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halbritter-lab
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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 months ago
0
Bug: uniprotID_pathogenicity_session.py coloring needs to match standard blue-white-red
#50
Claudia518
opened
2 months ago
0
bug: error - PDB file not found
#49
Claudia518
closed
2 months ago
0
Feature request: Create a Function to Generate a PyMOL Script in Analogy to the Chimera Script
#48
berntpopp
closed
2 months ago
0
Feature request: Update Chimera and PyMol Functions to Show ClinVar Variants as Spheres
#47
berntpopp
closed
2 months ago
0
fix: generate_pathogenicity_pdb updates bfactor
#46
Claudia518
closed
2 months ago
0
Feat: Add PDB file screenshot with coloring according to B-factors to output and in the report
#45
berntpopp
opened
2 months ago
1
Feat: Generate session for Chimera/PyMOL to open the PDB file and color according to B-factors
#44
berntpopp
opened
2 months ago
1
Bug: generate_pathogenicity_pdb no longer modifies PDB files
#43
berntpopp
opened
2 months ago
0
Bug: PDB file is named after UniProt, should also contain the source of the file
#42
berntpopp
opened
2 months ago
0
Docs: Update Documentation and Installation Instructions
#41
berntpopp
opened
2 months ago
0
Feat: Add a Logo to the Repository and CLI
#40
berntpopp
opened
2 months ago
0
Bug: Error Fetching ClinVar Summaries
#39
berntpopp
opened
2 months ago
0
Feat: Allow Output Image Type Selection
#38
berntpopp
opened
2 months ago
0
Feat: Implement Interactive CLI
#37
berntpopp
opened
2 months ago
0
Feat: Ensure Correct Mapping Between Gene Transcript, UniProt, and PDB
#36
berntpopp
opened
2 months ago
0
Feat: Add Support for Custom Mutations in Plots and PDB
#35
berntpopp
opened
2 months ago
0
Automate UniProt ID Retrieval, Improve Error Handling, Add Retry Mechanism, and Refactor pipeline.py
#34
berntpopp
closed
2 months ago
0
Integrate Static JSON API for AlphaMissense Scores and Structure Output Directory
#33
berntpopp
closed
2 months ago
0
Feature Request: Adapt Amissense Tool to Generate JSON Files Following New Schema
#32
berntpopp
opened
2 months ago
1
Feat: Structure Output Directory in a More Organized Way
#31
berntpopp
closed
2 months ago
0
Implement Testing: Test Coverage and CI Integration
#30
berntpopp
opened
2 months ago
0
Refactor: Ensure Consistent Formatting and Linting
#29
berntpopp
opened
2 months ago
0
Feat: Add Progress Bars for Long-Running Processes
#28
berntpopp
opened
2 months ago
0
Refactor: Clean Up pipeline.py
#27
berntpopp
closed
2 months ago
0
Feat: Add Retry Mechanism for API Calls
#26
berntpopp
closed
2 months ago
0
Feat: Use `get_uniprot_id` to Automate UniProt ID Retrieval
#25
berntpopp
closed
2 months ago
0
Refactor: Consolidate PDB Download Logic
#24
berntpopp
opened
2 months ago
0
Feat: Use Static JSON API for AlphaMissense Scores
#23
berntpopp
closed
2 months ago
0
Refactor: Regex in clinvar.py
#22
berntpopp
opened
2 months ago
0
Feat: Unit Tests
#21
berntpopp
opened
2 months ago
0
Feat: Generate an HTML Report
#20
berntpopp
opened
2 months ago
0
Feat: Interactive Plots
#19
berntpopp
opened
2 months ago
0
Feat: Caching Mechanism for API Calls
#18
berntpopp
opened
2 months ago
0
Refactor: Subcommand Abstraction
#17
berntpopp
opened
2 months ago
0
Refactor: Improve Argument Parsing
#16
berntpopp
opened
2 months ago
0
Refactor: Error Handling for Missing Configurations
#15
berntpopp
closed
2 months ago
0
Docs: Type Annotations and Documentation
#14
berntpopp
opened
2 months ago
0
Refactor: Config Path Handling
#13
berntpopp
closed
2 months ago
0
Convert script to CLI tool for better usability and integration
#12
berntpopp
closed
2 months ago
0
docs: Add License
#11
berntpopp
closed
2 months ago
0
feat: Convert to CLI
#10
berntpopp
closed
2 months ago
0
build: Create setup.py
#9
berntpopp
closed
2 months ago
0
refactor: Modularization
#8
berntpopp
opened
2 months ago
1
feat: Add Function to Download PDB Files
#7
berntpopp
opened
2 months ago
1
feat: Add Error Handling
#6
berntpopp
closed
2 months ago
0
feat: Add Semantic Versioning
#5
berntpopp
closed
2 months ago
0
refactor: Logging
#4
berntpopp
closed
2 months ago
0
refactor: Shared Utilities Module
#3
berntpopp
closed
2 months ago
0
refactor: Remove Redundancy (DRY Programming)
#2
berntpopp
closed
2 months ago
0
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