leonchaox/qinyan-academic-skills
59 skills · 2,786 total installs
$npx skills add leonchaox/qinyan-academic-skillsSkillInstalls
citation-managementComprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and…literature-reviewConduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.).research-lookupLook up current research information using the Parallel Chat API (primary) or Perplexity sonar-pro-search (academic paper searches).research-proposalGenerate academic research proposals for PhD applications. Use when user asks to "write a research proposal", "create PhD proposal", "generate research plan",…scientific-writingCore skill for the deep research and writing tool. Write scientific manuscripts in full paragraphs (never bullet points).paper-slide-deckGenerate professional slide deck images from academic papers and content.peer-reviewStructured manuscript/grant review with checklist-based evaluation.ggetFast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis.medical-imaging-reviewWrite comprehensive literature reviews for medical imaging AI research.openalex-databaseQuery and analyze scholarly literature using the OpenAlex database.paper-2-webThis skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation…pptx-postersCreate research posters using HTML/CSS that can be exported to PDF or PPTX.research-grantsWrite competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC.scholar-evaluationSystematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across research quality dimensions including problem…scientific-schematicsCreate publication-quality scientific diagrams using Nano Banana 2 AI with smart iterative refinement. Uses Gemini 3.1 Pro Preview for quality review.scientific-slidesBuild slide decks and presentations for research talks. Use this for making PowerPoint slides, conference presentations, seminar talks, research presentations,…scikit-bioBiological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick…arboretoInfer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3).bgpt-paper-searchSearch scientific papers and retrieve structured experimental data extracted from full-text studies via the BGPT MCP server.biorxiv-databaseEfficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or…bioservicesUnified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with…consciousness-councilRun a multi-perspective Mind Council deliberation on any question, decision, or creative challenge.deepchemMolecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive…dhdna-profilerExtract cognitive patterns and thinking fingerprints from any text.flowioParse 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…generate-imageGenerate or edit images using AI models (FLUX, Nano Banana 2).hypothesis-generationStructured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with…infographicsCreate professional infographics using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review.latex-postersCreate professional research posters in LaTeX using beamerposter, tikzposter, or baposter.markdown-mermaid-writingComprehensive markdown and Mermaid diagram writing skill. Use when creating any scientific document, report, analysis, or visualization.parallel-webSearch the web, extract URL content, and run deep research using the Parallel Chat API and Extract API.perplexity-searchPerform AI-powered web searches with real-time information using Perplexity models via LiteLLM and OpenRouter.pubmed-databaseDirect REST API access to PubMed. Advanced Boolean/MeSH queries, E-utilities API, batch processing, citation management.pyzoteroInteract with Zotero reference management libraries using the pyzotero Python client.scientific-brainstormingCreative research ideation and exploration. Use for open-ended brainstorming sessions, exploring interdisciplinary connections, challenging assumptions, or…scientific-critical-thinkingEvaluate scientific claims and evidence quality. Use for assessing experimental design validity, identifying biases and confounders, applying evidence grading…scientific-visualizationMeta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel layouts, significance annotations, error bars,…venue-templatesAccess comprehensive LaTeX templates, formatting requirements, and submission guidelines for major scientific publication venues (Nature, Science, PLOS, IEEE,…what-if-oracleRun structured What-If scenario analysis with multi-branch possibility exploration.anndataData structure for annotated matrices in single-cell analysis. Use when working with .h5ad files or integrating with the scverse ecosystem.biopythonComprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access…cellxgene-censusQuery the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated…datamolPythonic wrapper around RDKit with simplified interface and sensible defaults.deeptoolsNGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…diffdockDiffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design.etetoolkitPhylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for…genimlThis skill should be used when working with genomic interval data (BED files) for machine learning tasks.gtarsHigh-performance toolkit for genomic interval analysis in Rust with Python bindings.lamindbThis skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR.nssfc-proposal撰写国家社会科学基金（NSSFC）年度项目申请书，依据 2025…phylogeneticsBuild and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML).pydeseq2Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq…pysamGenomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing…scanpyStandard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and…scveloRNA velocity analysis with scVelo. Estimate cell state transitions from unspliced/spliced mRNA dynamics, infer trajectory directions, compute latent time, and…scvi-toolsDeep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with…tiledbvcfEfficient storage and retrieval of genomic variant data using TileDB.zarr-pythonChunked N-D arrays for cloud storage. Compressed arrays, parallel I/O, S3/GCS integration, NumPy/Dask/Xarray compatible, for large-scale scientific computing…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流：基本信息、摘要、立项依据、研究内容、研究基础、个人简历、伦理与AI辅助声明等模块；内置文献检索策略与质量自查清单。工具中性，适配 Claude Code…