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Use when selecting predictive genes or other molecular features from bulk expression matrices for binary case-vs-control classification with elastic net logistic regression, including coefficient path…
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Annotate variants with functional effects using SnpEff or Ensembl VEP, adding gene impact, population frequencies, and clinical significance.
Comprehensive geospatial science skill covering remote sensing, GIS, spatial analysis, machine learning for earth observation, and 30+ scientific domains. Supports satellite imagery processing (Sentin…
Converts a biomedical study storyline into a graphical abstract and, when direct image capability is available, generates the graphical abstract directly; otherwise it falls back to prompts, Mermaid f…
Parameter-efficient fine-tuning for LLMs using LoRA, QLoRA, and 25+ methods. Use when fine-tuning large models (7B-70B) with limited GPU memory, when you need to train <1% of parameters with minimal a…
Build a traceability manifest linking analysis scripts to inputs, outputs, and manuscript figures or tables. Use when documenting a computational pipeline or locating the source of a reported artefact…
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Use when validating an existing prognostic risk signature on an external bulk expression cohort with survival outcomes, producing risk scores, Kaplan-Meier curves, risk distribution plots, heatmap, an…
Assess alignment quality with coverage depth, mapping rates, insert size, and on-target metrics using samtools, mosdepth, and picard.
Call SNVs and indels from aligned BAMs using GATK HaplotypeCaller or DeepVariant with optional GVCF output for joint genotyping.
Writes Specific Aims pages for grant applications. Use when drafting or revising the Specific Aims page (NIH R01/R21/R03), NSF Project Summary, or equivalent for any major funding agency. Also trigger…
Expert guidance for GRPO/RL fine-tuning with TRL for reasoning and task-specific model training
Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial g…
Perform advanced PubMed search with field qualifiers - author, title, journal, MeSH, date range, article type. Constructs proper PubMed query syntax from natural language. Use for precise filtered sea…
Use this skill to compute ESTIMATE immune-related microenvironment scores from a bulk expression matrix, generate an ESTIMATE score heatmap, and optionally generate group-wise ESTIMATE score boxplots …
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Align short reads to a reference genome with BWA-MEM2, sort and index with samtools, and mark duplicates with picard.
Filter raw variant calls using GATK VQSR, GATK hard filters, or bcftools expression-based filtering.
Drafting and reviewing European fellowship and grant applications (Marie Skłodowska-Curie Actions, Horizon Europe, ERC, EIC). Covers the Excellence/Impact/Implementation triad, gender dimension and se…
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Export PubMed paper(s) to Zotero or save as RIS file. Supports single paper by PMID or batch export from search results. Use when user wants to save papers to their reference manager.