Skill directory

Agent skills

Focused instruction packs that teach a coding agent one job well. Browse the catalog and use any of them inside a RiverX project.

18,175Skills

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18,175 skills

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Tooluniverse Epigenomicsmims-harvard/tooluniverseGenomics and epigenomics analysis: DNA methylation (CpG, 5mC, 5hmC, bisulfite, RRBS), m6A RNA modification (MeRIP-seq), ChIP-seq peaks, ATAC-seq accessibility, histone modifications, chromatin state, multi-omics integration. Combines pandas/scipy/pysam computation with ToolUniverse annotation tools. Use for genome-wide epigenomic statistics, methylation analysis, and chromatin-genome integration.07 Tooluniverse Expression Data Retrievalmims-harvard/tooluniverseRetrieve gene expression and omics datasets from ArrayExpress and BioStudies with gene disambiguation and quality assessment. Use for finding RNA-seq/microarray datasets by organism/tissue/condition, comparing across studies (case-control, time-series, dose-response), and assessing dataset suitability before downloading. Always uses English search terms.03 Tooluniverse Gene Enrichmentmims-harvard/tooluniverseGene-set enrichment analysis — GO (Biological Process, Molecular Function, Cellular Component), KEGG, Reactome pathway enrichment via clusterProfiler, gseapy, ORA, GSEA. Use for interpreting DEG lists, screen hit lists, or any gene-list-to-pathways query. Includes simplify-cutoff handling and union-vs-total denominator conventions for percent-DE questions.011 Tooluniverse Gwas Drug Discoverymims-harvard/tooluniverseTransform GWAS signals into drug targets and repurposing opportunities. Connects GWAS-significant loci to causal genes via fine-mapping/eQTL, then to druggable proteins via DGIdb/OpenTargets, then to existing drugs via ChEMBL. Use for GWAS-to-target hypothesis generation, druggable-fraction analysis of disease loci, and human-genetics-validated drug-repurposing prioritization.07 Tooluniverse Gwas Snp Interpretationmims-harvard/tooluniverseInterpret a single GWAS SNP across multiple databases — GWAS Catalog hits, LD/haplotype context, eQTL evidence, regulatory annotation, ClinVar pathogenicity, gnomAD frequency. Use for 'what does this SNP do', SNP-to-mechanism tracing, and resolving lead-SNP-vs-causal-variant ambiguity. Always considers LD structure before claiming a SNP is mechanistically responsible.05 Tooluniverse Image Analysismims-harvard/tooluniverseMicroscopy and quantitative imaging analysis — colony morphometry, fluorescence intensity quantification, cell-count statistics, dose-response curves, and ANOVA/Dunnett on image-derived measurements. Uses pandas/numpy/scipy/scikit-image. Use for analyzing tabular outputs from CellProfiler/ImageJ, image-derived measurement statistics, and image-based assay quantification.010 Tooluniverse Infectious Diseasemims-harvard/tooluniverseRapid pathogen characterization and drug repurposing for outbreaks. Combines pathogen genomics (NCBI, BVBRC), host immune response (IEDB), drug-target databases (ChEMBL, DGIdb), and literature surveillance (PubMed/EuropePMC). Use for emerging-pathogen profiling, antiviral candidate identification, and outbreak intelligence reporting.06 Tooluniverse Literature Deep Researchmims-harvard/tooluniverseDeep literature review — PubMed, EuropePMC, bioRxiv preprints, citation networks, evidence synthesis. Disambiguates queries, runs collision-aware searches, grades evidence T1-T4, and produces structured reports. Use for systematic literature review, meta-analysis evidence collection, and detailed answer-with-citations workflows.07 Tooluniverse Metabolomics Analysismims-harvard/tooluniverseAnalyze metabolomics data end-to-end — metabolite identification, quantification (TIC normalization, batch correction), differential analysis, and pathway interpretation. Use for processing mass-spec metabolomics output, normalization choice, untargeted metabolomics workflows, and integrating with other omics layers.03 Tooluniverse Multi Omics Integrationmims-harvard/tooluniverseMulti-omics integration — orchestrate per-layer analysis (transcriptomics, proteomics, epigenomics, genomics, metabolomics) then perform cross-omics correlation, multi-omics clustering, and pathway-level integration. Use for integrative systems-biology analysis, multi-modal disease characterization, and cross-omics biomarker discovery.02 Tooluniverse Network Pharmacologymims-harvard/tooluniverseCompound-target-disease network construction and analysis for drug repurposing, polypharmacology discovery, and multi-target drug design. Uses STRING, BioGRID, ChEMBL, DGIdb, OMIM, OpenTargets. Use for off-target effect prediction, network-based drug repurposing, and identifying molecules with desired multi-target profile.08 Tooluniverse Pharmacovigilancemims-harvard/tooluniverseDrug safety and adverse event analysis — FAERS spontaneous-report mining, FDA black-box warnings, signal detection (PRR, ROR, IC), risk factors by demographic/comorbidity, and label change tracking. Use for post-market safety surveillance, AE signal investigation, drug-AE association strength scoring, and pharmacovigilance reports.07 Tooluniverse Precision Medicine Stratificationmims-harvard/tooluniversePatient stratification for precision medicine — integrate genomic, clinical, and therapeutic data to split patients into responder/non-responder groups, risk tiers, or treatment-decision groups. Use for stratification-by-biomarker, treatment-selection logic, and personalized therapeutic strategy reports per patient subgroup.07 Tooluniverse Precision Oncologymims-harvard/tooluniverseCancer treatment recommendations from molecular profile (mutations + cancer type + biomarkers) — FDA-approved + investigational therapies, resistance mechanisms, matching clinical trials, prognosis. Uses CIViC, ClinVar, OpenTargets, ClinicalTrials.gov. Use for tumor-board treatment recommendations, evidence-tiered actionability assessment, and FDA-precedent-driven therapy selection.08 Tooluniverse Protein Structure Retrievalmims-harvard/tooluniverseProtein structure retrieval from RCSB PDB, PDBe, and AlphaFold with disambiguation, quality assessment (resolution, R-factor, pLDDT), and metadata. Distinguishes high-quality experimental (X-ray under 2 Angstrom) vs predicted vs medium-quality structures. Use for fetching protein structures, structure-quality comparison, and selecting structures for drug design or modeling.03 Tooluniverse Protein Therapeutic Designmims-harvard/tooluniverseAI-guided de novo protein design — RFdiffusion backbone generation, ProteinMPNN sequence design, structure validation (pLDDT, pTM, MPNN scores). Use for designing therapeutic protein binders, novel scaffolds, enzyme variants, and miniprotein/protein-interface design before experimental validation.06 Tooluniverse Proteomics Analysismims-harvard/tooluniverseMass-spec proteomics analysis — protein identification, quantification (LFQ, TMT, iTRAQ), differential expression (tumor vs normal, treatment vs control), PTM identification, and pathway enrichment on protein lists. Use when you have proteomics MS output, asking about protein abundance differences, or doing systems-level proteomic interpretation.04 Tooluniverse Rare Disease Diagnosismims-harvard/tooluniverseRare disease differential diagnosis from patient phenotype — HPO term matching to candidate diseases (Orphanet, OMIM), gene panel prioritization, ACMG variant interpretation, and structure-based variant analysis. Use for diagnostic odyssey assistance, phenotype-to-disease ranking, and genetic-counseling differential generation.07 Tooluniverse Rnaseq Deseq2mims-harvard/tooluniverseRNA-seq differential expression analysis with DESeq2, edgeR, and limma-voom — DEG lists, fold changes, dispersion estimation, design formulas including covariates, multi-condition contrasts, and Venn-set operations across groups. Routes across DESeq2 (default), edgeR (QL-F / exact test for small replicate counts), and limma-voom (large n / complex designs). Use when you have a count matrix + metadata, want to find DEGs, or need dispersion/PCA/clustering analysis. Includes RULE ZERO precedence (read executed.ipynb if present).021 Tooluniverse SDKmims-harvard/tooluniverseBuild AI scientist systems with the ToolUniverse Python SDK for scientific research. Covers the 3 calling patterns (`tu.run` portable dict API, `tu.tools.X` function API, direct class instantiation), tool loading, batch execution, MCP server integration, and embedding-based tool search. Use for SDK programming, custom tool composition, benchmarking pipelines, and integrating ToolUniverse into research workflows.02 Tooluniverse Sequence Retrievalmims-harvard/tooluniverseRetrieve DNA/RNA/protein sequences from NCBI and ENA with disambiguation. Quality hierarchy: RefSeq (NM_/NP_) > RefSeq predicted (XM_/XP_) > GenBank submissions. Use for fetching specific sequences by accession, gene-symbol-to-sequence lookup, transcript-isoform retrieval, and curated-vs-raw-submission preference.03 Tooluniverse Spatial Transcriptomicsmims-harvard/tooluniverseSpatial transcriptomics analysis — Visium, MERFISH, seqFISH, Slide-seq. Maps gene expression to tissue architecture, identifies spatially variable genes (SVGs), tissue-domain segmentation, and cell-cell interaction inference. Use for spatial gene-expression questions, tissue architecture analysis, and SVG identification.03 Tooluniverse Statistical Modelingmims-harvard/tooluniverseStatistical modeling — linear/logistic/ordinal/Poisson regression, ANOVA, Kruskal-Wallis, chi-square, Mann-Whitney, Cox survival, spline fits (R `ns()`), odds ratios, Cohen's d, F-statistic, p-value computation. Specializes in clinical-trial AE analysis (SDTM DM/AE), severity ordinal regression, and per-feature stat workflows.021 Tooluniverse Systems Biologymims-harvard/tooluniverseSystems biology and pathway analysis integrating Reactome, KEGG, WikiPathways, BioCarta, NCI-Nature Pathway Interaction Database. Multi-database pathway enrichment, protein-pathway relationships, network reasoning. Use for pathway analysis on a gene list, multi-source pathway concordance, and systems-level interpretation across databases.07 Tooluniverse Target Researchmims-harvard/tooluniverseComprehensive drug-target intelligence — tissue expression (GTEx, HPA), pathways, protein interactions (STRING), variant landscape (ClinVar, gnomAD), druggability (DGIdb, ChEMBL approved drugs). 9 parallel research paths with citations. Use for full target profile reports, target characterization for drug discovery, and 'tell me about target X' queries.06 Toon Formatreason-machines/trending-skillsExpert skill for Token-Oriented Object Notation (TOON) — compact, schema-aware JSON encoding for LLM prompts that reduces tokens by ~40%.01 Top Banner Generatorkostja94/marketing-skillsWhen the user wants to add, optimize, or audit a top announcement bar or sticky banner. Also use when the user mentions "announcement bar," "top banner," "sticky bar," "promo banner," "discount banner," "student discount banner," "header banner," "announcement bar design," "sticky header," "promo bar," "urgency banner," or "lead capture bar." For promos, use discount-marketing-strategy.01 Top Designwondelai/skillsCreate award-winning, immersive web experiences at the level of Awwwards-featured agencies. Use when the user mentions "Awwwards quality", "make my site stunning", "scroll animations", "parallax storytelling", "cinematic web design", "portfolio site", or "brand experience". Also trigger when elevating a standard landing page into a memorable digital experience. Covers dramatic typography, purposeful motion, scroll-based composition, and performance-optimized animation. For foundational UI, see refactoring-ui. For type selection, see web-typography.06 Topic Monitorsundial-org/awesome-openclaw-skillsMonitor topics of interest and proactively alert when important developments occur. Use when user wants automated monitoring of specific subjects (e.g., product releases, price changes, news topics, technology updates). Supports scheduled web searches, AI-powered importance scoring, smart alerts vs weekly digests, and memory-aware contextual summaries.011 Torch Geometrick-dense-ai/scientific-agent-skillsPyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use when working with torch_geometric, not for general NetworkX analytics or non-graph PyTorch models.07 Torchcode Pytorch Interview Practicereason-machines/trending-skillsLeetCode-style PyTorch interview practice environment with auto-grading for implementing softmax, attention, GPT-2 and more from scratch.01 Torchdrugk-dense-ai/scientific-agent-skillsBuild and troubleshoot TorchDrug 0.2.1 workflows for molecular graphs, property prediction, self-supervised pretraining, molecule generation, retrosynthesis, protein representation learning, and knowledge graph reasoning. Use when code imports torchdrug or needs its datasets, models, tasks, or Engine.09 Torchforge Rl Trainingorchestra-research/ai-research-skillsProvides guidance for PyTorch-native agentic RL using torchforge, Meta's library separating infra from algorithms. Use when you want clean RL abstractions, easy algorithm experimentation, or scalable training with Monarch and TorchTitan.03 Toss Investmentnomadamas/k-skill토스증권 공식 Open API(OAuth2)로 계좌, 보유주식, 시세/종목/시장정보, 주문조회를 안전한 read-only 흐름으로 조회한다. 공식 credentials가 없거나 공식 API가 지원하지 않는 기능은 비공식 경로로 우회하지 않는다.05 Tourparcadei/continuous-claude-v3Friendly onboarding when users ask about capabilities01 Toutiao Publisherguanyang/super-publisherPublish or prepare articles for Toutiao/头条号, check or restore shared login state, fill Markdown drafts with inline images and covers, and optionally complete final publishing. Use for requests such as 发布到头条、检查头条登录、填充头条草稿、上传图文、人工审核 or explicitly authorized automatic publishing.020 Tower Defensegamedev-skills/awesome-gamedev-agent-skills>02 Traceyeachan-heo/oh-my-claudecodeEvidence-driven tracing lane that orchestrates competing tracer hypotheses in Claude built-in team mode01 Trace To Training Datawshobson/agentsConvert evaluation traces and production logs into SFT examples and preference pairs. Use when graded traces or failure examples exist and need to become training data, when applying rejection sampling to model outputs, or when building DPO pairs from passing and failing runs.02 Traceknotjin-doh/traceknotApply Traceknot's ISTQB-aligned, evidence-bound QA process to repository changes across OMP, Codex, GajaeCode, Claude Code, and OpenCode, including session-scoped QA Board publication. Use for implementation verification, bug fixes, release checks, repository audits, defect confirmation, and residual-risk decisions without treating an agent's own completion claim as proof.053 Tracing Downstream Lineageastronomer/agentsTrace downstream data lineage and impact analysis. Use when the user asks what depends on this data, what breaks if something changes, downstream dependencies, or needs to assess change risk before modifying a table or DAG.01 Tracing Knowledge Lineagesobra/superpowers-skillsUnderstand how ideas evolved over time to find old solutions for new problems and avoid repeating past failures01 Tracing Upstream Lineageastronomer/agentsTrace upstream data lineage. Use when the user asks where data comes from, what feeds a table, upstream dependencies, data sources, or needs to understand data origins.01 Track Managementwshobson/agentsUse this skill when creating, managing, or working with Conductor tracks - the logical work units for features, bugs, and refactors. Applies to spec.md, plan.md, and track lifecycle operations.02 Track Planes And Shipsuseosint/skills>-03 Tractiongetagentseal/founder-playbookApplies the Bullseye Framework from Traction by Gabriel Weinberg and Justin Mares. Use when choosing growth channels, testing customer acquisition strategies, or deciding where to spend marketing effort. Covers all 19 traction channels with selection methodology, testing protocol, and phase-matched channel advice. Triggers include 'how do we get customers', 'which marketing channel should we use', 'we have a product but no users', 'our growth has stalled', 'should we do content marketing or paid ads', 'how do we test traction channels', 'what channels work at our stage'. NOT for product development (use Lean Startup), not for positioning/messaging (use Obviously Awesome), not for pricing (use Monetizing Innovation), not for enterprise sales methodology (use SPIN Selling).05 Traction Eoswondelai/skillsImplement the Entrepreneurial Operating System (EOS) to align vision and execution across a company. Use when the user mentions "EOS", "Entrepreneurial Operating System", "V/TO", "quarterly rocks", "Level 10 meetings", "accountability chart", "IDS process", "my company feels chaotic", "we keep having the same problems", or "get the whole team aligned". Also trigger when a growing company needs meeting structure, goal-setting frameworks, or a systematic way to solve recurring organizational issues. Covers the six EOS components: Vision, People, Data, Issues, Process, Traction. For team motivation design, see drive-motivation. For lean experimentation, see lean-startup.010 Trade Accountingagiprolabs/claude-trading-skillsDouble-entry bookkeeping for trading operations with ledger management, P&L statements, balance sheets, and cash flow reporting03

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