https://github.com/tlnagy/ms-analysis

Analysis of MS results for PUBS
https://github.com/tlnagy/ms-analysis

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Analysis of MS results for PUBS

• Host: GitHub
• URL: https://github.com/tlnagy/ms-analysis
• Owner: tlnagy
• License: mpl-2.0
• Created: 2015-10-05T20:16:55.000Z (about 9 years ago)
• Default Branch: master
• Last Pushed: 2015-10-18T21:48:12.000Z (about 9 years ago)
• Last Synced: 2024-10-12T14:54:47.468Z (about 1 month ago)
• Language: Python
• Size: 12.1 MB
• Stars: 1
• Watchers: 4
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# ms-analysis

Analysis of MS results for PUBS

## Reproducing results

The code can be run by 

```

./run_analysis.py -d ms_data

```

## Development

To build on top of this code, first import it (if it is in the current

directory) like so

```

import run_analysis as ra

```

then make sure to run the `process_data` function and point it to the

location of the ms_data directory containing the data from the MS

experiment e.g.

```

ms_data/

├── Phospho\ (STY)Sites.txt

├── experimentalDesignTemplate.txt

├── parameters.txt

├── peptides.txt

├── proteinGroups.txt

├── summary.txt

└── tables.pdf

0 directories, 7 files

```

so we have 

```

path = "ms_data"

prot_groups, intensity_cols, normed_intensities, log_ratios = run_analysis.process_data(path)

```

where `path` is the location of the ms_data folder relative to the current

directory. And that's it! Now you access to the processed data. The other

functions within `run_analysis` can be accessed similarly