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Code comments and annotations
bio-splicing-qc
by GPTomics
Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC. Use when evaluating data suitability for splicing analysis or troubleshooting low event detection.
bio-clinical-databases-dbsnp-queries
by GPTomics
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
academic-paper-reviewer
by brycewang-stanford
"Multi-perspective academic paper review with dynamic reviewer personas. Simulates 5 independent reviewers (EIC + 3 peer reviewers + Devil's Advocate) with field-specific expertise. Supports full review, re-review (verification), quick assessment, methodology focus, and Socratic guided modes. Triggers on: review paper, peer review, manuscript review, referee report, review my paper, critique paper, simulate review, editorial review."
Statistical Writing (One Skill)
by brycewang-stanford
🔬 A curated collection of 23,000+ agent skills for empirical research across 8 social science disciplines. 精选 23,000+ AI Agent 技能库，覆盖8大社会科学学科的实证研究。CoPaper.AI 20分钟完成一篇可复现的规范实证论文，并支持用户上传 Skills。-- Maintained by CoPaper.AI from Stanford REAP.
bio-differential-splicing
by GPTomics
Detects differential alternative splicing between conditions using rMATS-turbo (BAM-based) or SUPPA2 diffSplice (TPM-based). Reports events with FDR-corrected significance and delta PSI effect sizes. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
bio-sashimi-plots
by GPTomics
Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes differential splicing events with grouped samples and junction read support. Use when visualizing specific splicing events or validating differential splicing results.
econ-write
by brycewang-stanford
"Expert economics paper writing assistant synthesizing advice from 50+ top guides by Cochrane, McCloskey, Shapiro, Head, Bellemare, Goldin, Glaeser, Kremer, and other leading economists. USE THIS SKILL whenever the user writes, edits, reviews, rewrites, or structures any economics paper, thesis, job market paper, abstract, introduction, conclusion, results section, literature review, or referee response. Also handles LaTeX formatting, presentations, and paper audits. Covers all paper types (applied, theory, structural, mixed) and all sections."
bayesian-workflow
by brycewang-stanford
Opinionated Bayesian modeling workflow with PyMC and ArviZ. Contains critical guardrails (nutpie sampler, prior/posterior predictive checks, LOO-PIT calibration, prior sensitivity checks, 94% HDI, non-centered parameterizations, reproducible seeds) that agents won't apply unprompted — always consult before writing Bayesian model code. Trigger on: building probabilistic/Bayesian models, prior elicitation, MCMC inference, convergence diagnostics (divergences, R-hat, ESS), model comparison (LOO-CV, ELPD, stacking weights), hierarchical/multilevel models, count regressions, logistic regression with uncertainty, prior sensitivity analysis, reporting Bayesian results, or mentions of PyMC, ArviZ, InferenceData, credible intervals, posterior distributions, shrinkage, uncertainty quantification. Also trigger for model comparison, diagnosing sampling problems, choosing priors, or presenting stats to non-technical audiences.
flutter-add-widget-preview
by flutter
Adds interactive widget previews to the project using the previews.dart system. Use when creating new UI components or updating existing screens to ensure consistent design and interactive testing.
Solution Brief
by product-on-purpose
A curated collection of 24 best-practice, plug-and-play product management “agent skills” plus templates and workflow bundles for consistent, professional PM outputs.
etetoolkit
by jaechang-hits
"ETE Toolkit (ETE3) is a Python environment for phylogenetic tree analysis, manipulation, and visualization. Parse Newick/NHX/PhyloXML trees, traverse and annotate nodes, render publication-quality figures with TreeStyle/NodeStyle, integrate NCBI taxonomy for taxon-aware operations, and run PhyloTree workflows for comparative genomics. Use for building species trees, gene family evolution analysis, and annotated tree figures."
bedtools-genomic-intervals
by jaechang-hits
"Toolkit for genomic interval operations on BED, BAM, GFF, VCF files. Find overlapping regions, merge adjacent intervals, calculate coverage depth, extract FASTA sequences, find nearest features, and manipulate interval coordinates. Essential for ChIP-seq peak annotation, target region filtering, and genome arithmetic. Use tabix instead for indexed single-region queries; use deeptools for normalized bigWig coverage."
architectural-analysis
by pedronauck
Deep architectural audit focused on finding dead code, duplicated functionality, architectural anti-patterns, type confusion, and code smells. Use when user asks for architectural analysis, find dead code, identify duplication, or assess codebase health.
geo-database
by jaechang-hits
"Query NCBI Gene Expression Omnibus (GEO) for gene expression datasets and sample metadata via GEOparse Python library and E-utilities. Search datasets by keyword/organism/platform, download GSE series matrices, parse GPL platform annotations, extract GSM sample metadata, and load expression matrices into pandas. For single-cell data use cellxgene-census; for programmatic multi-DB access use gget-genomic-databases."
gene-database
by jaechang-hits
"Query NCBI Gene via E-utilities for curated gene records across 1M+ taxa. Retrieve official gene symbols, aliases, RefSeq accessions, summary descriptions, genomic coordinates, GO annotations, and interaction data. Use for gene ID resolution, cross-species queries, and gene function summaries. For sequence retrieval use Ensembl; for expression data use geo-database."
ensembl-database
by jaechang-hits
"Query Ensembl REST API for gene/transcript/variant annotations across 300+ species. Retrieve gene info by symbol/ID, sequence, cross-references (HGNC, RefSeq, UniProt), variants, regulatory features, comparative genomics. For bulk local access use pyensembl; for pathway lookups use kegg-database or reactome-database."
github-code-review
by NousResearch
Review code changes by analyzing git diffs, leaving inline comments on PRs, and performing thorough pre-push review. Works with gh CLI or falls back to git + GitHub REST API via curl.
omero-integration
by jaechang-hits
"OMERO is an open-source platform for biological image data management. Use the omero-py Python client to connect to an OMERO server, search and retrieve images as numpy arrays, annotate images with tags and key-value pairs, manage ROIs, and integrate OMERO image data into downstream analysis pipelines — all programmatically without the OMERO desktop GUI."
cosmic-database
by jaechang-hits
"Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity."
featurecounts-rna-counting
by jaechang-hits
"Counts aligned RNA-seq reads overlapping gene features in a GTF annotation. Takes sorted BAM files from STAR alignment and a GTF file; outputs a tab-delimited count matrix per gene across all samples. Handles strandedness (0=unstranded, 1=stranded, 2=reverse-stranded), paired-end, and multi-sample batch counting in a single command. Use Salmon instead for alignment-free quantification; use featureCounts when STAR BAMs already exist and a gene-level count matrix is needed."
docstring
by pipecat-ai
Document a Python module and its classes using Google style
cellxgene-census
by jaechang-hits
"Query CELLxGENE Census (61M+ cells) programmatically. Search by cell type, tissue, disease, organism. Get expression matrices as AnnData, stream large queries out-of-core, train PyTorch models on single-cell data. For analyzing your own data use scanpy; for annotated data manipulation use anndata."
clinvar-database
by K-Dense-AI
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
etetoolkit
by K-Dense-AI
Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.