Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.
Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
Evaluate a skill's effectiveness by running test cases and grading results. Use when you want to test whether a skill produces correct guidance, validate skill improvements, or benchmark a skill before release.
Synchronize dev and main branches for LAMB releases, including merging changes, creating version tags, and bumping version numbers in code. Use this skill when creating a new release, syncing branches, or tagging a version.
Retrieves, organizes, and interprets laboratory Observation resources with clinical context. Use when user asks to "interpret labs", "review lab results", "what do these labs mean", "explain my bloodwork", "check labs", "lab trends", "abnormal labs", or needs clinical interpretation of laboratory values. Do NOT use for vital signs, imaging results, pathology reports, or non-laboratory Observations.
Assign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and identify emerging variants of concern. Use when classifying viral sequences, tracking lineage dynamics, or monitoring for variants of concern.
Calculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing repertoire diversity, finding shared clonotypes, or comparing immune profiles between conditions.
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying problematic samples before analysis.
Differential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.
Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality.
Quality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when assessing data quality before analysis or troubleshooting problematic acquisitions.
Designs experiments to minimize and account for batch effects using balanced layouts and blocking strategies. Use when planning multi-batch experiments, assigning samples to sequencing lanes, or designing studies where technical variation could confound biological signals.
Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes.
Mass spectrometry raw data quality control using PTXQC, rawTools, or MSstatsQC.
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka). Essential for improving long-read assembly accuracy. Use when improving assembly accuracy with polishing tools.
Validate, gap-fill, and curate genome-scale metabolic models using memote for quality scores and COBRApy for manual curation. Ensure models meet SBML standards and produce biologically meaningful predictions. Use when improving draft models or preparing models for publication.
Print labels on the lab's Zebra ZD411 printer (2"x1" labels). Use when asked to print labels, tube labels, box labels, sample labels, or anything involving the Zebra/label printer. Supports text labels, barcodes, and raw ZPL.
Remote debugging for BEAM/Elixir in production-like environments. Use when you need to enter a live container or host via kubectl exec or ssh to run IEx/remote RPC, reproduce issues, and collect telemetry/metrics safely with human-in-the-loop approval.
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
