteins.txt' file, however you can also upload a generic tab-separated format which can easily be processed by the addition of a file that maps relevant search engine-specific columns to a standard format.
After uploading all required files and pressing the 'Upload' button
a new field becomes accessible which allows for changing analysis parameters:
One property that can be changed in the 'Input' tab are the colors for all upcoming plots. Press on 'Choose colors' to toggle the color selection that is separated into different categories, depending on which plots are outputted. The selected colors propagate to all subsequent visualizations (e.g groups from the exp. design will always have the same color in a plot legend.)
