Add scVelo RNA velocity analysis workflow and IQ-TREE reference documentation

- Introduced a comprehensive RNA velocity analysis pipeline using scVelo, including data loading, preprocessing, velocity estimation, and visualization.
- Added a script for running RNA velocity analysis with customizable parameters and output options.
- Created detailed documentation for IQ-TREE 2 phylogenetic inference, covering command syntax, model selection, bootstrapping methods, and output interpretation.
- Included references for velocity models and their mathematical framework, along with a comparison of different models.
- Enhanced the scVelo skill documentation with installation instructions, use cases, and best practices for RNA velocity analysis.

scientific-skills/gnomad-database/references/variant_interpretation.md

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+# gnomAD Variant Interpretation Guide
+
+## Allele Frequency Thresholds for Disease Interpretation
+
+### ACMG/AMP Criteria
+
+| Criterion | AF threshold | Classification |
+|-----------|-------------|----------------|
+| BA1 | > 0.05 (5%) | Benign Stand-Alone |
+| BS1 | > disease prevalence | Benign Supporting |
+| PM2_Supporting | < 0.0001 (0.01%) for dominant; absent for recessive | Pathogenic Moderate → Supporting |
+
+**Notes:**
+- BA1 applies to most conditions; exceptions include autosomal dominant with high penetrance (e.g., LDLR for FH: BA1 threshold is ~0.1%)
+- BS1 requires knowing disease prevalence; for rare diseases (1:10,000), BS1 if AF > 0.01%
+- Homozygous counts (`ac_hom`) matter for recessive diseases
+
+### Practical Thresholds
+
+| Inheritance | Suggested max AF |
+|-------------|-----------------|
+| Autosomal Dominant (high penetrance) | < 0.001 (0.1%) |
+| Autosomal Dominant (reduced penetrance) | < 0.01 (1%) |
+| Autosomal Recessive | < 0.01 (1%) |
+| X-linked recessive | < 0.001 in females |
+
+## Absence in gnomAD
+
+A variant **absent in gnomAD** (ac = 0) is evidence of rarity, but interpret carefully:
+- gnomAD does not capture all rare variants (sequencing depth, coverage, calling thresholds)
+- A variant absent in 730K exomes is very strong evidence of rarity for PM2
+- Check coverage at the position: if < 10x, absence is less informative
+
+## Loss-of-Function Variant Assessment
+
+### LOFTEE Classification (lof field)
+
+- **HC (High Confidence):** Predicted to truncate functional protein
+  - Stop-gained, splice site (±1,2), frameshift variants
+  - Passes all LOFTEE quality filters
+
+- **LC (Low Confidence):** LoF annotation with quality concerns
+  - Check `lof_flags` for specific reason
+  - May still be pathogenic — requires manual review
+
+### Common lof_flags
+
+| Flag | Meaning |
+|------|---------|
+| `NAGNAG_SITE` | Splice site may be rescued by nearby alternative site |
+| `NON_CANONICAL_SPLICE_SITE` | Not a canonical splice donor/acceptor |
+| `PHYLOCSF_WEAK` | Weak phylogenetic conservation signal |
+| `SMALL_INTRON` | Intron too small to affect splicing |
+| `SINGLE_EXON` | Single-exon gene (no splicing) |
+| `LAST_EXON` | In last exon (NMD may not apply) |
+
+## Homozygous Observations
+
+The `ac_hom` field counts homozygous (or hemizygous in males for chrX) observations.
+
+**For recessive diseases:**
+- If a variant is observed homozygous in healthy individuals in gnomAD, it is strong evidence against pathogenicity (BS2 criterion)
+- Even a single homozygous observation can be informative
+
+## Coverage at Position
+
+Always check that gnomAD has adequate coverage at the variant position before concluding absence is meaningful. The gnomAD browser shows coverage tracks, and coverage data can be downloaded from:
+- https://gnomad.broadinstitute.org/downloads#v4-coverage
+
+## In Silico Predictor Scores
+
+| Predictor | Score Range | Pathogenic Threshold |
+|-----------|-------------|---------------------|
+| CADD PHRED | 0–99 | > 20 deleterious; > 30 highly deleterious |
+| REVEL | 0–1 | > 0.75 likely pathogenic (for missense) |
+| SpliceAI max_ds | 0–1 | > 0.5 likely splice-altering |
+| SIFT | 0–1 | < 0.05 deleterious |
+| PolyPhen-2 | 0–1 | > 0.909 probably damaging |
+
+## Ancestry-Specific Considerations
+
+- A variant rare overall may be a common founder variant in a specific population
+- Always check all ancestry-specific AFs, not just the total
+- Finnish and Ashkenazi Jewish populations have high rates of founder variants
+- Report ancestry-specific frequencies when relevant to patient ancestry