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geniml
by K-Dense-AI
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), building consensus peaks (universes), or any ML-based analysis of genomic regions. Applies to BED file collections, scATAC-seq data, chromatin accessibility datasets, and region-based genomic feature learning.
dhdna-profiler
by K-Dense-AI
Extract cognitive patterns and thinking fingerprints from any text. Use this skill when the user wants to analyze how someone thinks, understand cognitive style, profile writing or speech patterns, compare thinking styles between people, asks "what's my thinking style", "analyze how this person reasons", "cognitive profile", "thinking pattern", "DHDNA", "digital DNA", or wants to understand the mind behind any text. Also trigger when the user provides text and wants deeper insight into the author's reasoning patterns, decision-making style, or cognitive signature.
clinpgx-database
by K-Dense-AI
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
docx
by K-Dense-AI
"Use this skill whenever the user wants to create, read, edit, or manipulate Word documents (.docx files). Triggers include: any mention of 'Word doc', 'word document', '.docx', or requests to produce professional documents with formatting like tables of contents, headings, page numbers, or letterheads. Also use when extracting or reorganizing content from .docx files, inserting or replacing images in documents, performing find-and-replace in Word files, working with tracked changes or comments, or converting content into a polished Word document. If the user asks for a 'report', 'memo', 'letter', 'template', or similar deliverable as a Word or .docx file, use this skill. Do NOT use for PDFs, spreadsheets, Google Docs, or general coding tasks unrelated to document generation."
biopython
by K-Dense-AI
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioinformatics pipelines, BLAST automation. For quick lookups use gget; for multi-service integration use bioservices.
histolab
by K-Dense-AI
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
earnings-analysis
by anthropics
Create professional equity research earnings update reports (8-12 pages, 3,000-5,000 words) analyzing quarterly results for companies already under coverage. Fast-turnaround format focusing on beat/miss analysis, key metrics, updated estimates, and revised thesis. Includes 1-3 summary tables and 8-12 charts. Use when user requests "earnings update", "quarterly update", "earnings analysis", "Q1/Q2/Q3/Q4 results", or post-earnings report.
gene-database
by K-Dense-AI
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
fluidsim
by K-Dense-AI
Framework for computational fluid dynamics simulations using Python. Use when running fluid dynamics simulations including Navier-Stokes equations (2D/3D), shallow water equations, stratified flows, or when analyzing turbulence, vortex dynamics, or geophysical flows. Provides pseudospectral methods with FFT, HPC support, and comprehensive output analysis.
learn-about-omx
by Yeachan-Heo
Learn about your OMX usage patterns and get personalized recommendations
ultraqa
by Yeachan-Heo
QA cycling workflow - test, verify, fix, repeat until goal met
frontend-ui-ux
by Yeachan-Heo
Designer-developer for UI/UX work
pipeline
by Yeachan-Heo
Configurable pipeline orchestrator for sequencing stages
help
by Yeachan-Heo
Guide on using oh-my-codex plugin
hud
by Yeachan-Heo
"Show or configure the OMX HUD (two-layer statusline)"
citation-management
by K-Dense-AI
Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.
exploratory-data-analysis
by K-Dense-AI
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats. This skill should be used when analyzing any scientific data file to understand its structure, content, quality, and characteristics. Automatically detects file type and generates detailed markdown reports with format-specific analysis, quality metrics, and downstream analysis recommendations. Covers chemistry, bioinformatics, microscopy, spectroscopy, proteomics, metabolomics, and general scientific data formats.
e2e-tests-studio
by mastra-ai
REQUIRED when modifying any file in packages/playground-ui or packages/playground. Triggers on: React component creation/modification/refactoring, UI changes, new playground features, bug fixes affecting studio UI. Generates Playwright E2E tests that validate PRODUCT BEHAVIOR, not just UI states.
deeptools
by K-Dense-AI
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
esm
by K-Dense-AI
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.
get-available-resources
by K-Dense-AI
This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.
cbioportal-database
by K-Dense-AI
Query cBioPortal for cancer genomics data including somatic mutations, copy number alterations, gene expression, and survival data across hundreds of cancer studies. Essential for cancer target validation, oncogene/tumor suppressor analysis, and patient-level genomic profiling.
bindingdb-database
by K-Dense-AI
Query BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50). Search by target (UniProt ID), compound (SMILES/name), or pathogen. Essential for drug discovery, lead optimization, polypharmacology analysis, and structure-activity relationship (SAR) studies.
chembl-database
by K-Dense-AI
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.