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Generate Circos configuration files for circular genomics data visualization. Supports genomic variations (SNPs, CNVs, structural variants), cell-cell communication networks, and custom track configurations for publication-ready circular plots.
Automated generation of baseline characteristics tables (Table 1) for clinical research papers.
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, process FASTQ/BAM/VCF, for developing and executing genomics pipelines.
Use when building a sample-level hierarchical clustering dendrogram from a bulk expression matrix and sample annotation table, especially for QC, batch inspection, or sample similarity assessment. Trigger keywords: hierarchical clustering, dendrogram, sample QC, batch inspection, sample similarit...
Use Bio.PDB to parse and analyze protein structures (PDB/mmCIF) for structural bioinformatics tasks; use when you need structure parsing, geometry calculations, or structural comparison/superposition.
Query the ChEMBL database for bioactive molecules, targets, bioactivities, and approved drugs; use this when you need to filter by physicochemical properties (e.g., MW, LogP), chemical structure (SMILES), or retrieve drug mechanism information.
Use when performing sample-level dimensionality reduction and visualization on abundance or OTU-style matrices with a companion group file, generating UMAP and/or t-SNE coordinates and plots for group separation assessment. NOT for: differential expression testing, single-cell workflows requiring...
Generates complete non-tumor biomedical machine learning research designs from a user-provided research direction. Always use this skill when users want to plan bioinformatics + ML papers for non-cancer diseases (metabolic, cardiovascular, kidney, inflammatory, autoimmune, infectious, neurologica...
Use when you need a standardized R CLI workflow to build a protein-protein interaction network from a local gene list and an offline STRING cache, export node and edge tables, and render a reproducible PDF network plot. NOT for online API fetching, arbitrary graph databases, multi-omics integrati...
Generates complete network toxicology + molecular docking research designs from a user-provided toxicant and disease/phenotype. Always use this skill when users want to investigate how an environmental toxicant, endocrine disruptor, heavy metal, food contaminant, pharmaceutical residue, or consum...
Access bioDBnet REST services for biological identifier conversion, pathway retrieval, and ortholog mapping. Use when you need to convert gene/protein IDs, find pathways, or retrieve biological annotations via bioDBnet.
Virtual gene knockout simulation using foundation models to predict transcriptional
PyTorch-native Graph Neural Network framework for molecules and proteins. Suitable for building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, and retrosynthesis. If you need pretrained m...
Detect copy number variations from whole genome sequencing data and generate publication-quality genome-wide CNV plots. Supports CNV calling, segmentation, and visualization for cancer genomics and rare disease analysis.
Generate forest plots for meta-analysis of continuous data. Input a CSV file containing study names, means, standard deviations, and sample sizes for experimental and control groups. Output forest plot PNG and data table CSV.
Predict neoantigens that may be recognized by the immune system based.
Extracts and summarizes key takeaways from documents, meeting notes, articles, and other text content. Use when the user asks for summaries, bullet points, main points, highlights, or a TL;DR of any document or body of text. Produces structured outputs such as numbered lists, executive summaries,...
Automatically summarize scientific podcasts like Huberman Lab and Nature.
Generates high-quality promotional soft articles with structured outlines, tailored introductions, and optimized titles based on product info and hot topics. Use when you need to write promotional content, "soft articles" (), or marketing copy that integrates product highlights with current trend...
Transform academic papers into university press releases for general.
Use this skill when converting academic papers to promotional and presentation formats, including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). This skill is suitable for paper dissemination, conference preparation, creating explorable...
Generates science popularization articles with titles and outlines based on medical topics and style preferences. Invoke when user needs to create medical/science popular content for public education.
Generates academic conference tweets and summaries by filtering abstracts, translating content, and creating engaging titles. Use when you need to process conference abstracts into social media content.
Generates a structured reading tweet from an academic paper (PDF, Word, or Text), highlighting specific product advantages. Use when the user wants to turn a document into a social media post or reading summary.
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