bg-szy

@bg-szy source repo

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Bio Variant Normalization · bg-szy bundle
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.

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Bio Population Genetics Association Testing 2 · bg-szy bundle
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result visualization. Use when running GWAS or association tests.

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Bio Rna Quantification Alignment Free Quant · bg-szy bundle
Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.

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Bio Comparative Genomics Ancestral Reconstruction · bg-szy bundle
Reconstruct ancestral sequences at phylogenetic nodes using PAML and IQ-TREE marginal likelihood methods. Infer ancient protein sequences and trace evolutionary trajectories through sequence history. Use when inferring ancestral states for protein resurrection or tracing evolutionary history.

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Bio Spatial Transcriptomics Image Analysis · bg-szy bundle
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.

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Bio Spatial Transcriptomics Spatial Data Io · bg-szy bundle
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other spatial data.

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Bio Spatial Transcriptomics Spatial Domains · bg-szy bundle
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions.

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Bio Variant Calling Clinical Interpretation · bg-szy bundle
Clinical variant interpretation using ClinVar, ACMG guidelines, and pathogenicity predictors. Prioritize variants for diagnostic and research applications. Use when interpreting clinical significance of variants.

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Bio Spatial Transcriptomics Spatial Neighbors · bg-szy bundle
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.

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Bio Variant Calling Filtering Best Practices · bg-szy bundle
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.

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Bio Spatial Transcriptomics Spatial Multiomics · bg-szy bundle
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.

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Bio Spatial Transcriptomics Spatial Proteomics · bg-szy bundle
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with transcriptomics.

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Bio Spatial Transcriptomics Spatial Statistics · bg-szy bundle
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment. Use when computing spatial autocorrelation or co-occurrence statistics.

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Bio Variant Calling Structural Variant Calling · bg-szy bundle
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions, inversions, duplications, and translocations that are too large for standard SNV callers. Use when detecting structural variants from short-read data.

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Bio Spatial Transcriptomics Spatial Communication · bg-szy bundle
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks. Use when analyzing cell-cell communication in spatial context.

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Bio Spatial Transcriptomics Spatial Deconvolution · bg-szy bundle
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type proportions from scRNA-seq references. Use when estimating cell type composition in spatial spots.

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Bio Spatial Transcriptomics Spatial Preprocessing · bg-szy bundle
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data.

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Bio Spatial Transcriptomics Spatial Visualization · bg-szy bundle
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.

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Bio Primer Design Primer Basics · bg-szy bundle
Design PCR primers for a target sequence using primer3-py. Specify target regions, product size, melting temperature, and other constraints. Returns ranked primer pairs with quality metrics. Use when designing standard PCR primers.

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Bio Reporting Rmarkdown Reports · bg-szy bundle
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.

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Bio Workflows Fastq To Variants · bg-szy bundle
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.

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Bio Workflows Multiome Pipeline · bg-szy bundle
End-to-end multiome workflow for joint scRNA-seq + scATAC-seq analysis. Covers data loading, separate modality processing, and WNN integration with Seurat/Signac. Use when analyzing joint scRNA+scATAC data.

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Bio Workflows Outbreak Pipeline · bg-szy bundle
End-to-end outbreak investigation from pathogen isolates to transmission networks. Orchestrates MLST typing, AMR surveillance, phylodynamic dating, and transmission inference with TransPhylo. Use when investigating disease outbreaks or tracking pathogen transmission chains.

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Bio Workflows Scrnaseq Pipeline · bg-szy bundle
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, clustering, marker detection, and cell type annotation. Use when analyzing single-cell RNA-seq data.

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Carrier Relationship Management · bg-szy
Codified expertise for managing carrier portfolios, negotiating freight rates, tracking carrier performance, allocating freight, and maintaining strategic carrier relationships. Informed by transportation managers with 15+ years experience. Includes scorecarding frameworks, RFP processes, market intelligence, and compliance vetting. Use when managing carriers, negotiating rates, evaluating carrier performance, or building freight strategies.

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Chip Clonal Hematopoiesis Agent · bg-szy
AI-powered clonal hematopoiesis of indeterminate potential (CHIP) detection, risk stratification, and cardiovascular/malignancy risk prediction using genomic and clinical data.

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Hemoglobinopathy Analysis Agent · bg-szy
AI-powered analysis of hemoglobin disorders including sickle cell disease, thalassemias, and variant hemoglobins using HPLC, electrophoresis, and molecular data.

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Multimodal Radpath Fusion Agent · bg-szy
AI-powered multimodal diagnostic fusion integrating radiology imaging (CT/MRI/PET), digital pathology (WSI), genomics, and clinical data for comprehensive cancer diagnosis and treatment planning.

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Pytdc Therapeutics Data Commons · bg-szy
Therapeutics Data Commons (TDC) AI-ready drug discovery datasets. Curated ADME, toxicity, DTI, DDI with scaffold/cold splits, standardized metrics, molecular oracles, and ADMET benchmarks for therapeutic ML and property prediction. For chemical database queries use chembl-database-bioactivity; for featurization use molfeat.

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Tcell Exhaustion Analysis Agent · bg-szy
AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.

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Universal Single Cell Annotator · bg-szy bundle
Annotate scRNA-seq

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Knowledge Base Health Check · bg-szy
Audits a local Claude-managed knowledge base in Simon's '/Users/simon/Claude CoWork/Knowledge Base/' system. Surfaces contradictions between articles, broken backlinks, unsourced claims, stale articles, writing-rules violations, and three suggested new articles. Files a full report into the KB's 'Outputs/' folder, appends a one-line CHANGELOG entry, and (in interactive sessions) walks through which findings to action. Use this skill whenever the user says "run a health check", "audit the [name] KB", "audit my knowledge base", "check the wiki", "let's go through the health check report", or "action the latest health check". Also use when the monthly scheduled task 'knowledge-base-monthly-health-check' fires. Use this skill for any audit-style request against a folder under 'Knowledge Base/' even if the user doesn't say the word "health check" - the protocol is the same.

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Obsidian Claude Integration · bg-szy
Comprehensive guide for integrating Obsidian vaults as AI-powered second brains with Claude Code. Covers MCP integration, vault manifests, self-evolving patterns, auto-linking, and knowledge graph automation. Use when setting up Claude Code + Obsidian workflows, implementing bidirectional sync, creating CLAUDE.md manifests, or building self-healing knowledge systems.

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Social Selling Content Generator · bg-szy
Generate 30+ LinkedIn posts that attract your target prospects. Creates industry insights, thought leadership, engagement prompts, and comment strategies. Use when building personal brand to attract inbound leads through social selling.

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Shictonghua Zhuangxiu Zhinan Ready · bg-szy bundle
【儿童房装修必看】家里有小孩、正准备要孩子、或想给儿童房做环保安全装修？这个 Skill 内置装修课堂知识库，专门讲"适童化"——儿童是最易受甲醛伤害的人群，儿童房必须实木/ENF/控总量。问儿童房怎么装环保、问儿童房墙面地面用什么、问儿童家具选实木还是人造板、问孩子学习/游戏专区怎么规划、问有娃家庭怎么防磕碰防污染，全部覆盖。适合家里有娃、备孕婚房、想装出健康儿童房的业主。

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Bio Clip Seq Clip Motif Analysis · bg-szy bundle
Identify enriched sequence motifs at CLIP-seq binding sites for RBP binding specificity. Use when characterizing the sequence preferences of an RNA-binding protein.

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Bio Read Alignment Bwa Alignment · bg-szy bundle
Align DNA short reads to reference genomes using bwa-mem2, the faster successor to BWA-MEM. Use when aligning DNA short reads to a reference genome.

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Bio Restriction Enzyme Selection · bg-szy bundle
Select restriction enzymes by criteria using Biopython Bio.Restriction. Find enzymes that cut once, don't cut, produce specific overhangs, are commercially available, or have compatible ends for cloning. Use when selecting restriction enzymes for cloning or analysis.

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Bio Workflows Biomarker Pipeline · bg-szy bundle
End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, classifier training with nested CV, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.

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Bio Workflows Cytometry Pipeline · bg-szy bundle
End-to-end flow cytometry workflow from FCS files to differential analysis. Orchestrates compensation, transformation, gating/clustering, and statistical testing with CATALYST/diffcyt. Use when processing flow or mass cytometry data end-to-end.

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Radiomics Pathomics Fusion Agent · bg-szy
AI-powered multimodal fusion of radiology (CT/MRI/PET) and pathology (H&E/IHC) imaging with clinical and genomic data for comprehensive cancer diagnostics and treatment prediction.

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Spatial Transcriptomics Analysis · bg-szy bundle
Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.

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Azure Landing Zone Checklist · bg-szy
Fill out Microsoft Azure Landing Zone (ALZ) Accelerator checklists by interviewing the user, mapping their Azure subscriptions, integrating IP addressing documentation, and applying Microsoft Cloud Adoption Framework best practices. Produces a completed Excel checklist (.xlsx) ready for ALZ deployment. Use this skill whenever the user mentions Azure Landing Zone, ALZ checklist, landing zone accelerator, platform landing zone configuration, ALZ bootstrap, hub-and-spoke setup, Azure network topology planning, or wants to fill out any ALZ-related checklist or configuration file. Also trigger when the user uploads an Excel file that contains tabs like "Accelerator - Bootstrap", "Accelerator - Bicep", or "Accelerator - Terraform".

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App Store Listing Optimizer · bg-szy
Optimize iOS App Store and Google Play Store listings for maximum discoverability and conversion. Perform competitive keyword research, craft keyword-optimized titles/subtitles/descriptions, design screenshot sequences, and generate A/B test variants. Use when the user has a built app and needs to write or improve their store listing, do ASO keyword research, optimize app metadata, plan screenshot strategy, or create listing variants for testing. Triggers on "optimize my app listing", "ASO", "app store optimization", "keyword research for my app", "improve my store listing", "screenshot strategy", "app store keywords", "play store listing".

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Mobile App Launch Checklist · bg-szy
Comprehensive step-by-step launch checklist for shipping mobile apps to the iOS App Store and Google Play Store. Covers pre-submission preparation, store asset creation, build and submission, launch day execution, and post-launch monitoring. Use when the user wants to launch a mobile app, prepare for App Store or Google Play submission, create a launch plan, review submission requirements, or ensure nothing is missed before releasing an app. Triggers on "launch checklist", "app submission", "prepare for launch", "app store submission", "google play submission", "ready to ship", "pre-launch review", "launch day plan".

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Stop Slop · bg-szy bundle
Use for durable prose artifacts: docs, README, release notes, UI copy, comments, commit messages, PR/issue text. Skip ordinary chat replies.

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Bio Genome Assembly Hifi Assembly · bg-szy bundle
High-quality genome assembly from PacBio HiFi reads using hifiasm with phasing support. Use when building reference-quality diploid assemblies from HiFi data, especially with trio or Hi-C phasing for fully resolved haplotypes.

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Bio Methylation Epigenetic Clocks · bg-szy bundle
Computes DNA methylation age (DNAm age) and pace of aging by applying frozen elastic-net epigenetic clocks to a clean beta matrix with methylclock, dnaMethyAge, or methylCIPHER. Covers the clock menu by question (chronological Horvath/Hannum/skin&blood; health-mortality PhenoAge/GrimAge; DunedinPACE pace; pediatric/gestational; mitotic epiTOC), age acceleration (EAA/IEAA/EEAA) as the real endpoint, the principal-component (PC) clock fix for the per-CpG reliability crisis, and EPICv2 clock-CpG dropout with missing-CpG imputation bias. Use when estimating epigenetic age, computing age acceleration, choosing a clock for an outcome, assessing clock reliability, or porting a clock to EPICv2. A clock is a frozen predictor: do not GO-enrich its CpGs and do not train it here. For cell-count adjustment (IEAA) see cell-type-deconvolution; for predictor training/validation/leakage see machine-learning/model-validation; for survival modeling of age acceleration see clinical-biostatistics/survival-analysis.

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Bio Read Alignment Star Alignment · bg-szy bundle
Align RNA-seq reads with STAR (Spliced Transcripts Alignment to a Reference). Supports two-pass mode for novel splice junction discovery. Use when aligning RNA-seq data requiring splice-aware alignment.

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Bio Restriction Fragment Analysis · bg-szy bundle
Analyze restriction digest fragments using Biopython Bio.Restriction. Predict fragment sizes, get fragment sequences, simulate gel electrophoresis patterns, and perform double digests. Use when analyzing restriction digest fragment patterns.

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Bio Small Rna Seq Mirge3 Analysis · bg-szy bundle
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.

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Bio Workflows Microbiome Pipeline · bg-szy bundle
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy assignment, diversity analysis, and compositional testing with ALDEx2. Use when processing 16S/ITS amplicon data.

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Bio Workflows Neoantigen Pipeline · bg-szy bundle
End-to-end neoantigen discovery from somatic variants to ranked vaccine candidates. Integrates HLA typing, MHC binding prediction, pVACtools neoantigen calling, and immunogenicity scoring. Use when identifying tumor neoantigens for personalized vaccine design or checkpoint biomarkers.

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Bio Workflows Proteomics Pipeline · bg-szy bundle
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with MSstats or limma. Use when processing mass spectrometry proteomics.

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Pdb Database · bg-szy
Use when you want to search for or download experimentally-determined 3D structures for biomolecules (proteins, nucleic acids, bound ligands). Supports searching by sequence similarity, structure similarity, chemical and other attributes. Also use to get metadata about biomolecular structure experiments.

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Simo Multiomics Integration Agent · bg-szy
AI-powered spatial integration of multi-omics datasets using probabilistic alignment for comprehensive tissue atlas construction and cellular state mapping.

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Bio Alignment Files Bam Statistics · bg-szy bundle
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Bio Data Visualization Upset Plots · bg-szy bundle
Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets.

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Bio Methylation Array Qc Filtering · bg-szy bundle
Performs probe filtering and sample-level QC on Illumina Infinium methylation arrays (450K / EPIC / EPICv2) to decide which probes and samples to trust. Drops detection-p-failed and low-bead-count probes, removes cross-reactive/non-specific probes (Chen 2013 / Pidsley 2016 lists via maxprobes), excludes SNP-overlapping probes with dropLociWithSnps, and handles sex-chromosome probes. Collapses EPICv2 replicate probes with betasCollapseToPfx and harmonizes across array versions (EPICv2 hg38 vs 450K/EPIC hg19, intersect plus mLiftOver). Runs sample-identity QC: getSex sex prediction vs sample sheet for swap detection, rs-SNP fingerprint clustering for duplicates/swaps, and Sentrix chip/array-position batch diagnosis. Use when filtering methylation array probes, detecting sample swaps or mislabels, collapsing EPICv2 replicates, or merging 450K/EPIC/EPICv2 cohorts. For IDAT-to-corrected-beta normalization see array-preprocessing; for batch correction and study design see ewas-design.

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Bio Pathway Enrichment Foundations · bg-szy bundle
Chooses the enrichment generation before any tool runs, mapping the input shape to a method class - a pre-selected gene list plus a background to over-representation analysis (ORA, hypergeometric), a ranked statistic for all genes to gene set enrichment (GSEA), a signed signaling topology to pathway-topology (SPIA) - then making the null explicit (competitive vs self-contained, gene vs subject sampling) and running a trustworthiness checklist (testable-gene universe, FDR, redundancy collapse, leading-edge check, version reporting). Covers why every clusterProfiler GSEA is the inter-gene-correlation-uncorrected competitive null, why the background not the gene list decides ORA significance, and why no method is universally best. Use when deciding ORA vs GSEA vs topology, which gene-set DB, whether a result is trustworthy, or which null a tool computes. For ORA see go-enrichment, GSEA see gsea, databases kegg-pathways/reactome-pathways/wikipathways; the ranking comes from differential-expression/de-results.

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Bio Phasing Imputation Foundations · bg-szy bundle
Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (recombination is the transition, mutation the emission, the genetic map and Ne set the rates), imputation's honest output is a dosage with a self-estimated quality (INFO/R2/DR2) not a hard genotype, and the stages are ordered and each fails silently (QC, align build and strand to the panel, phase, impute per chromosome, filter by INFO/R2 plus a MAF floor, carry dosages to GWAS). Covers the strategy fork (array vs low-coverage WGS plus genotype-likelihood imputation), why the panel ancestry is the prior, and why a flipped strand or build mismatch destroys accuracy without an error. Use when deciding a genotyping strategy, sequencing the pipeline, choosing array vs low-coverage WGS, or diagnosing silently-wrong imputation. Mechanics route to reference-panels, haplotype-phasing, genotype-imputation, imputation-qc; read-backed phasing is long-read-sequencing/haplotype-phasing.

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Bio Systems Biology Model Curation · bg-szy bundle
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.

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Bio Workflows Longread Sv Pipeline · bg-szy bundle
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with minimap2 and SV calling with Sniffles or cuteSV. Use when detecting structural variants from long reads.

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Bio Workflows Methylation Pipeline · bg-szy bundle
End-to-end bisulfite sequencing workflow from FASTQ to differentially methylated regions. Covers Bismark alignment, methylation calling, and DMR detection with methylKit. Use when analyzing bisulfite sequencing data.

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Bio Workflows Multi Omics Pipeline · bg-szy bundle
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.

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Protein Sequence Similarity Search · bg-szy
Searches for homologous protein sequences using MMseqs2 (fast, default) or BLAST (comprehensive, fallback). Trigger this whenever the user provides a protein sequence or FASTA file and asks to find homologues, sequence matches, or wants to infer protein function based on sequence similarity, but not when the user wants to infer protein function based on structural similarity.

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Alphagenome Single Variant Analysis · bg-szy bundle
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API. Use when the user asks about non-coding variant effects, pathogenicity, clinical significance, disease associations, functional effects, gene expression changes, splicing disruption, or regulatory effects in promoters and enhancers. Also use for resolving biological terms to tissue/cell-type ontologies (UBERON/CL) or analyzing variants in chr:pos:ref>alt format.

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Bio Data Visualization Circos Plots · bg-szy bundle
Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs. Use when creating circular genome visualizations.

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Bio Experimental Design Sample Size · bg-szy bundle
Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.

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Bio Expression Matrix Counts Ingest · bg-szy bundle
Load gene expression count matrices from various formats including CSV, TSV, featureCounts, Salmon, kallisto, and 10X. Use when importing quantification results for downstream analysis.

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Bio Primer Design Primer Validation · bg-szy bundle
Validate PCR primers for specificity, dimers, hairpins, and secondary structures using primer3-py thermodynamic calculations. Check self-complementarity, heterodimer formation, and 3' stability. Use when validating primer specificity and properties.

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Bio Read Alignment Hisat2 Alignment · bg-szy bundle
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.

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Bio Small Rna Seq Mirdeep2 Analysis · bg-szy bundle
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data. Use when identifying new miRNAs or performing comprehensive miRNA profiling with discovery.

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Bio Small Rna Seq Target Prediction · bg-szy bundle
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.

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Bio Workflows Metabolomics Pipeline · bg-szy bundle
End-to-end metabolomics workflow from raw MS data to pathway analysis. Orchestrates XCMS preprocessing, annotation, normalization, statistical analysis, and pathway mapping. Use when processing LC-MS metabolomics data.

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Bio Workflows Metagenomics Pipeline · bg-szy bundle
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken abundance estimation, and HUMAnN functional profiling. Use when profiling metagenomic samples.

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Gtex Database · bg-szy
Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

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Immune Checkpoint Combination Agent · bg-szy
AI-powered analysis for predicting optimal immune checkpoint inhibitor combinations based on tumor microenvironment, biomarkers, and molecular profiling.

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App Store Opportunity Research · bg-szy
Full-pipeline iOS App Store opportunity research. Discovers underserved niches, analyzes competitor gaps, estimates revenue, produces scored top-3 opportunity reports, and writes MVP PRDs — all through browser and web research. Use when the user wants to find profitable iOS app ideas, research App Store charts, analyze competitor apps (ratings, reviews, revenue, gaps), generate opportunity reports, or write MVP PRDs. Triggers on "find app opportunities", "app store research", "what app should I build", "research this app category", "find a gap in the app store", "ios app ideas".

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AI Music · bg-szy bundle
Generate AI music on RunComfy via the `runcomfy` CLI. Routes to ElevenLabs Music (premium vocal, $0.0083/s) or ACE Step / 1.5 (open-weights, $0.0002–0.0003/s, multilingual), plus ACE Step audio-inpaint and audio-outpaint for editing. Picks the right model for the user's intent and ships the `runcomfy run` invoke. Triggers on "generate music", "make a song", "background music", "jingle", "theme music", "extend music", "fix this song", or any ask to generate or edit music.

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Alphafold Database Fetch And Analyze · bg-szy
Retrieve and analyze AlphaFold predicted structures for a protein. Use when the user provides a specific UniProt Accession ID and wants structural confidence metrics (pLDDT), domain boundary analysis, or disorder assessment. Do not use if the user only has a protein name, gene name, or amino acid sequence — ask for a UniProt ID first.

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Bio Data Visualization Genome Tracks · bg-szy bundle
Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tracks.

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Bio Expression Matrix Metadata Joins · bg-szy bundle
Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization.

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Bio Phasing Imputation Imputation Qc · bg-szy bundle
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputation accuracy before GWAS.

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Bio Population Genetics Plink Basics · bg-szy bundle
PLINK file formats, format conversion, and quality control filtering for population genetics. Convert between VCF, BED/BIM/FAM, and PED/MAP formats, apply MAF, genotyping rate, and HWE filters using PLINK 1.9 and 2.0. Use when working with PLINK format files or running QC.

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Bio Read Alignment Bowtie2 Alignment · bg-szy bundle
Align short reads using Bowtie2 with local or end-to-end modes. Supports gapped alignment. Use when aligning ChIP-seq, ATAC-seq, or when flexible alignment modes are needed.

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Bio Small Rna Seq Differential Mirna · bg-szy bundle
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.

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Bio Workflows Crispr Screen Pipeline · bg-szy bundle
End-to-end CRISPR screen analysis from FASTQ to hit genes. Orchestrates guide counting, QC, statistical analysis with MAGeCK, and hit calling with multiple methods. Use when analyzing pooled CRISPR screens from count data to hit calling.

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Bio Workflows Expression To Pathways · bg-szy bundle
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization. Use when taking DE results to pathway enrichment.

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Bio Data Visualization Color Palettes · bg-szy bundle
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.

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Bio Expression Matrix Gene Id Mapping · bg-szy bundle
Convert between gene identifier systems including Ensembl, Entrez, HGNC symbols, and UniProt. Use when mapping IDs for pathway analysis or matching different data sources.

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Bio Expression Matrix Sparse Handling · bg-szy bundle
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.

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Bio Genome Intervals Gtf Gff Handling · bg-szy bundle
Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread, gtfparse, and gffutils. Use when extracting specific features from gene annotations or converting between annotation formats.

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Bio Machine Learning Model Validation · bg-szy bundle
Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfitting in biomarker discovery. Use when validating classifiers or optimizing hyperparameters on omics data.

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Bio Small Rna Seq Smrna Preprocessing · bg-szy bundle
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.

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Bio Systems Biology Gene Essentiality · bg-szy bundle
Perform in silico gene knockout analysis and synthetic lethality screens using COBRApy single and double deletions. Predict essential genes and identify synthetic lethal pairs for drug target discovery. Use when identifying essential genes or finding synthetic lethal drug targets.

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Bio Workflow Management Cwl Workflows · bg-szy bundle
Create portable, standards-based bioinformatics pipelines with Common Workflow Language (CWL). Use when building workflows that need maximum portability across execution platforms, sharing pipelines with collaborators using different systems, or contributing to community workflow registries.

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Bio Workflow Management Wdl Workflows · bg-szy bundle
Create portable bioinformatics pipelines with Workflow Description Language (WDL) using Cromwell or miniwdl execution engines. Use when running GATK best practices pipelines, working with Terra/AnVIL platforms, or building workflows for cloud execution on Google Cloud or AWS.

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Bio Workflows Crispr Editing Pipeline · bg-szy bundle
End-to-end CRISPR experiment design from target selection to delivery-ready constructs. Covers guide RNA design, off-target assessment, and specialized editing strategies including knockouts, base editing, and HDR knockins. Use when designing complete CRISPR editing experiments for gene knockout, correction, or tagging.

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Dbsnp Database · bg-szy
Use when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database. Resolves between rsIDs, genomic coordinates in VCF format, and HGVS strings. For an rsID, returns variant type, gene associations, clinical significance, allele frequencies, and genomic coordinates (GRCh38).

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1099 published skills · page 1 of 11