SPA_STOCSY

SPA_STOCSY is a R pipeline for the automatic identification of both "known" and "unknown" metabolites in given samples.
With given input samples, SPA_STOCSY offers automatic algorithms to estimate all the parameters and generatet the final results.
Here is an example of using SPA_STOCSY to analyze on 10 NMR samples from brain homogenates of Drosophila melanogaster.
Click here

Data

All the data listed in the paper are stored in input_data/ foler.

• 10_meta_simulation.csv : 50 synthesized samples from 10 metabolites
• htt_c12.csv: 10 NMR samples from brain homogenates of Drosophila melanogaster
• human_cell_data.csv: 22 NMR samples from human cells
• chx_lib_trunc.csv: reference library for 257 metabolites with their cluster information

Source code

The main functions in SPA_STOCSY are stored in source_codes/ folder.
Load these R files before running the tool as in the example.

Input

• The input file takes multiple NMR samples as columns. The first column should be specified as a list of chemical shift values.
• The NMR samples are highly recommended to get normalized on integral.

Output

• The output location is defined by user before running the tool as in the example
• The output files contain:
  • Multiple visualization plots during the running process
  • 'SPA_cluster_peaks.csv': peaks detected in each SPA cluster
  • 'STOCSY_corr_clusters.csv': correlated SPA clusters generated from STOCSY
  • 'auto_identify_metabolites.csv': list of identified metabolites with a set detection rate