Product & Planning

oimiragieo Bundle

Semantic tool search with embeddings for scalable tool discovery. Enables on-demand tool loading to reduce context usage by 90%+ for large tool libraries.

ariffazil Bundle

Operate Google Workspace from one CLI using dynamic API discovery, secure OAuth flows, and agent-ready automation patterns for Drive and

oimiragieo Bundle

Access and analyze comprehensive drug information from the DrugBank database including drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. This skill should be used when working with pharmaceutical data, drug discovery research, pharmacology studies, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task requiring detailed drug and drug target information from DrugBank.

boshi-xixixi Bundle

当用户在开始开发前需要搜索现有的开源库、工具、MCP Server 或最佳实践代码时使用。帮助避免重复造轮子，找到最适合当前需求的现成解决方案。

oimiragieo Bundle

Use when monitoring online forums (Reddit, HN, ProductHunt) for recurring user pain points, feature requests, and unmet needs. Invoke for market research, pain-point discovery, trend detection, and competitive intelligence. Designed for scheduled execution via CronCreate.

ariffazil Skill

Unified MCP server testing, probing, and conformance validation. Covers MCPJam Inspector methodology for deep conformance testing, MCPJam CLI/SDK probing for protocol version and stateless transport discovery, and quick smoke tests for federation organ health. Merges: FORGE-mcp-smoke-test, FORGE-mcp-probe, FORGE-mcp-testing.

oimiragieo Bundle

Access AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.

oimiragieo Bundle

Generate structured Product Requirements Documents using hypothesis-driven methodology with Implementation Phases tracking.

oimiragieo Bundle

Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.

tibsfox Bundle

Use when the user asks "what should I work on", mentions GSD phases, ROADMAP, or .planning/ artifacts. Routes to the correct GSD command for the current project state.

oimiragieo Bundle

Integration with protocols.io API for managing scientific protocols. This skill should be used when working with protocols.io to search, create, update, or publish protocols; manage protocol steps and materials; handle discussions and comments; organize workspaces; upload and manage files; or integrate protocols.io functionality into workflows. Applicable for protocol discovery, collaborative protocol development, experiment tracking, lab protocol management, and scientific documentation.

oimiragieo Bundle

Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.

ariffazil Bundle

Real apex-judge skill. Gödel lock + strange-loop zen: doer ≠ judge lane, evidence-only packages, kernel arif_judge is sole effective_verdict source, F13 is true external for critical. FORBIDS free-text self-SEAL and same-agent self-audit. Default: apex-judge isolate. Option 2 A2A 888-APEX is backlog.

oimiragieo Bundle

How agents discover and use skills. Use to understand skill invocation protocol.

ariffazil Skill

Private, self-hosted web search and URL content reader via SearXNG MCP server (mcp-searxng). Use for privacy-preserving web searches, query suggestions, instance discovery, and converting web pages to markdown.

oimiragieo Bundle

Customer feedback analysis — sentiment detection, NPS/CSAT frameworks, feature request clustering, support ticket triage, churn signal detection, and feedback-to-roadmap translation

gptomics Bundle

Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets, chaining kit-aware cutadapt trimming (adapter on every read, UMI/4N handling), miRge3 known+isomiR quantification or miRDeep2 novel discovery, compositionally-aware DESeq2, and miRanda target prediction. Use when committing the library-kit adapter/UMI handling once, choosing the NORMALIZER (which drives which miRNAs are called DE more than the DE model does), deciding known quantification vs novel discovery, handling biofluid/plasma libraries that lack a trustworthy endogenous normalizer, routing tRF/piRNA reads to their own profiling, or feeding RAW (not RPM) counts with size-factor inspection into DE. Hands mechanism to the small-rna-seq component skills; not a re-teach of any single step.

gptomics Bundle

Trains and applies base-resolution deep learning models on ChIP-seq / ChIP-nexus / CUT&RUN data. Uses BPNet (Avsec 2021 Nat Genet 53:354; soft motif syntax from ChIP-nexus), chromBPNet (Pampari A et al 2024 bioRxiv; bias-factorized base-resolution profiles), EnFormer (Avsec 2021 Nat Methods 18:1196; 196 kb input, ~100 kb effective receptive field), DeepSEA (Zhou 2015; multi-task CNN), and JASPAR 2026 deep-learning collection (1259 BPNet ChIP models). Performs in silico mutagenesis for variant-effect prediction, DeepLIFT/Grad attribution, and TF-MoDISco motif discovery from attribution scores. Use when predicting variant effects on TF binding, discovering soft motif syntax / cooperativity, integrating ChIP-seq with sequence-only predictions, or applying precomputed JASPAR Deep Learning models to new variants.

gptomics Bundle

Predict RBP binding from RNA sequence using deep learning models (RBPNet sequence-to-signal, RNAProt RNN, GraphProt2 GCN with structure, DeepCLIP, DeepRiPe multi-modal CNN) for variant-effect prediction, in silico binding-site discovery, model interpretation, and transfer learning from CLIP and RBNS datasets. Use when computational prediction of RBP binding from sequence is needed, evaluating variant effects on binding without further wet-lab experiments, comparing model performance, or training a custom model on ENCODE eCLIP data.

sboghossian-mini-claude-for-legal Skill

Use when applying specific product management tools and processes — roadmapping, prioritisation frameworks (RICE, MoSCoW), stakeholder management, sprint planning, and how to run these processes effectively in a legal-AI product team context. Reach for this skill when the user asks about how to build a product roadmap, how to prioritise between competing features, or how to manage stakeholders (legal domain experts, engineers, investors) in a legal-tech product organisation.

gptomics Bundle

End-to-end biomarker discovery workflow from expression data to validated biomarker panels. Covers feature selection with Boruta/LASSO, leakage-safe cross-validation, calibration, and SHAP interpretation. Use when building and validating diagnostic or prognostic biomarker signatures from omics data.

roadsidedev Bundle

Multi-agent autonomous startup system for Claude Code. Triggers on "Loki Mode". Orchestrates 100+ specialized agents across engineering, QA, DevOps, security, data/ML, business operations, marketing, HR, and customer success. Takes PRD to fully deployed, revenue-generating product with zero human intervention. Features Task tool for subagent dispatch, parallel code review with 3 specialized reviewers, severity-based issue triage, distributed task queue with dead letter handling, automatic deployment to cloud providers, A/B testing, customer feedback loops, incident response, circuit breakers, and self-healing. Handles rate limits via distributed state checkpoints and auto-resume with exponential backoff. Requires --dangerously-skip-permissions flag.

gptomics Bundle

Aligns RNA-seq reads to a genome with STAR, the fast splice-aware aligner whose splice-junction database (built from a GTF at sjdbOverhang = readlength-1) and two-pass mode set junction sensitivity, whose 255-for-unique MAPQ breaks GATK, and whose GeneCounts output reveals library strandedness. Use when RNA reads must be placed on the genome for novel-isoform discovery, fusion detection, RNA variant calling, coverage tracks, splicing QC, or single-cell (STARsolo). Memory-constrained RNA alignment is hisat2-alignment; DE on known transcripts only should skip alignment for rna-quantification/alignment-free-quant; the QC gate and contig-naming reconciliation are alignment-files; counting is rna-quantification; DNA is bwa-alignment/bowtie2-alignment.

sboghossian-mini-claude-for-legal Skill

Use when a prospect, customer, IT/security team, or procurement evaluator asks about Louis's security posture, data handling practices, compliance certifications, or infrastructure protections. Covers encryption standards, tenant isolation, access controls, certification roadmap (SOC 2, ISO 27001), no-training defaults, and zero-trust architecture. Applicable to all enterprise and regulated-sector deployments across all jurisdictions.

gptomics Bundle

Orchestrates neoantigen discovery from somatic variants to ranked vaccine candidates, chaining HLA typing (OptiType/arcasHLA + LOHHLA), VEP annotation (Wildtype+Frameshift plugins) + expression/readcount annotation, proximal-variant phasing, pVACseq MHC-I/II binding, CCF/clonality, and immunogenicity/quality ranking. Use when recognizing that binding is single-digit PPV and the critical steps are downstream (full-resolution HLA + LOH gating, proximal-variant phasing, clonality from purity+CN not raw VAF, expression), sequencing normalize+annotate -> phase -> HLA -> binding -> quality in the defensible order, dropping candidates on LOH-lost alleles, supplying --phased-proximal-variants-vcf so the mutant peptide is real, or ranking WITHIN patient rather than a fixed IC50 threshold. Hands mechanism to the immunoinformatics component skills; not a re-teach of any single step.

gptomics Bundle

End-to-end bulk time-course analysis from an expression matrix to temporal gene modules and per-cluster pathway enrichment. Orchestrates temporal DE (limma splines or DESeq2 LRT), Mfuzz/tslearn soft clustering of expression-profile shapes, GAM trajectory fitting, per-cluster GO enrichment against a temporal-gene background, and an OPTIONAL circadian rhythm-detection branch (MetaCycle/CosinorPy) that runs only when the design covers >=2 full cycles with >=6-8 evenly spaced samples per cycle. Use when analyzing a bulk time-series expression experiment from any omics platform and deciding limma-splines vs DESeq2-LRT for temporal DE, soft vs hard clustering, whether the sampling design even licenses rhythm detection, and which background to use for enrichment. Not for single-cell pseudotime (see temporal-genomics/trajectory-modeling for the bulk-vs-pseudotime boundary) or unknown-period discovery (see temporal-genomics/periodicity-detection).

gptomics Bundle

Predict enhancer-gene regulatory connections from ATAC-seq using ABC, ENCODE-rE2G, HiChIP, or Cicero. Use when linking distal enhancers to target genes, choosing between contact-aware (ABC, ENCODE-rE2G), accessibility-only (Cicero), and orthogonal (HiChIP H3K27ac, EpiMap) approaches, validating predictions against CRISPRi-FlowFISH gold-standard, or building cell-type-specific regulatory maps for fine-mapping or therapeutic target discovery.

oimiragieo Bundle

Audit memory retrieval quality (drift, staleness, citation-groundedness) and produce remediation backlog.

sboghossian-mini-claude-for-legal Skill

Use when a user asks about the publicly accessible tools available through Louis — both the free public tools (NDA generator, contract summarizer, statute explainer, legal translator AR-EN) and the paid professional tools. Delivers a structured catalog with tool descriptions, access tier, supported jurisdictions, and use cases. Triggers on "what free tools do you have?", "can I try something without signing up?", or tool-discovery queries from visitors not yet committed to a subscription.

sboghossian-mini-claude-for-legal Skill

Use when a user asks where their data is hosted, which data residency options are available, or how to configure their workspace for MENA-region data hosting. This is a platform documentation skill covering data residency options (EU Frankfurt default, MENA/GCC on request, Saudi-region roadmap), per-tenant configuration, and the regulatory drivers that make data residency critical for MENA legal professionals.

intent-solutions-io Bundle

Generate comprehensive pytest test suites from PRD functional requirements with fixtures, parameterization, and coverage tracking. Use when creating tests for new plugins, validating PRD requirements, or scaffolding test infrastructure. Trigger with 'generate tests from PRD', 'create test suite', or 'scaffold pytest tests'.

sboghossian-mini-claude-for-legal Skill

Use when preparing investor materials, responding to due diligence questions, or planning HAQQ's capital-raise roadmap. Covers the seed and Series A thesis, traction milestones, target investor profiles, and narrative framing for a MENA-first legal AI company. Internal use only.

gptomics Bundle

Discovers novel miRNAs and quantifies known miRNAs with miRDeep2 by scoring genome-mapped read stacks against the Dicer/Drosha biogenesis signature. Use when deciding whether a study needs de novo discovery at all versus known-miRNA quantification; choosing the species and related-species miRBase references; reading the miRDeep2 score as a signal-to-noise hypothesis rather than a fixed cutoff; or filtering novel candidates against tRNA/rRNA loci to reject the classic false positives.

gptomics Bundle

Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio diagnostics, junction-overhang distribution, splice-site strength scoring (MaxEntScan intrinsic + SpliceAI context-aware), strandedness verification, GENCODE basic vs comprehensive choice, and rRNA contamination screening. Splicing analysis is more demanding than DGE on read length, depth, library prep, alignment strategy, and annotation choice — failures silently bias PSI estimates and inflate novel-junction false positives. Use when evaluating data suitability for splicing analysis, troubleshooting low event detection, or designing sequencing experiments where AS is a primary endpoint.

intent-solutions-io Skill

This skill generates comprehensive test reports with coverage metrics, trends, and stakeholder-friendly formats (HTML, PDF, JSON). It aggregates test results from various frameworks, calculates key metrics (coverage, pass rate, duration), and performs trend analysis. Use this skill when the user requests a test report, coverage analysis, failure analysis, or historical comparisons of test runs. Trigger terms include "test report", "coverage report", "testing trends", "failure analysis", and "historical test data".

gptomics Bundle

Validates predictive models on omics and biomedical data with nested cross-validation, group/batch/temporal-aware splits, the full data-leakage taxonomy, probability calibration, decision-curve net benefit, optimism correction, sample-size planning, and TRIPOD+AI reporting. Use when estimating model performance honestly, choosing a CV scheme, detecting leakage, or judging whether reported discrimination means the model is actually useful. For feature selection itself see machine-learning/biomarker-discovery; for confirmatory-trial inference see clinical-biostatistics/trial-reporting.