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Use when analyzing bulk RNA-seq or microarray expression data to identify differentially expressed genes between two biological groups (case vs control), with volcano plots and heatmap visualization. …
Download files from the NCI Genomic Data Commons (GDC) using the GDC Data Transfer Tool and REST API, supporting both open-access and controlled-access data.
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…
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Download supplementary data files, series matrices, and raw FASTQ links from NCBI GEO for a given GSE series or GSM sample accession.
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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
Composes a Discussion around key findings, mechanisms, clinical relevance, and limitations. Use when writing or improving a Discussion section for any biomedical manuscript — including interpreting re…
Download raw sequencing data from NCBI SRA as FASTQ files using prefetch and fasterq-dump, with support for single accessions, batch lists, and BioProject expansion.
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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