数据处理
数据转换、清洗与 ETL
yao-geo-execution-roadmap
yaojingang
当用户需要把 GEO 全景诊断、机会地图、AI 平台采样结论或品牌事实底座转成 30/60/90 天综合实施方案时使用，输出页面技术、内容矩阵、标题体系、知识库、外部证据、监测闭环、角色分工、验收指标和四格式报告；覆盖 DeepSeek、豆包、千问、Kimi、元宝；不用于从零做全景采样诊断或只写单篇内容。
yao-geo-intent-miner
yaojingang
Use when a user asks for GEO 意图拓词、AI 搜索意图挖掘、AI 搜索问题集、问题簇、追问链路、查询重写、内容选题库、FAQ 题库、监测 Prompt 库, or AI Intent Miner.
depmap
K-Dense-AI
Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for identifying cancer-specific vulnerabilities, synthetic lethal interactions, and validating oncology drug targets.
query-finelog
marin-community
Query Finelog logs and telemetry for Iris tasks, workers, profiles, training, vLLM, and cross-cluster forwarding. Use for schema discovery, SQL, memory or CPU summaries, hub-versus-regional comparisons, counter semantics, and query-performance diagnosis.
organize-experiments
marin-community
Harvest experiment issue reports and curate docs/reports/index.md only when explicitly requested.
trace-pulumi-diff
marin-community
Run a read-only preview for a specified Marin infra/pulumi stack and trace each pending resource change to merged pull requests since its latest successful update when that update records a clean Git checkout. Use when a stack has unapplied changes or drift and someone needs to know which PRs explain the preview.
add-sfx
remotion-dev
Add a new sound effect to @remotion/sfx
gtars
K-Dense-AI
High-performance toolkit for genomic interval analysis in Rust with Python bindings. Use when working with genomic regions, BED files, coverage tracks, overlap detection, tokenization for ML models, or fragment analysis in computational genomics and machine learning applications.
datamol
K-Dense-AI
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including 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.
dnanexus-integration
K-Dense-AI
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.
astropy
K-Dense-AI
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.
flowio
K-Dense-AI
Parse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arrays, read metadata/channels, convert to CSV/DataFrame, for flow cytometry data preprocessing.
anndata
K-Dense-AI
Data structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem. This is the data format skill—for analysis workflows use scanpy; for probabilistic models use scvi-tools; for population-scale queries use cellxgene-census.
dask
K-Dense-AI
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best for parallel file processing, distributed ML, integration with existing pandas code. For out-of-core analytics on single machine use vaex; for in-memory speed use polars.
arboreto
K-Dense-AI
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.
gget
K-Dense-AI
"Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices."
exploratory-data-analysis
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.
aeon
K-Dense-AI
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
adaptyv
K-Dense-AI
"How to use the Adaptyv Bio Foundry API and Python SDK for protein experiment design, submission, and results retrieval. Use this skill whenever the user mentions Adaptyv, Foundry API, protein binding assays, protein screening experiments, BLI/SPR assays, thermostability assays, or wants to submit protein sequences for experimental characterization. Also trigger when code imports adaptyv, adaptyv_sdk, or FoundryClient, or references foundry-api-public.adaptyvbio.com."
bgpt-paper-search
K-Dense-AI
Search scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server. Returns 25+ fields per paper including methods, results, sample sizes, quality scores, and conclusions. Use for literature reviews, evidence synthesis, and finding experimental details not available in abstracts alone.
glycoengineering
K-Dense-AI
Analyze and engineer protein glycosylation. Scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and access curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). For glycoprotein engineering, therapeutic antibody optimization, and vaccine design.
labarchive-integration
K-Dense-AI
Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows.
geopandas
K-Dense-AI
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.
imaging-data-commons
K-Dense-AI
Query and download public cancer imaging data from NCI Imaging Data Commons using idc-index. Use for accessing large-scale radiology (CT, MR, PET) and pathology datasets for AI training or research. No authentication required. Query by metadata, visualize in browser, check licenses.