LeonChaoX/qinyan-academic-skills

这个仓库里有 187 个技能，GitHub 星标 ★ 899。

• bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted fro
• biorxiv-databaseEfficient database search tool for bioRxiv preprint server. Use this skill when
• citation-managementComprehensive citation management for academic research. Search Google Scholar a
• literature-reviewConduct comprehensive, systematic literature reviews using multiple academic dat
• openalex-databaseQuery and analyze scholarly literature using the OpenAlex database. This skill s
• parallel-webSearch the web, extract URL content, and run deep research using the Parallel Ch
• perplexity-searchPerform AI-powered web searches with real-time information using Perplexity mode
• pubmed-databaseDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API
• pyzoteroInteract with Zotero reference management libraries using the pyzotero Python cl
• research-lookupLook up current research information using the Parallel Chat API (primary) or Pe
• medical-imaging-review>
• paper-2-webThis skill should be used when converting academic papers into promotional and p
• peer-reviewStructured manuscript/grant review with checklist-based evaluation. Use when wri
• research-proposal>
• scientific-writingCore skill for the deep research and writing tool. Write scientific manuscripts
• venue-templatesAccess comprehensive LaTeX templates, formatting requirements, and submission gu
• generate-imageGenerate or edit images using AI models (FLUX, Nano Banana 2). Use for general-p
• infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative r
• latex-postersCreate professional research posters in LaTeX using beamerposter, tikzposter, or
• markdown-mermaid-writingComprehensive markdown and Mermaid diagram writing skill. Use when creating any
• paper-slide-deckGenerate professional slide deck images from academic papers and content. Create
• pptx-postersCreate research posters using HTML/CSS that can be exported to PDF or PPTX. Use
• scientific-schematicsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart
• scientific-slidesBuild slide decks and presentations for research talks. Use this for making Powe
• scientific-visualizationMeta-skill for publication-ready figures. Use when creating journal submission f
• consciousness-councilRun a multi-perspective Mind Council deliberation on any question, decision, or
• dhdna-profilerExtract cognitive patterns and thinking fingerprints from any text. Use this ski
• hypothesis-generationStructured hypothesis formulation from observations. Use when you have experimen
• nsfc-proposal撰写国家自然科学基金（NSFC）申请书，覆盖青年科学基金（C类）、优秀青年科学基金（B类）、国家杰出青年科学基金（A类）2026年度最新规范。提供分阶段写作工作
• nssfc-proposal撰写国家社会科学基金（NSSFC）年度项目申请书，依据 2025 年全国哲学社会科学工作办公室官方模板，覆盖重点项目（A）、一般项目（B）、青年项目（C）、西部
• research-grantsWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC.
• scholar-evaluationSystematically evaluate scholarly work using the ScholarEval framework, providin
• scientific-brainstormingCreative research ideation and exploration. Use for open-ended brainstorming ses
• scientific-critical-thinkingEvaluate scientific claims and evidence quality. Use for assessing experimental
• what-if-oracleRun structured What-If scenario analysis with multi-branch possibility explorati
• anndataData structure for annotated matrices in single-cell analysis. Use when working
• arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable a
• biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file par
• bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multi
• cellxgene-censusQuery the CELLxGENE Census (61M+ cells) programmatically. Use when you need expr
• deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprin
• etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary ev
• flowioParse FCS (Flow Cytometry Standard) files v2.0-3.1. Extract events as NumPy arra
• genimlThis skill should be used when working with genomic interval data (BED files) fo
• ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups:
• gtarsHigh-performance toolkit for genomic interval analysis in Rust with Python bindi
• lamindbThis skill should be used when working with LaminDB, an open-source data framewo
• phylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2
• pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bu
• pysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FAST
• scanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimen
• scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, dive
• scveloRNA velocity analysis with scVelo. Estimate cell state transitions from unsplice
• scvi-toolsDeep generative models for single-cell omics. Use when you need probabilistic ba
• tiledbvcfEfficient storage and retrieval of genomic variant data using TileDB. Scalable V
• zarr-pythonChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS in
• datamolPythonic wrapper around RDKit with simplified interface and sensible defaults. P
• deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property p
• diffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB
• matchmsSpectral similarity and compound identification for metabolomics. Use for compar
• medchemMedicinal chemistry filters. Apply drug-likeness rules (Lipinski, Veber), PAINS
• molecular-dynamicsRun and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set u
• molfeatMolecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pre
• pyopenmsComplete mass spectrometry analysis platform. Use for proteomics workflows featu
• pytdcTherapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI
• rdkitCheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing,
• rowanCloud-based quantum chemistry platform with Python API. Preferred for computatio
• torchdrugPyTorch-native graph neural networks for molecules and proteins. Use when buildi
• cbioportal-databaseQuery cBioPortal for cancer genomics data including somatic mutations, copy numb
• clinical-decision-supportGenerate professional clinical decision support (CDS) documents for pharmaceutic
• clinical-reportsWrite comprehensive clinical reports including case reports (CARE guidelines), d
• clinicaltrials-databaseQuery ClinicalTrials.gov via API v2. Search trials by condition, drug, location,
• clinpgx-databaseAccess ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug in
• clinvar-databaseQuery NCBI ClinVar for variant clinical significance. Search by gene/position, i
• cosmic-databaseAccess COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Cen
• depmapQuery the Cancer Dependency Map (DepMap) for cancer cell line gene dependency sc
• fda-databaseQuery openFDA API for drugs, devices, adverse events, recalls, regulatory submis
• histolabLightweight WSI tile extraction and preprocessing. Use for basic slide processin
• imaging-data-commonsQuery and download public cancer imaging data from NCI Imaging Data Commons usin
• monarch-databaseQuery the Monarch Initiative knowledge graph for disease-gene-phenotype associat
• neurokit2Comprehensive biosignal processing toolkit for analyzing physiological data incl
• neuropixels-analysisNeuropixels neural recording analysis. Load SpikeGLX/OpenEphys data, preprocess,
• pathmlFull-featured computational pathology toolkit. Use for advanced WSI analysis inc
• pydicomPython library for working with DICOM (Digital Imaging and Communications in Med
• pyhealthComprehensive healthcare AI toolkit for developing, testing, and deploying machi
• treatment-plansGenerate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format
• adaptyvCloud laboratory platform for automated protein testing and validation. Use when
• alphafold-databaseAccess AlphaFold 200M+ AI-predicted protein structures. Retrieve structures by U
• esmComprehensive toolkit for protein language models including ESM3 (generative mul
• glycoengineeringAnalyze and engineer protein glycosylation. Scan sequences for N-glycosylation s
• interpro-databaseQuery InterPro for protein family, domain, and functional site annotations. Inte
• pdb-databaseAccess RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/
• uniprot-databaseDirect REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping
• aeonThis skill should be used for time series machine learning tasks including class
• hypogenicAutomated LLM-driven hypothesis generation and testing on tabular datasets. Use
• pufferlibHigh-performance reinforcement learning framework optimized for speed and scale.
• pymcBayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational
• pymooMulti-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts
• pytorch-lightningDeep learning framework (PyTorch Lightning). Organize PyTorch code into Lightnin
• scikit-learnMachine learning in Python with scikit-learn. Use when working with supervised l
• scikit-survivalComprehensive toolkit for survival analysis and time-to-event modeling in Python
• shapModel interpretability and explainability using SHAP (SHapley Additive exPlanati
• stable-baselines3Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2
• timesfm-forecastingZero-shot time series forecasting with Google's TimesFM foundation model. Use fo
• torch-geometricGraph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GA
• transformersThis skill should be used when working with pre-trained transformer models for n
• umap-learnUMAP dimensionality reduction. Fast nonlinear manifold learning for 2D/3D visual
• astropyComprehensive Python library for astronomy and astrophysics. This skill should b
• cirqGoogle quantum computing framework. Use when targeting Google Quantum AI hardwar
• cobrapyConstraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux samp
• fluidsimFramework for computational fluid dynamics simulations using Python. Use when ru
• matlabMATLAB and GNU Octave numerical computing for matrix operations, data analysis,
• pennylaneHardware-agnostic quantum ML framework with automatic differentiation. Use when
• pymatgenMaterials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, ban
• qiskitIBM quantum computing framework. Use when targeting IBM Quantum hardware, workin
• qutipQuantum physics simulation library for open quantum systems. Use when studying m
• simpyProcess-based discrete-event simulation framework in Python. Use this skill when
• daskDistributed computing for larger-than-RAM pandas/NumPy workflows. Use when you n
• exploratory-data-analysisPerform comprehensive exploratory data analysis on scientific data files across
• matplotlibLow-level plotting library for full customization. Use when you need fine-graine
• networkxComprehensive toolkit for creating, analyzing, and visualizing complex networks
• plotlyInteractive visualization library. Use when you need hover info, zoom, pan, or w
• polarsFast in-memory DataFrame library for datasets that fit in RAM. Use when pandas i
• seabornStatistical visualization with pandas integration. Use for quick exploration of
• statistical-analysisGuided statistical analysis with test selection and reporting. Use when you need
• statsmodelsStatistical models library for Python. Use when you need specific model classes
• sympyUse this skill when working with symbolic mathematics in Python. This skill shou
• vaexUse this skill for processing and analyzing large tabular datasets (billions of
• bindingdb-databaseQuery BindingDB for measured drug-target binding affinities (Ki, Kd, IC50, EC50)
• brenda-databaseAccess BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kca
• chembl-databaseQuery ChEMBL bioactive molecules and drug discovery data. Search compounds by st
• datacommons-clientWork with Data Commons, a platform providing programmatic access to public stati
• drugbank-databaseAccess and analyze comprehensive drug information from the DrugBank database inc
• ena-databaseAccess European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw
• ensembl-databaseQuery Ensembl genome database REST API for 250+ species. Gene lookups, sequence
• gene-databaseQuery NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene
• geo-databaseAccess NCBI GEO for gene expression/genomics data. Search/download microarray an
• gnomad-databaseQuery gnomAD (Genome Aggregation Database) for population allele frequencies, va
• gtex-databaseQuery GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expressi
• gwas-databaseQuery NHGRI-EBI GWAS Catalog for SNP-trait associations. Search variants by rs I
• hmdb-databaseAccess Human Metabolome Database (220K+ metabolites). Search by name/ID/structur
• jaspar-databaseQuery JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs).
• kegg-databaseDirect REST API access to KEGG (academic use only). Pathway analysis, gene-pathw
• metabolomics-workbench-databaseAccess NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolit
• opentargets-databaseQuery Open Targets Platform for target-disease associations, drug target discove
• pubchem-databaseQuery PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/S
• reactome-databaseQuery Reactome REST API for pathway analysis, enrichment, gene-pathway mapping,
• string-databaseQuery STRING API for protein-protein interactions (59M proteins, 20B interaction
• uspto-databaseAccess USPTO APIs for patent/trademark searches, examination history (PEDS), ass
• zinc-databaseAccess ZINC (230M+ purchasable compounds). Search by ZINC ID/SMILES, similarity
• benchling-integrationBenchling R&D platform integration. Access registry (DNA, proteins), inventory,
• dnanexus-integrationDNAnexus cloud genomics platform. Build apps/applets, manage data (upload/downlo
• ginkgo-cloud-labSubmit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a w
• labarchive-integrationElectronic lab notebook API integration. Access notebooks, manage entries/attach
• latchbio-integrationLatch platform for bioinformatics workflows. Build pipelines with Latch SDK, @wo
• omero-integrationMicroscopy data management platform. Access images via Python, retrieve datasets
• opentrons-integrationOfficial Opentrons Protocol API for OT-2 and Flex robots. Use when writing proto
• protocolsio-integrationIntegration with protocols.io API for managing scientific protocols. This skill
• pylabrobotVendor-agnostic lab automation framework. Use when controlling multiple equipmen
• denarioMultiagent AI system for scientific research assistance that automates research
• docxUse this skill whenever the user wants to create, read, edit, or manipulate Word
• markitdownConvert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX,
• open-notebookSelf-hosted, open-source alternative to Google NotebookLM for AI-powered researc
• pdfUse this skill whenever the user wants to do anything with PDF files. This inclu
• pptxUse this skill any time a .pptx file is involved in any way — as input, output,
• xlsxUse this skill any time a spreadsheet file is the primary input or output. This
• alpha-vantageAccess real-time and historical stock market data, forex rates, cryptocurrency p
• edgartoolsPython library for accessing, analyzing, and extracting data from SEC EDGAR fili
• fred-economic-dataQuery FRED (Federal Reserve Economic Data) API for 800,000+ economic time series
• hedgefundmonitorQuery the OFR (Office of Financial Research) Hedge Fund Monitor API for hedge fu
• market-research-reportsGenerate comprehensive market research reports (50+ pages) in the style of top c
• usfiscaldataQuery the U.S. Treasury Fiscal Data API for federal financial data including nat
• geomasterComprehensive geospatial science skill covering remote sensing, GIS, spatial ana
• geopandasPython library for working with geospatial vector data including shapefiles, Geo
• get-available-resourcesThis skill should be used at the start of any computationally intensive scientif
• iso-13485-certificationComprehensive toolkit for preparing ISO 13485 certification documentation for me
• modalRun Python code in the cloud with serverless containers, GPUs, and autoscaling.
• qinyan-citation沁言学术文献引用 - 先通过沁言学术OpenAPI检索文献，然后按照GB/T 7714、IEEE、APA、MLA、Chicago、Harvard等标准格式输出引
• qinyan-nature-figures面向 Nature Portfolio 与高影响力期刊的证据驱动科研绘图技能。用于从原始或汇总数据设计单图与多面板 figure、选择合适图形语法、编写 Pyt
• qinyan-nature-polishing面向 Nature、Nature Communications 及高影响力期刊的学术语言重构与润色技能。用于中译英、英文精修、摘要压缩、段落逻辑修复、术语统一、
• qinyan-nature-review面向 Nature、Nature Communications 及高影响力期刊的可追溯投稿前评审技能。用于模拟同行评审、检查原创性与广泛意义、压力测试技术严谨性
• qinyan-nature-statistics面向 Nature Portfolio 与高影响力期刊的实验设计一致型统计分析、审查和报告技能。用于定义独立实验单位与重复层级、制定统计分析计划、检查数据质量、
• qinyan-nature-writing面向 Nature、Nature Communications 及同等级综合期刊的证据驱动论文写作技能。用于从已核验的结果、图表、实验记录或中英文草稿构建标题、
• qinyan-paper-analysis沁言学术论文分析 - 对单篇学术论文进行深度分析解读，提取研究目标、方法论、主要发现和研究限制。通过沁言学术OpenAPI的analyze接口实现。触发词：论文
• qinyan-paper-polish沁言学术通用论文润色优化 - 按照专业学术规范对中英文学术论文、学位论文和专业报告进行语言润色，提升表达质量、逻辑连贯性和格式规范性。适用于未指定期刊的常规润色
• qinyan-paper-search沁言学术文献检索 - 支持从 Google Scholar、万方(Wanfang)、PubMed、ArXiv 四大学术数据库检索文献。智能选择检索策略：中文优先
• qinyan-topic-analysis沁言学术AI选题分析 - 基于大量文献检索结果，为科研人员提供智能选题建议，包括选题方向、研究价值、研究内容概述、研究难点分析和相关文献推荐。使用沁言学术Ope