halbritter-lab Amissense issues

halbritter-lab / Amissense

The Amissense Tool analyzes and visualizes AlphaMissense pathogenicity scores, integrating AlphaFold structures and ClinVar data. It offers automated pipelines, visualizations, and versatile command-line utilities.

MIT License

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Bug: uniprotID_pathogenicity_session.py strand needs to be specified

#51 Claudia518 opened 2 weeks ago
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Bug: uniprotID_pathogenicity_session.py coloring needs to match standard blue-white-red

#50 Claudia518 opened 2 weeks ago
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bug: error - PDB file not found

#49 Claudia518 closed 2 weeks ago
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Feature request: Create a Function to Generate a PyMOL Script in Analogy to the Chimera Script

#48 berntpopp closed 2 weeks ago
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Feature request: Update Chimera and PyMol Functions to Show ClinVar Variants as Spheres

#47 berntpopp closed 2 weeks ago
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fix: generate_pathogenicity_pdb updates bfactor

#46 Claudia518 closed 2 weeks ago
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Feat: Add PDB file screenshot with coloring according to B-factors to output and in the report

#45 berntpopp opened 3 weeks ago
1
Feat: Generate session for Chimera/PyMOL to open the PDB file and color according to B-factors

#44 berntpopp opened 3 weeks ago
1
Bug: generate_pathogenicity_pdb no longer modifies PDB files

#43 berntpopp opened 3 weeks ago
0
Bug: PDB file is named after UniProt, should also contain the source of the file

#42 berntpopp opened 3 weeks ago
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Docs: Update Documentation and Installation Instructions

#41 berntpopp opened 3 weeks ago
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Feat: Add a Logo to the Repository and CLI

#40 berntpopp opened 3 weeks ago
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Bug: Error Fetching ClinVar Summaries

#39 berntpopp opened 3 weeks ago
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Feat: Allow Output Image Type Selection

#38 berntpopp opened 3 weeks ago
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Feat: Implement Interactive CLI

#37 berntpopp opened 3 weeks ago
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Feat: Ensure Correct Mapping Between Gene Transcript, UniProt, and PDB

#36 berntpopp opened 3 weeks ago
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Feat: Add Support for Custom Mutations in Plots and PDB

#35 berntpopp opened 3 weeks ago
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Automate UniProt ID Retrieval, Improve Error Handling, Add Retry Mechanism, and Refactor pipeline.py

#34 berntpopp closed 3 weeks ago
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Integrate Static JSON API for AlphaMissense Scores and Structure Output Directory

#33 berntpopp closed 3 weeks ago
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Feature Request: Adapt Amissense Tool to Generate JSON Files Following New Schema

#32 berntpopp opened 3 weeks ago
1
Feat: Structure Output Directory in a More Organized Way

#31 berntpopp closed 3 weeks ago
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Implement Testing: Test Coverage and CI Integration

#30 berntpopp opened 3 weeks ago
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Refactor: Ensure Consistent Formatting and Linting

#29 berntpopp opened 3 weeks ago
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Feat: Add Progress Bars for Long-Running Processes

#28 berntpopp opened 3 weeks ago
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Refactor: Clean Up pipeline.py

#27 berntpopp closed 3 weeks ago
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Feat: Add Retry Mechanism for API Calls

#26 berntpopp closed 3 weeks ago
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Feat: Use `get_uniprot_id` to Automate UniProt ID Retrieval

#25 berntpopp closed 3 weeks ago
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Refactor: Consolidate PDB Download Logic

#24 berntpopp opened 3 weeks ago
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Feat: Use Static JSON API for AlphaMissense Scores

#23 berntpopp closed 3 weeks ago
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Refactor: Regex in clinvar.py

#22 berntpopp opened 3 weeks ago
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Feat: Unit Tests

#21 berntpopp opened 3 weeks ago
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Feat: Generate an HTML Report

#20 berntpopp opened 3 weeks ago
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Feat: Interactive Plots

#19 berntpopp opened 3 weeks ago
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Feat: Caching Mechanism for API Calls

#18 berntpopp opened 3 weeks ago
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Refactor: Subcommand Abstraction

#17 berntpopp opened 3 weeks ago
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Refactor: Improve Argument Parsing

#16 berntpopp opened 3 weeks ago
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Refactor: Error Handling for Missing Configurations

#15 berntpopp closed 3 weeks ago
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Docs: Type Annotations and Documentation

#14 berntpopp opened 3 weeks ago
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Refactor: Config Path Handling

#13 berntpopp closed 3 weeks ago
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Convert script to CLI tool for better usability and integration

#12 berntpopp closed 3 weeks ago
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docs: Add License

#11 berntpopp closed 3 weeks ago
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feat: Convert to CLI

#10 berntpopp closed 3 weeks ago
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build: Create setup.py

#9 berntpopp closed 3 weeks ago
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refactor: Modularization

#8 berntpopp opened 3 weeks ago
1
feat: Add Function to Download PDB Files

#7 berntpopp opened 3 weeks ago
1
feat: Add Error Handling

#6 berntpopp closed 3 weeks ago
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feat: Add Semantic Versioning

#5 berntpopp closed 3 weeks ago
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refactor: Logging

#4 berntpopp closed 3 weeks ago
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refactor: Shared Utilities Module

#3 berntpopp closed 3 weeks ago
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refactor: Remove Redundancy (DRY Programming)

#2 berntpopp closed 3 weeks ago
0