This tool launches a local Shiny-based web application that enables an overall analysis of a DIA proteomics data matrix (from FragPipe DIA-NN). It provides an interactive interface, easy to use for those users with little or no experience in the R programming language, and outputs an HTML report, a .pptx file with the figures, and an Excel file with different types of data.
An Excel (.xlsx) or .tsv file.
The data matrix should be the output of FragPipe's DIA-NN, which means that it has to include the following annotation columns: "Protein.Group", "Protein.Ids", "Protein.Names", "Genes" and "First.Protein.Description"; and the columns with the actual data (with their names matching the BioReplicate column from the Metadata file).
An Excel (.xlsx) file.
For the app to work, the following variables, with those exact same names (capital letters included), have to be present:
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BioReplicate: each sample within each condition - it should be copy-pasted from the column names of the raw data matrix file
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Group: which group the sample belongs to - the names should be informative and always the same (i.e., GAPDH in all instances, not variations like Gapdh)
An Excel (.xlsx) file.
For the app to work, the following variables, with those exact same names (capital letters included), have to be present:
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Condition: name of the group that is acting as treatment/mutated, or simply one of the groups
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Control: name of the group that is acting as control/wildtype, or simply one of the groups
The names given to the Condition and Control must be written exactly the same as in the Group column of the Metadata file
For the app to work, it is mandatory that all headers of all files are written correctly, that the BioReplicates are written (copy-pasted) as in the data matrix file, and that de Control-Condition names are the same as in the Group variable of the Metadata file.