This pipeline processes mass spec data for Metaboanalyst 5.0 analysis. Further compound specific reports can also be generated using Metaboanalyst's volcano data.
- Install Python3 and the following packages: numpy, pandas, and statistics
- Update SAMPLE_ID.txt with the {root sample ID} (e.g., "example" is the root sample ID in "example.xlsx")
- Place the abundance XLS data file in the "input_files" folder. Note that this file must match the format of the "example.xlsx" file, including the sheet name.
- Run "python3 part1_annotation_transform.py" from your terminal or code IDE in the location of this code pipeline
- Use the file named "{root sample ID} + -transposed_p1.csv" the "output_files" folder for Metaboanalyst 5.0 analysis, looking over results first for gut-check and adding sample group IDs
- Place the resulting volcano plot data in a CSV file in the "input_files" folder, titled "{root sample ID} + _ volcano.csv"
- Run "python3 part2_compound_trackback.py"
- The resulting output file, "{root sample ID} + _ p2.csv", located in the "output_files" folder, is the end result of the pipeline for analysis