Modified the program to allow users to specify how many experiments and controls they have
- A GUI via tkinter
- Streamlining the application/reducing overlapping code
To compare results of two MaxQuant experiments and their respective controls from a run by normalizing data from the output peptides.txt file.
Users can selected data by PEP and MS/MS count thresholds, proteins marked by MaxQuant as potential contaminats are removed by default.
Data is normalized by count and intensity columns: (Experiment 1 - Control 1, Experiment 2 - Control 2).
- A .csv file containing aggregated, normalized data
- A .csv file containing differentially expressed proteins + log2 fold change of intensity
- .csv files containing proteins expressed in either Experiment 1 or Experiment 2
After uploading peptides.csv to the experimental_data folder, run tools through run_all_functions.py or individually.