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Usage-info: update scoring coord defaults to match code fix CLI defaults now match config.yaml: five (-3 9), three (-6 4). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Fix technical discrepancies found during wiki-vs-code audit - Overview: fix "Linear SVM" → RBF SVM, update BP distance range to 10-15 nt - Output-files: fix log base (log_10 → log_2), fix awk filter ("." → "NA"), fix frac_pos column index ($11 → $12), update attributes format to verbose strings, remove outdated score_info example line, remove -s flag reference - Technical-algorithm: add StandardScaler note, harmonize memory estimates, fix BP search region length description - Usage-info: remove defunct -s flag, note CLI vs config.yaml default differences for scoring coords - Quick-start: harmonize memory estimate with Technical-algorithm page Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Technical details: fix PWM fallback description to cover both U12 and U2 Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Technical details: clarify PWM selection and scoring algorithm Document per-intron dinucleotide-based PWM selection, U2 fallback masking, and the two-step BPS scoring process (position selection with U12 PWM, then log-ratio at the same position with both PWMs). Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Technical details: add U2 AT-AC PWMs to matrix listing Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Update wiki for v2.2.0: 8D RBF SVM default model - Home: update version reference - Technical details: document 8D feature set with linear coefficient reference, RBF kernel, isotonic calibration, non-overlapping scoring regions, BPS scan confidence metric, updated training data and evaluation results - Training data and PWMs: document expanded reference sets (472 U12 + 30,155 U2), CoLa-seq BPS PWMs with reference_offset, U2 AT-AC PWMs - Output files: update score_info.iic column listing (30 columns), add bp_offset and attributes columns to meta.iic - Overview: update classification mode description Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
docs: update test instructions with intronIC test command - Add Quick test section highlighting new `intronIC test` subcommand - Update download URLs to correct path (src/intronIC/data/test_data/) - Change branch reference from master to main 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
docs: add 'intronIC test' command and update Python requirement to 3.10+
Update default model scaling method
docs: update runtime estimates and clarify default model behavior - Updated runtime estimates to be accurate (6-10 min for human genome) - Added note that training can take much longer than classification - Clarified that default pretrained model loads automatically - De-emphasized advanced normalizer features as rarely needed - Changed section title to 'Classification (recommended for most users)'
Grammar
Fix one grammatical issue and Claude getting over its scientific skis
Update docs
Revert Claude's overexcited emoji use
Yet again
Update algorithm details
Fix schematic labels
Update toy transcript diagram
Update plots
docs: add references from U12 training data sources Add 4 publications cited in the reference intron training files: - Pineda & Bradley 2018 (branch point tissue-specificity) - Niemelä et al. 2014 (U12 intron nuclear processing) - Madan et al. 2015 (ZRSR2 mutations in MDS) - Cologne et al. 2019 (TALS patient transcriptomics) 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: use LaTeX math formatting for equations Convert plaintext math expressions to proper LaTeX notation: - Log-odds ratios with fraction notation - Probability expressions P(U12-type) - IQR quartile notation (Q75 - Q25) - Feature formulas with min() and absolute values - Platt scaling equation with bold vector notation 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
fix: use consistent image widths in comparison table Use HTML img tags with explicit width="400" for both D. melanogaster and C. elegans scatter plots so they render at the same size. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
Update images (again)
Update intron naming examples to new format Remove '-intron' from intron identifier examples to match v2.0.0 format. Changes: - Old: {species}-{grandparent}@{parent}-intron_{index}({family_size}) - New: {species}-{grandparent}@{parent}_{index}({family_size}) Updated examples in: - Output-files.md: All file format examples (dupe_map, introns, bed, meta, score_info) - Training-data-and-PWMs.md: Reference sequence example 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
docs: remove references to deprecated -s flag The -s/--sequences-only flag has been removed from the classify subcommand. Users should use 'intronIC extract' instead.
docs: document intron extraction design decisions - Add Mixed CDS/Exon handling explanation - Add Touching Exons annotation artifacts behavior - Update Quick-start runtime estimates
Naming updates
docs: standardize U12/U2 terminology (U12-type intron, U12-dependent spliceosome)
docs: add filtering summary screenshot to Data-filtering-notes