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Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics. Use when verifying alignment data quality before variant calling or quantification.
Maps GWAS-implicated loci to candidate effector (causal) genes by integrating variant-to-gene (V2G) features via Open Targets L2G (Mountjoy 2021), MAGMA gene-based association (de Leeuw 2015), FUMA SNP2GENE, cS2G combined SNP-to-gene scores (Gazal 2022), Polygenic Priority Scores (PoPS, Weeks 202...
Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pathway collection with clusterProfiler and rWikiPathways. Covers why a WikiPathways result is a snapshot of a live, monthly-updated database (enrichWP/gseWP/gson_WP silently pull da...
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
Build reproducible scientific documents, presentations, and websites with Quarto supporting R, Python, Julia, and Observable JS. Use when creating reproducible reports with Quarto.
Orchestrates the full path from differential expression results to redundancy-collapsed functional enrichment: choose ORA vs GSEA, convert gene IDs per method, run enrichGO/enrichKEGG/enrichPathway/enrichWP or gseGO/gseKEGG (clusterProfiler, ReactomePA, rWikiPathways), and visualize. Routes the O...
Performs subgroup and heterogeneous treatment effect (HTE) analyses for clinical trials. Covers Mantel-Haenszel pooling, Breslow-Day, interaction tests in regression, RERI for additive interaction, modern data-adaptive HTE methods (STEPP, SIDES, causal forests, X/R-learners), Bayesian shrinkage (...
Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-v...
Parses, queries, converts, and extracts from GTF and GFF3 gene-model annotation files - walking the gene/transcript/exon/CDS hierarchy with gffutils (queryable SQLite DB), converting formats and extracting transcript/CDS/protein FASTA with gffread, slurping to dataframes with gtfparse/pyranges, a...
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological ...
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathwa...
Builds QSAR / QSPR models using chemprop D-MPNN, MolFormer, Uni-Mol, ChemBERTa, random forest baselines, and Gaussian processes with explicit handling of OECD 5 principles, applicability domain (kNN, leverage, conformal prediction, Mahalanobis), scaffold-balanced splits, ensemble uncertainty, cal...
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector graphics for presentations, or ensuring consistent figure styling across analyses.
Execute Speak primary workflow: AI Conversation Practice with real-time
Write a structured clinical case summary or case presentation. Use when asked to write a clinical case summary, case presentation, patient case report, or clinical handover. Produces a structured summary using SBAR or SOAP format. For educational and documentation purposes only — not a substitute...
Mobile specialist for Flutter, React Native, and Swift native iOS development. Use for mobile app, Flutter, Dart, React Native, Swift, SwiftUI, iOS, Android, Riverpod, swift-openapi-generator, and widget work.
Use when debugging Purchasely SDK issues — diagnoses common problems like blank paywalls, frozen UI, missing callbacks, purchase failures, and initialization errors across all platforms.
Use when integrating the Purchasely SDK into a mobile app — guides through installation, initialization, paywall display, purchase handling, and action interceptor setup for iOS, Android, React Native, Flutter, and Cordova.
Add local notifications to .NET MAUI apps on Android, iOS, and Mac Catalyst. Covers notification channels, permissions, scheduling, foreground/background handling, and DI registration. Works with XAML/MVVM, C# Markup, and MauiReactor. USE FOR: "local notification", "schedule notification", "notif...
Integrate your app with iOS Visual Intelligence for camera-based search and object recognition. Use when adding visual search capabilities.
Use when reviewing an existing Purchasely SDK integration — checks initialization, paywall display, action interceptor, deeplinks, user management, and production readiness across iOS, Android, React Native, Flutter, and Cordova.
SettingsKit for SwiftUI settings interfaces (iOS, macOS, watchOS, tvOS, visionOS). Use for settings/preferences screens, searchable settings, nested navigation, @Observable/@Bindable state, or encountering settings update errors, navigation state issues.
Generates customized business agreements for 10 common relationship
Build a Quarterly Business Review (QBR) deck structure and narrative for a customer account. Use when asked to prepare a QBR, business review meeting, executive review, or quarterly check-in with a customer. Produces a slide-by-slide QBR structure with talking points, metrics review, value narrat...
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