Research & Knowledge
Research, retrieval, summarization, and knowledge work
Skills List
geo-fundamentals
Generative Engine Optimization for AI search engines (ChatGPT, Claude, Perplexity).
sickn33ai-engineer
Build production-ready LLM applications, advanced RAG systems, and intelligent agents. Implements vector search, multimodal AI, agent orchestration, and enterprise AI integrations.
sickn33audio-transcriber
Transform audio recordings into professional Markdown documentation with intelligent summaries using LLM integration
sickn33
bulk-rnaseq
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathway-enrichment), and publication figures (scientific-visualization). Use whenever the user has bulk RNA-seq reads or quant output and wants a complete, reproducible differential-expression workflow — e.g. "analyze my RNA-seq", "FASTQ to DESeq2", "run nf-core/rnaseq", "STAR/Salmon quantification", "build a counts matrix for DESeq2", or "go from reads to differentially expressed genes and enriched pathways". Routes between an nf-core/rnaseq (Nextflow) path and a standalone STAR/Salmon path, and covers experimental design, strandedness, and QC gates. For single-cell RNA-seq use the scanpy skill instead.
k-dense-aipathway-enrichment
Run pathway and gene-set enrichment analysis on gene lists or ranked gene data, then interpret the results. Use whenever the user has a set of genes (differentially expressed genes from PyDESeq2/Scanpy, CRISPR-screen hits, cluster marker genes, proteomics hits) and wants to know which biological pathways, GO terms, or gene sets are over-represented or enriched. Covers over-representation analysis (ORA / Enrichr / Fisher / hypergeometric), ranked Gene Set Enrichment Analysis (GSEA / preranked), single-sample scoring (ssGSEA/GSVA), and functional profiling via gseapy, g:Profiler, Enrichr libraries, MSigDB, GO, KEGG, Reactome, and WikiPathways — plus gene-ID mapping, choosing the right background universe, multiple-testing correction, redundancy reduction, dotplots/enrichment maps, and publication-ready tables. Use this for "pathway analysis", "enrichment analysis", "GO enrichment", "KEGG/Reactome pathways", "GSEA", "over-representation", "functional annotation", or "what pathways are my genes in".
k-dense-aicontext-window-management
Strategies for managing LLM context windows including
sickn33conversation-memory
Persistent memory systems for LLM conversations including
sickn33last30days
Research a topic from the last 30 days on Reddit + X + Web, become an expert, and write copy-paste-ready prompts for the user's target tool.
sickn33documentation-templates
Documentation templates and structure guidelines. README, API docs, code comments, and AI-friendly documentation.
sickn33liteparse
Local document and PDF parsing that returns spatial text with bounding boxes. Use for extracting text from PDFs, DOCX, Office files, and images; running OCR on scans; producing layout-preserved JSON for RAG; batch-ingesting folders of papers; or rendering pages to PNG for multimodal agents. Distinguishing capabilities are per-token bounding boxes, page raster output, and fully local processing with no cloud API.
k-dense-aiagent-memory-systems
"Memory is the cornerstone of intelligent agents. Without it, every
sickn33youtube-summarizer
Extract transcripts from YouTube videos and generate comprehensive, detailed summaries using intelligent analysis frameworks
sickn33brainstorming
Use before creative or constructive work (features, architecture, behavior). Transforms vague ideas into validated designs through disciplined reasoning and collaboration.
sickn33bids
Use this skill when working with Brain Imaging Data Structure (BIDS) datasets: organizing neuroscience and biomedical data (MRI, EEG, MEG, iEEG, PET, microscopy, NIRS, motion capture, EMG, MR spectroscopy, behavioral), querying BIDS layouts, validating compliance, converting DICOM to BIDS, writing metadata sidecars, or creating BIDS derivatives.
k-dense-aibrainstorming
Use before creative or constructive work (features, architecture, behavior). Transforms vague ideas into validated designs through disciplined reasoning and collaboration.
sickn33exa-search
Web toolkit powered by Exa, tuned for scientific and technical content. Use this skill when the user needs to search the web or fetch/extract URL content. Covers: web search (semantic lookups, research, current info — with optional research-paper category and academic domain filtering) and URL extraction (fetching pages, articles, academic PDFs in batch). Use this skill for web-related tasks when the user wants high-quality search or scholarly filtering via category=research paper. Triggers on requests to search, look up, fetch a page, or extract an article.
k-dense-aiautoskill
Observe the user's screen via screenpipe, detect repeated research workflows, match them against existing scientific-agent-skills, and draft new skills (or composition recipes that chain existing ones) for the patterns not yet covered. Use when the user asks to analyze their recent work and propose skills based on what they actually do. Requires the screenpipe daemon (https://github.com/screenpipe/screenpipe) running locally on port 3030 — the skill has no other data source and will refuse to run if screenpipe is unreachable. All detection runs locally; only redacted cluster summaries reach the LLM.
k-dense-aihugging-science
Use when the user is doing AI/ML work in a scientific domain such as biology, chemistry, physics, astronomy, climate, genomics, materials, medicine, ecology, energy, engineering, math, drug discovery, protein design, weather modeling, theorem proving, single-cell, or PDE solving. Hugging Science is a curated catalog of scientific datasets, models, blog posts, and interactive Spaces. This skill helps discover and use resources via `datasets`, `transformers`, the HF Inference API, `gradio_client`, and methodology citations.
k-dense-ai
attribution
When the user wants to figure out which marketing actually drives conversions and revenue, choose or interpret an attribution model, or reconcile conflicting numbers across tools. Also use when the user mentions "attribution," "attribution model," "first-touch vs last-touch," "multi-touch," "which channel drives revenue," "what's my real CAC," "my dashboards disagree," "Google/Meta says X but GA says Y," "media mix model," "MMM," "incrementality," "geo lift," "holdout test," "how did you hear about us," "self-reported attribution," "dark social," or wants to instrument attribution themselves — "stitch my bookings to their source," "SavvyCal/Calendly attribution," "close the identify gap," "track conversions on a third-party domain," "first-party / self-hosted attribution." For event tracking setup and UTMs, see analytics. For ad-platform pixels/CAPI, see ads. For pipeline and CRM revenue reporting, see revops. For the AI-search attribution blind spot, see ai-seo.
coreyhaines31opentrons-integration
Author, review, migrate, simulate, and troubleshoot official Opentrons Python Protocol API v2 protocols for Flex and OT-2 robots. Use for robot-specific liquid handling, deck and labware setup, pipettes, modules, runtime parameters, liquid classes, and Opentrons App analysis. Use pylabrobot instead when one workflow must support multiple robot vendors.
k-dense-aicobrapy
Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.
k-dense-aiqiskit
Build, simulate, transpile, and execute quantum circuits with Qiskit and IBM Quantum Runtime. Use for Qiskit 2.x circuits and operators, V2 Sampler or Estimator primitives, target-aware transpilation, local or noisy simulation, IBM QPU execution, Runtime sessions or batches, error mitigation, and Qiskit ecosystem packages.
k-dense-aipylabrobot
Develop and review PyLabRobot lab-automation resources, liquid-handling plans, offline simulations, and supported-device integrations. Use for PyLabRobot protocols or API questions; keep physical execution behind an explicit operator safety gate.
k-dense-aineuropixels-analysis
Analyze Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion correction, Kilosort4 (and CPU) spike sorting, quality metrics, and unit curation (threshold-based, model-based UnitRefine, and AI-assisted visual review). Use when working with Neuropixels 1.0/2.0 recordings, spike sorting, or extracellular electrophysiology analysis.
k-dense-ai