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Use when evaluating the clinical utility of a binary prediction model from a single clinical CSV file by fitting a logistic decision-curve model, plotting decision and clinical-impact curves, and expo…
Analyzes clinical diagnostic accuracy studies for bias using the QUADAS-2 tool. Use when Claude needs to assess the quality, risk of bias, or applicability of diagnostic accuracy studies (e.g., \"Asse…
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.
Use when building a decision tree model in R and generating feature importance ranking outputs. Supports classification and regression, automatic task detection, parameter validation, model evaluation…
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…
Use when screening differentially expressed genes from a bulk expression matrix between two user-specified groups, producing DEG tables, a volcano plot, and a clustered heatmap. Triggers include DEG a…
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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…