How crisprking/nka-pump-genomics works
This repository is a reproducible genomics analysis of disease-associated variants in Na⁺/K⁺-ATPase subunits. Its principal workflow gathers and aligns sequences, derives conservation, maps and validates ClinVar variants, adds population and predictor evidence, then tests biological associations and produces reports. The graph preserves documented structure, topology, paralogue and classifier analyses as capabilities. Sampled source confirms the variant, population and statistical wiring; connections for unsampled pipeline stages are limited to documented inputs and outputs rather than inferred from their numbering.
Main entry points: results Analysis tables · 03_variants.py ClinVar variants · 06_analysis.py Association analysis · 00_fetch_sequences.py Fetch sequences
Components 21
Sequence analysis
- Fetch sequences
scripts/00_fetch_sequences.py - Align orthologues
scripts/01_align.py - Conservation scores
scripts/02_conservation.py - Canonical sequences
data/reference/canonical.fasta - Sequence alignments
data/alignments
Variant evidence
- ClinVar variants
scripts/03_variants.py - Variant mapping
src/nka/variants.py - Quality gates
src/nka/qc.py - gnomAD evidence
scripts/04_population.py - AlphaMissense evidence
scripts/05_alphamissense.py
Statistical analysis
- Structure analysis
scripts - Topology analysis
scripts - Evidence integration
scripts - Association analysis
scripts/06_analysis.py - Variant classifiers
src/nka/model.py - Statistical tests
src/nka/stats.py
Results and reporting
- Analysis tables
results - Report generation
scripts/07_report.py - Reports and figures
docs
Other components
- Researcher
- External databases
Connections 24
- Researcher → Fetch sequences: runs pipeline
- Fetch sequences → External databases: fetches sequences
- Fetch sequences → Canonical sequences: writes sequences
- Align orthologues → Canonical sequences: reads sequences
- Align orthologues → Sequence alignments: writes alignments
- Conservation scores → Sequence alignments: reads alignments
- Conservation scores → Analysis tables: writes scores
- ClinVar variants → Variant mapping: maps variants
- ClinVar variants → External databases: queries ClinVar and VEP
- ClinVar variants → Canonical sequences: validates residues
- ClinVar variants → Quality gates: records mapping QC
- ClinVar variants → Analysis tables: writes variants
- gnomAD evidence → External databases: queries gnomAD
- gnomAD evidence → Analysis tables: writes population evidence
- AlphaMissense evidence → Analysis tables: writes predictions
- Structure analysis → Analysis tables: records structure analyses
- Topology analysis → Analysis tables: records enrichment
- Evidence integration → Analysis tables: writes integrated evidence
- Association analysis → Analysis tables: reads analysis inputs
- Association analysis → Statistical tests: computes permutations and intervals
- Association analysis → Variant classifiers: scores classifiers
- Association analysis → Analysis tables: writes statistics and validation
- Report generation → Analysis tables: reads results
- Report generation → Reports and figures: produces reports