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Add use cases for Gen/Prot in README.md #607

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Jan 14, 2025
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Add use cases for Gen/Prot in README.md #607

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Add use cases for Gen/Prot in README.md
cristinaetrv Nov 27, 2024
58e906d
Fix grammar
cristinaetrv Nov 27, 2024
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25 changes: 21 additions & 4 deletions README.md
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Expand Up @@ -53,13 +53,30 @@ from bystro.supervised_ppca import *

## Applications in Proteomics

Description coming soon

For proteomics analyses, we have 4 modular steps that can be applied alone or combined:

1. Imputation
- Recommended if there are missing values within your data, demo here: [Soft Impute Demo](python/python/bystro/examples/Demo_Imputing_Missing_Data.ipynb)
2. Batch Correction
- Recommended for TMT data that has a control per batch to correct for small batches, demo here: [Small sample batch correction Demo](python/python/bystro/examples/Demo_accounting_for_batch_effects_with_control.ipynb)
3. Removal of Confounding factors
- Recommended if there are confounding factors such as sex or ancestry that you want to remove from your data, demo here: [Fair PCA Demo](python/python/bystro/examples/Demo_Fair_PCA.ipynb)
4. Network Analysis
- Recommended if you want to discover predictive networks in your proteomic data, demo here: [Learning Predictive Network Demo](python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb)
<br>

## Applications in Genetics

Description coming soon
Make genetic results more generalizable by removing information from confounding factors:
- Remove ancestry-related information in multi-ancestry cohorts to reduce bias
- Remove effect of batch in meta-analyses
- See demo here: [Fair PCA Demo](python/python/bystro/examples/Demo_Fair_PCA.ipynb)
<br>

## Combined (Multi-omics) Applications

Combine genomic and proteomic data for any downstream analyses or data exploration
- Read more here: [Proteomics combine README.md](python/python/bystro/proteomics/README.md)
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💡 Codebase verification

Fix incorrect path in proteomics README link

The proteomics README exists but the path in the main README is incorrect. The actual path is python/python/bystro/proteomics/README.md while the link references python/bystro/proteomics/README.md. Additionally, the README contains comprehensive information about combining genomic annotations with proteomics data, particularly in the "Annotation Interface" section, which aligns with the purpose mentioned in the main README.

  • Update the link path in README.md to: [Proteomics combine README.md](python/python/bystro/proteomics/README.md)
🔗 Analysis chain

Verify the proteomics README link

Let's ensure the referenced proteomics README exists and contains relevant information.

Let me verify the content of the README file to better understand what information it contains.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if the referenced README exists
if [ ! -f "python/python/bystro/proteomics/README.md" ]; then
    echo "Warning: Proteomics README not found"
else
    # Check if it contains multi-omics content
    if ! grep -i "multi-omics\|combined" "python/python/bystro/proteomics/README.md" > /dev/null; then
        echo "Warning: No multi-omics content found in proteomics README"
    fi
fi

Length of output: 261

Script:

#!/bin/bash
# Check the content of the proteomics README
cat python/python/bystro/proteomics/README.md

Length of output: 5014


<br>

Expand Down Expand Up @@ -92,4 +109,4 @@ Bystro is compatible with Linux and MacOS. Windows support is experimental. If y
brew install cmake
```

Please refer to [INSTALL.md](INSTALL.md) for more details.
Please refer to [INSTALL.md](INSTALL.md) for more details.