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

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@cristinaetrv cristinaetrv commented Nov 27, 2024

Summary by CodeRabbit

  • Documentation
    • Updated the README.md to enhance the documentation of the Bystro platform in proteomics and genetics.
    • Introduced a new section detailing modular steps for proteomics analyses, including Imputation, Batch Correction, Removal of Confounding Factors, and Network Analysis, with descriptions and demo links.
    • Expanded the genetics section to highlight the significance of removing confounding factors, providing specific examples for improved generalizability.
    • Added a section on combined (multi-omics) applications discussing the integration of genomic and proteomic data for downstream analyses.
    • Made minor formatting adjustments for better readability.

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coderabbitai bot commented Nov 27, 2024

Walkthrough

The README.md file has been significantly updated to enhance the documentation of the Bystro platform's applications in proteomics and genetics. A new section detailing four modular steps for proteomics analyses has been introduced, including Imputation, Batch Correction, Removal of Confounding Factors, and Network Analysis. The genetics section has been expanded to emphasize the importance of removing confounding factors, with specific examples provided. Additionally, a new section on combined multi-omics applications has been added. Minor formatting adjustments were made for improved readability.

Changes

File Change Summary
README.md Updated to include details on proteomics analyses, expanded genetics section, and introduced multi-omics applications. Minor formatting adjustments made.

Poem

In the garden where knowledge grows,
Bystro's secrets now brightly show.
With steps for proteomics, clear and bright,
Genetics shines with new insights!
Multi-omics dance in a lovely array,
A rabbit's joy in the light of day! 🐇✨


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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (2)
README.md (2)

56-56: Remove redundant wording

The phrase "combined together" is redundant. "Combined" alone conveys the same meaning.

-For proteomics analyses, we have 4 modular steps that can be applied alone or combined together:
+For proteomics analyses, we have 4 modular steps that can be applied alone or combined:
🧰 Tools
🪛 LanguageTool

[style] ~56-~56: ‘combined together’ is redundant. Use “combined”
Context: ...ular steps that can be applied alone or combined together: 1. Imputation - Recommended if...

(COMBINE_TOGETHER)


70-73: Fix list indentation for better markdown formatting

The unordered list items should be properly indented according to markdown standards.

 Make genetic results more generalizable by removing 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)
+ - 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)
🧰 Tools
🪛 Markdownlint (0.35.0)

71-71: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


72-72: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


73-73: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 9bccb40 and bad807e.

📒 Files selected for processing (1)
  • README.md (2 hunks)
🧰 Additional context used
🪛 LanguageTool
README.md

[style] ~56-~56: ‘combined together’ is redundant. Use “combined”
Context: ...ular steps that can be applied alone or combined together: 1. Imputation - Recommended if...

(COMBINE_TOGETHER)


[style] ~65-~65: Consider using an alternative to strengthen your wording.
Context: ...twork Analysis - Recommended if you want to discover predictive networks in your...

(WANT_KEEN)

🪛 Markdownlint (0.35.0)
README.md

71-71: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


72-72: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


73-73: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)

🔇 Additional comments (3)
README.md (3)

56-79: Documentation improvements look great!

The additions effectively document the platform's capabilities in proteomics and genetics. The structure is clear, with well-organized sections and helpful references to demos and documentation. The modular approach to describing the analysis steps makes it easy for users to understand the available options.

🧰 Tools
🪛 LanguageTool

[style] ~56-~56: ‘combined together’ is redundant. Use “combined”
Context: ...ular steps that can be applied alone or combined together: 1. Imputation - Recommended if...

(COMBINE_TOGETHER)


[style] ~65-~65: Consider using an alternative to strengthen your wording.
Context: ...twork Analysis - Recommended if you want to discover predictive networks in your...

(WANT_KEEN)

🪛 Markdownlint (0.35.0)

71-71: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


72-72: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


73-73: Expected: 0; Actual: 2
Unordered list indentation

(MD007, ul-indent)


78-79: Verify the referenced documentation file

Let's ensure the referenced proteomics README file exists and is accessible.

✅ Verification successful

Referenced documentation file exists and is correctly linked

The proteomics README file exists at the exact path mentioned in the main README: python/python/bystro/proteomics/README.md. The directory structure is also properly set up.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the referenced README file exists
if [ ! -f "python/python/bystro/proteomics/README.md" ]; then
  echo "Warning: Referenced README file not found: python/python/bystro/proteomics/README.md"
fi

Length of output: 58


Script:

#!/bin/bash
# Let's try to find the actual location of the proteomics README file
fd -t f "README.md" | grep -i "proteomics"

# Also search for the proteomics directory structure
fd -t d "proteomics"

Length of output: 136


59-59: Verify the demo notebook paths

Let's verify that all the demo notebook links are valid and accessible.

Also applies to: 61-61, 63-63, 65-65

✅ Verification successful

All demo notebook links are valid and accessible

Based on the fd command output, all the demo notebooks mentioned in the README.md are present in the repository at the exact paths specified:

  • python/python/bystro/examples/Demo_Imputing_Missing_Data.ipynb
  • python/python/bystro/examples/Demo_accounting_for_batch_effects_with_control.ipynb
  • python/python/bystro/examples/Demo_Fair_PCA.ipynb
  • python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if the demo notebooks exist in the specified paths
for notebook in \
  "python/python/bystro/examples/Demo_Imputing_Missing_Data.ipynb" \
  "python/python/bystro/examples/Demo_accounting_for_batch_effects_with_control.ipynb" \
  "python/python/bystro/examples/Demo_Fair_PCA.ipynb" \
  "python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb"; do
  if [ ! -f "$notebook" ]; then
    echo "Warning: Demo notebook not found: $notebook"
  fi
done

Length of output: 1496


Script:

#!/bin/bash
# Let's use fd to find all .ipynb files in the repository
fd -e ipynb

# Also let's check the actual content of README.md to see the exact paths mentioned
cat README.md

Length of output: 5462

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Actionable comments posted: 1

🧹 Outside diff range and nitpick comments (2)
README.md (2)

64-65: Consider strengthening the wording in the Network Analysis description

The current wording "if you want to" could be more assertive. Consider revising to emphasize the value proposition.

-    - 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)
+    - Recommended for discovering predictive networks in your proteomic data, demo here: [Learning Predictive Network Demo](python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb)
🧰 Tools
🪛 LanguageTool

[style] ~65-~65: Consider using an alternative to strengthen your wording.
Context: ...twork Analysis - Recommended if you want to discover predictive networks in your...

(WANT_KEEN)


70-73: Consider adding brief examples or expected outcomes

While the use cases are clear, adding brief examples of expected outcomes or benefits for each scenario would help users better understand the impact.

For example:

- Remove ancestry-related information in multi-ancestry cohorts to reduce bias
+ Remove ancestry-related information in multi-ancestry cohorts to reduce bias (e.g., improves replication across populations)
- Remove effect of batch in meta-analyses
+ Remove effect of batch in meta-analyses (e.g., increases statistical power by reducing technical variation)
📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between bad807e and 58e906d.

📒 Files selected for processing (1)
  • README.md (2 hunks)
🧰 Additional context used
🪛 LanguageTool
README.md

[style] ~65-~65: Consider using an alternative to strengthen your wording.
Context: ...twork Analysis - Recommended if you want to discover predictive networks in your...

(WANT_KEEN)

🔇 Additional comments (2)
README.md (2)

112-112: Verify the INSTALL.md reference

Let's ensure the referenced INSTALL.md file exists and contains installation instructions.

✅ Verification successful

INSTALL.md file exists and contains appropriate installation instructions

The INSTALL.md file is present and contains comprehensive installation instructions, including:

  • Package installation via pip
  • Platform compatibility information
  • Development environment setup
  • Additional dependencies for MacOS
  • Instructions for working with Cython and Rust code
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if INSTALL.md exists and contains installation content
if [ ! -f "INSTALL.md" ]; then
    echo "Warning: INSTALL.md not found"
else
    # Check for installation-related content
    if ! grep -i "install\|setup\|requirement" "INSTALL.md" > /dev/null; then
        echo "Warning: No installation content found in INSTALL.md"
    fi
fi

Length of output: 78


Script:

#!/bin/bash
# Let's first check if the file exists and show its contents
if [ -f "INSTALL.md" ]; then
    echo "=== INSTALL.md contents ==="
    cat INSTALL.md
else
    echo "INSTALL.md file does not exist"
fi

# Also check for any other installation-related files
echo -e "\n=== Other potential installation files ==="
fd -i "install|setup" -e md

Length of output: 1418


58-65: Verify the notebook demo links

The documentation references several Jupyter notebook demos. Let's ensure these links are valid and accessible.

✅ Verification successful

The previous script's output was not conclusive as it only showed the command execution but not the actual file check results. Let's use fd to search for these notebooks with more flexible pattern matching to ensure we find them even if they might be in slightly different locations or have slightly different names.


All demo notebook links are valid and correctly referenced

The documentation accurately references all four Jupyter notebook demos, which are present in the repository at the exact paths specified:

  • python/python/bystro/examples/Demo_Imputing_Missing_Data.ipynb
  • python/python/bystro/examples/Demo_accounting_for_batch_effects_with_control.ipynb
  • python/python/bystro/examples/Demo_Fair_PCA.ipynb
  • python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb
🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Check if the referenced demo notebooks exist
for notebook in \
    "python/python/bystro/examples/Demo_Imputing_Missing_Data.ipynb" \
    "python/python/bystro/examples/Demo_accounting_for_batch_effects_with_control.ipynb" \
    "python/python/bystro/examples/Demo_Fair_PCA.ipynb" \
    "python/python/bystro/examples/Demo_Learning_Predictive_Network.ipynb"; do
    if [ ! -f "$notebook" ]; then
        echo "Warning: Demo notebook not found: $notebook"
    fi
done

Length of output: 1496


Script:

#!/bin/bash
# Let's use fd to search for these notebooks with case-insensitive matching
fd -i "demo.*missing.*data.*ipynb" 
fd -i "demo.*batch.*effects.*control.*ipynb"
fd -i "demo.*fair.*pca.*ipynb"
fd -i "demo.*predictive.*network.*ipynb"

Length of output: 424

🧰 Tools
🪛 LanguageTool

[style] ~65-~65: Consider using an alternative to strengthen your wording.
Context: ...twork Analysis - Recommended if you want to discover predictive networks in your...

(WANT_KEEN)

Comment on lines +78 to +79
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

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