「sam」の検索結果

Build a differential-ready consensus peakset from per-replicate ATAC-seq peaks using iterative overlap removal, fixed-width re-centering, and majority-rule overlap. Use when generating a stable peak coordinate system for downstream differential accessibility, ML feature engineering, cross-sample comparison, or fixed-width peak counts; covers Corces 2018 iterative overlap (501 bp), DiffBind summit re-centering, and ENCODE consistency rules.

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Generates 3D conformer ensembles using RDKit ETKDGv3 with knowledge-enhanced distance geometry, MMFF94/UFF force-field optimization, CREST + GFN2-xTB semi-empirical refinement, and macrocycle-aware torsion preferences. Provides explicit decision rules for single vs ensemble conformer use, RMSD pruning, energy windows, conformer count, and force-field choice. Use when preparing 3D ligands for docking, generating descriptor input for 3D QSAR, or sampling macrocycle/peptide conformational ensembles.

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Plot per-group distributions of continuous data using boxplots, violins, beeswarms, quasirandom jitter, and raincloud plots with sample-size honesty (Weissgerber 2015), KDE-bandwidth awareness, and N-aware encoding choices. Use when comparing distributions across a small number of groups — expression per cluster, biomarker per arm, scores per condition — and the bar-of-mean default is misleading.

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Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts, plotBCV, sample distance heatmaps, and p-value histograms. Use when visualizing differential expression results.

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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.

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Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.

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Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating sample-specific reference sequences or reconstructing haplotypes.

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Visualizes ChIP-seq data using deepTools (computeMatrix, plotHeatmap, plotProfile, bamCoverage, bamCompare), pyGenomeTracks (modern INI-driven track plots), Gviz (R browser-style), EnrichedHeatmap (ComplexHeatmap-based), ChIPseeker tag heatmaps, and IGV batch screenshots. Handles bigWig normalization choices (CPM, BPM, RPGC, spike-in scaled), bamCompare operations (log2 ratio, subtract, SES), k-means clustering of heatmaps for biological subgrouping, and spike-in-scaled tracks for global-shift experiments. Use when generating publication-quality ChIP-seq signal heatmaps, profile plots, genome-browser tracks, or comparing samples visually.

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Call protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.

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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.

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Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.

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Run Bayesian phylogenetic analysis with MrBayes, BEAST2, RevBayes, and PhyloBayes including MCMC convergence diagnostics and model comparison. Use when needing posterior probability support, Bayesian model averaging, site-heterogeneous models for deep phylogenies, or formal model comparison via stepping-stone sampling.

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Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when annotating a new assembly of a species with an existing reference annotation or mapping annotations across related species.

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Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC. Use when summarizing QC metrics across samples, creating shareable quality reports, or building automated QC pipelines.

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Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.

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Trim PCR primers from aligned reads in amplicon-panel BAMs using samtools ampliconclip. Use when processing SARS-CoV-2 ARTIC, hereditary cancer panels, ctDNA hot-spot panels, or any amplicon assay where primer-derived bases would falsely confirm reference at primer footprints.

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Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences. Use when integrating multiple scRNA-seq batches or datasets.

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Proteina-Complexa flow-based protein backbone generation with fold-conditioned sampling guidance. Use this skill when: (1) Generating de novo protein backbones with hierarchical fold conditioning, (2) Exploring long-chain backbone generation beyond standard diffusion baselines, (3) Using NVIDIA Proteina-style flow matching workflows for controllable backbone design, (4) Comparing flow-based backbone generation against RFdiffusion or BoltzGen, (5) Prototyping fold-guided backbone campaigns before sequence design. This skill is based on the public NVIDIA Digital Bio Proteina project and uses "Proteina-Complexa" as the BioClaw-facing skill label. For sequence design after backbone generation, use proteinmpnn or solublempnn. For QC thresholds, use protein-design-qc.

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Python-first workflow for bulk RNA-seq expression intake, normalization, sample QC, and downstream-ready matrices.

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Use trace-mcp apply_codemod for any bulk mechanical change instead of repeated Edit calls. Activate whenever the same edit pattern would be applied 2+ times, across one file or many.

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CesiumJS terrain, globe, and environment - TerrainProvider, Globe, sampleTerrain, atmosphere, sky, fog, lighting, shadows, panoramas. Use when configuring terrain providers, querying terrain heights, customizing atmosphere or sky rendering, adding panoramas, or adjusting scene lighting and shadows.

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Run the konsistent CLI, review all reported violations, and fix them in the codebase. Use when the user wants to "fix konsistent violations", "resolve konsistent errors", "clean up konsistent diagnostics", "make konsistent pass", "address structural convention violations", or asks to run konsistent and act on the results. The skill is interactive: it requires explicit user decisions when many violations stem from the same rule (rule vs. code question), explicit user confirmation before modifying any code, and a triage step for non-trivial violations. For editing `konsistent.json`, this skill defers to the `konsistent-config` skill.

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Orchestrate approved, bounded work through a same-directory Codex App fork: create and name the execution task, ask it to run spec-executor, route decisions through Codex Task Messenger, validate the returned receipt, and archive a completed child. The source may come from any planning workflow. Requires Codex App task tools and codex-task-messenger.

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Migrate a test suite from one framework to another, incrementally and without losing coverage. Covers Selenium→Playwright, Cypress→Playwright, Jest→Vitest, Mocha→Vitest, and Protractor→Playwright, with parallel CI running, locator/assertion translation, and a coverage-parity track. Use when: "migrate tests," "switch framework," "Selenium to Playwright," "Jest to Vitest," "framework migration." Not for: bulk selector regeneration after a UI refactor on the SAME framework — use selector-drift-recovery. Not for: healing one flaky test at runtime — use test-reliability. Not for: modernizing patterns without changing framework — use ai-qa-review. Related: playwright-automation, cypress-automation, unit-testing, ci-cd-integration, test-reliability.

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