mdbabumiamssm/LLMs-Universal-Life-Science-and-Clinical-Skills- - الصفحة ١١

prs-net-deep-learning-agent

Geometric deep learning-based polygenic risk score prediction using PRS-Net for modeling gene interactions, enhanced disease prediction, and cross-ancestry portability.

لغة النص الأصلي: الإنجليزية

deep-visual-proteomics-agent

AI-driven integration of cellular imaging, laser microdissection, and ultra-sensitive mass spectrometry for spatially-resolved single-cell proteomics.

لغة النص الأصلي: الإنجليزية

core-python-best-practices

Essential guidelines for writing modern, type-safe, and idiomatic Python 3 code.

لغة النص الأصلي: الإنجليزية

pandas-best-practices

Standards for efficient, readable, and performant data manipulation using Python's Pandas library.

لغة النص الأصلي: الإنجليزية

nextjs-best-practices

Guidelines for building scalable, SEO-friendly applications with Next.js (App Router).

لغة النص الأصلي: الإنجليزية

react-best-practices

A comprehensive guide and rule set for writing clean, performant, and maintainable React code.

لغة النص الأصلي: الإنجليزية

cryoem-ai-drug-design-agent

AI-powered integration of cryo-EM structural data with generative AI and molecular dynamics for structure-based drug design targeting flexible proteins and membrane complexes.

لغة النص الأصلي: الإنجليزية

time-resolved-cryoem-agent

AI-powered time-resolved cryo-EM analysis for capturing protein dynamics, drug-binding kinetics, and conformational transitions for dynamics-based drug discovery.

لغة النص الأصلي: الإنجليزية

deep-research-swarm

Multi-agent research literature analysis

لغة النص الأصلي: الإنجليزية

bio-single-cell-clustering

scRNA-seq clustering analysis

لغة النص الأصلي: الإنجليزية

biokernel

Biomedical OS Core & MCP Server

لغة النص الأصلي: الإنجليزية

meta-prompter

Automatic prompt engineering & optimization

لغة النص الأصلي: الإنجليزية

nano-banana

AI-powered reasoning image engine for generating and editing high-quality biomedical infographics and realistic images.

لغة النص الأصلي: الإنجليزية

paper-banana

Agentic framework for automating the generation of publication-ready academic illustrations and statistical plots.

لغة النص الأصلي: الإنجليزية

clinical-trial-protocol-skill

Generate clinical trial protocols for medical devices or drugs. This skill should be used when users say "Create a clinical trial protocol", "Generate protocol for [device/drug]", "Help me design a clinical study", "Research similar trials for…

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-compartment-analysis

Detect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B) chromatin compartments from contact matrices. Use when identifying A/B compartments from Hi-C data.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-contact-pairs

Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data. Use when processing raw Hi-C read pairs.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-hic-data-io

Load, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format, access matrix data, and export to different formats. Use when loading or converting Hi-C contact matrices.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-hic-differential

Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-hic-visualization

Visualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle plots, virtual 4C, and multi-track figures. Use when visualizing contact matrices or genomic features.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-loop-calling

Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-matrix-operations

Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.

لغة النص الأصلي: الإنجليزية

bio-hi-c-analysis-tad-detection

Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-clinvar-lookup

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-dbsnp-queries

Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-gnomad-frequencies

Query gnomAD for population allele frequencies to assess variant rarity. Use when filtering variants by population frequency for rare disease analysis or determining if a variant is common in the general population.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-hla-typing

Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-myvariant-queries

Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-pharmacogenomics

Query PharmGKB and CPIC for drug-gene interactions, pharmacogenomic annotations, and dosing guidelines. Use when predicting drug response from genetic variants or implementing clinical pharmacogenomics.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-polygenic-risk

Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-somatic-signatures

Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes. Use when identifying DNA damage mechanisms or etiology in cancer genomes.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-tumor-mutational-burden

Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

لغة النص الأصلي: الإنجليزية

bio-clinical-databases-variant-prioritization

Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-circos-plots

Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, variants, CNVs, and interaction arcs. Use when creating circular genome visualizations.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-color-palettes

Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-genome-browser-tracks

Generate genome browser visualizations using pyGenomeTracks or IGV batch scripting for publication figures. Use when creating publication figures of genomic regions with multiple data tracks.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-genome-tracks

Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks, Gviz, and IGV. Use when visualizing genomic data at specific loci with multiple aligned tracks.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-ggplot2-fundamentals

Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-panel layouts. Use when creating static figures for papers, presentations, or reports in R.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-heatmaps-clustering

Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization. Use when visualizing expression patterns across samples or identifying co-expressed gene clusters.

لغة النص الأصلي: الإنجليزية

bio-data-visualization-interactive-visualization

Create interactive HTML plots with plotly and bokeh for exploratory data analysis and web-based sharing of omics visualizations. Use when building zoomable, hoverable plots for data exploration or web dashboards.

لغة النص الأصلي: الإنجليزية