Project Tracking
System for tracking work across AI sessions. Use when starting or ending work sessions, managing initiatives, capturing ideas or todos, or when needing to understand what work is in progress. Handles knowledge transfer between sessions.
Documentation System
Standards for documenting codebases. Use when writing documentation, deciding where docs should go, reviewing doc quality, or updating docs after code changes. Covers folder structure, content guidelines, and maintenance workflows.
OpenCode SDK Development
This skill should be used when the user asks to "create an OpenCode tool", "build an OpenCode plugin", "write a custom tool for OpenCode", "use @opencode-ai/sdk", "use @opencode-ai/plugin", "integrate with OpenCode", "create OpenCode hooks", "define tool schema", "use tool.schema", "work with OpenCode sessions", or needs guidance on OpenCode SDK patterns, plugin development, or custom tool creation.
Agent Design
This skill should be used when the user asks to "configure agent profile", "add skills to agent", "set up MCP servers", "configure agent tools", "write system prompt", "create agent workflow", "define agent commands", "add subagents", or needs to define what capabilities an agent has and how to orchestrate complex workflows in the runtime.
hc-ingest-ads
Import selected Google Ads or Meta Ads reports into HC with account identity, attribution settings, currencies, reporting periods and revision-aware metrics.
hc-ingest-analytics
Import selected PostHog, GA4 or database analytics into HC as scoped measurements with query definitions, time windows, sampling and freshness evidence.
hc-ingest-billing
Import selected Stripe subscription, invoice, payment and refund records or aggregate billing reports into HC while keeping live/test accounts and revenue definitions distinct.
hc-ingest-claude
Import selected Claude Code session transcripts or Claude conversation exports into HC with conversation identity, revision tracking and explicit content exclusions.
hc-ingest-codex
Import selected Codex conversation exports or local session transcripts into HC, preserving user/assistant turns and excluding hidden reasoning, credentials and unrelated sessions.
hc-ingest-crm
Import selected Attio or HubSpot contacts, companies, deals, notes and task records into HC without changing CRM data or merging uncertain identities.
hc-ingest-docs-tasks
Import selected Notion pages, Linear issues or Markdown knowledge exports into HC while preserving document identity, revisions, linked context and task states.
hc-ingest-github
Import selected GitHub repositories, issues, pull requests, reviews and release or workflow records into HC through an existing GitHub reader.
hc-ingest-google-workspace
Import selected Gmail, Drive, Docs, Calendar and available Meet records into HC through existing Google access or exports, keeping mailboxes and sharing scopes separate.
hc-ingest-infra
Import scoped operational summaries from AWS, Google Cloud, Cloudflare, Vercel or Sentry into HC through existing read access, excluding secrets and raw production payloads.
hc-ingest-marketing
Import selected Buffer, HeyReach or Loops campaign, post and delivery records into HC with provider status, audience scope and metric freshness preserved.
hc-ingest-meetings
Import selected meeting notes, transcripts or Zoom and Cal.com records into HC, separating scheduling, attendance, speaker evidence and derived decisions.
hc-ingest-slack
Import selected Slack channels, messages and thread replies into HC using existing authorized access, with edit, deletion and thread-coverage tracking.
hc-ingest-support
Import selected Intercom, Zendesk or Discord support conversations into HC with thread, author, status and coverage evidence, excluding unrelated private content.
hc-ingest
Import authorized source records into an existing HC store with provenance, versioned retries, freshness metadata and readback verification. Use for ingestion or import requests, not ordinary questions about records already in HC.
hyperconsciousness-ops
Operate, inspect, sync, recover, and connect agents or phones to a private HC store safely. Use for HC CLI work, second-brain replication across macOS/Windows/Linux, device or bucket sync, workspace projections, grants and revocation, MCP/HTTP access, mobile pairing, integrity checks, or determining whether a brain is actually running and current on a device.
hyperconsciousness
Recall facts and decisions from HC with source-backed answers, including when the question uses different wording from the records. Find local skills, PKM notes and opaque capabilities; operate encrypted knowledge storage. Use for questions requiring saved knowledge, not unrelated questions or device control.
ralphie-spec
Generate project specifications in V2 format through structured user interviews. Requires user presence.
home-assistant-manager
Manage Home Assistant configuration safely and fast — edit and deploy YAML (automations, blueprints, scripts, scenes, templates, MQTT), validate with ha core check, deploy via git or rapid scp, reload-vs-restart correctly, verify changes from logs, traces and entity state, and build Lovelace dashboards. Use for any Home Assistant config, automation, template, or dashboard work over SSH/hass-cli/MCP.
scientific-slides
Build slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations, thesis defense slides, or any scientific talk. Provides slide structure, design templates, timing guidance, and visual validation. Works with PowerPoint and LaTeX Beamer.
literature-review
Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).
latex-posters
Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. Support for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices for visual communication.
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
arboreto
Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
scientific-visualization
Create publication figures with matplotlib/seaborn/plotly. Multi-panel layouts, error bars, significance markers, colorblind-safe, export PDF/EPS/TIFF, for journal-ready scientific plots.
cobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
anndata
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.
astropy
Comprehensive Python library for astronomy and astrophysics. This skill should be used when working with astronomical data including celestial coordinates, physical units, FITS files, cosmological calculations, time systems, tables, world coordinate systems (WCS), and astronomical data analysis. Use when tasks involve coordinate transformations, unit conversions, FITS file manipulation, cosmological distance calculations, time scale conversions, or astronomical data processing.
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
biomni
Autonomous biomedical AI agent framework for executing complex research tasks across genomics, drug discovery, molecular biology, and clinical analysis. Use this skill when conducting multi-step biomedical research including CRISPR screening design, single-cell RNA-seq analysis, ADMET prediction, GWAS interpretation, rare disease diagnosis, or lab protocol optimization. Leverages LLM reasoning with code execution and integrated biomedical databases.
biopython
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
biorxiv-database
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
cellxgene-census
Query CZ CELLxGENE Census (61M+ cells). Filter by cell type/tissue/disease, retrieve expression data, integrate with scanpy/PyTorch, for population-scale single-cell analysis.
chembl-database
Query ChEMBL's bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
clinicaltrials-database
Query ClinicalTrials.gov via API v2. Search trials by condition, drug, location, status, or phase. Retrieve trial details by NCT ID, export data, for clinical research and patient matching.
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
clinvar-database
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.
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
datacommons-client
Work with Data Commons, a platform providing programmatic access to public statistical data from global sources. Use this skill when working with demographic data, economic indicators, health statistics, environmental data, or any public datasets available through Data Commons. Applicable for querying population statistics, GDP figures, unemployment rates, disease prevalence, geographic entity resolution, and exploring relationships between statistical entities.
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.
deepchem
Molecular machine learning toolkit. Property prediction (ADMET, toxicity), GNNs (GCN, MPNN), MoleculeNet benchmarks, pretrained models, featurization, for drug discovery ML.
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing research methodologies, executing computational experiments, performing literature searches, or generating publication-ready papers in LaTeX format. Supports end-to-end research pipelines with customizable agent orchestration.
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
docx
Document toolkit (.docx). Create/edit documents, tracked changes, comments, formatting preservation, text extraction, for professional document processing.
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