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概要と使いどころ
A set of resources to help me write all kinds of internal communications, using the formats that my company likes to use. Claude should use this skill whenever asked to write some sort of internal communications (status reports, leadership updates, 3P updates, company newsletters, FAQs, incident reports, project updates, etc.).
日本語の概要は準備中です。原文の説明を表示しています。
Performs set operations on genomic intervals - intersect (-wa/-wb/-wo/-wao/-loj/-c/-v/-u), subtract (-A), merge (-d, -c/-o), complement, cluster, multiinter, unionbedg, map, and groupby - with bedtools (CLI) and pybedtools/pyranges/bioframe (Python). Covers the sorted-input contract and the -sorted chromosome-order footgun, reciprocal/fractional overlap (-f/-F/-r/-e) and the A-vs-B asymmetry, -split for spliced/BED12/BAM features, and jaccard/fisher as mechanics only. Use when finding overlapping or unique regions between BED/peak/feature files, building consensus peaksets, removing blacklisted regions, transferring annotation values onto intervals, or computing interval-set similarity; route overlap-significance testing to overlap-significance.
日本語の概要は準備中です。原文の説明を表示しています。
Performs proximity operations on genomic intervals with bedtools (closest, window, flank, slop) and pybedtools - nearest-feature queries with signed/strand-aware distance, fixed-radius window searches, strand-aware promoter construction, and interval extension. Covers the closest -d/-D a/b/ref/-t/-k/-io/-iu/-id flags, the -D ref strand sign-flip, silent chromosome-end clipping in slop/flank, -t all tie double-counting, and the critical distinction between a geometry answer (nearest TSS) and a biology answer (which gene an element regulates). Use when assigning peaks or variants to genes, defining promoters from a gene model, building distance-to-TSS distributions, finding features within a window, or extending intervals - and when deciding whether nearest-gene is a fair prior (GWAS locus) or a trap (distal enhancer).
日本語の概要は準備中です。原文の説明を表示しています。
Assign cell types from marker expression in IMC/MIBI data using clustering (PhenoGraph/FlowSOM/Leiden/Pixie), marker-based probabilistic classifiers (Astir), or image-context CNNs (CellSighter), covering the double-positive segmentation artifact, lineage-vs-state markers, the two spillover types, and why a "cell type" in imaging is conditioned on a segmentation guess. Use when phenotyping segmented IMC cells, choosing clustering vs classification, diagnosing implausible double-positive populations, separating lineage from functional markers, or transferring labels across a cohort.
日本語の概要は準備中です。原文の説明を表示しています。
Identify tumor neoantigens from somatic variants with pVACtools (pVACseq/pVACfuse/pVACbind/pVACvector/pVACview) for personalized cancer vaccines and checkpoint biomarkers. Encodes the field's hard truth that binding prediction is the easy, near-solved part and single-digit-percent PPV lives downstream — so it centers clonality/CCF, HLA LOH (the silent invalidator), expression, proximal-variant phasing, agretopicity/foreignness quality, and the predicted->presented->immunogenic validation tiers. Use when nominating vaccine targets, ranking neoantigens, or building a tumor-to-candidate pipeline. Binding details in mhc-binding-prediction; ranking in immunogenicity-scoring.
日本語の概要は準備中です。原文の説明を表示しています。
Detects acquired antimicrobial-resistance determinants and chromosomal point-mutation resistance in bacterial assemblies using AMRFinderPlus, ResFinder 4.0 (acquired + PointFinder), CARD-RGI, abritAMR, staramr, and species-specific callers (TB-Profiler, Mykrobe). Harmonises cross-tool output via hAMRonization, contextualises determinants with mobile-genetic-element annotation (MOB-suite, PlasmidFinder, MobileElementFinder, ICEberg), predicts phenotype against EUCAST or CLSI breakpoints, and translates calls into WHO GLASS reporting categories. Use when screening clinical or surveillance isolates for AMR, distinguishing acquired vs intrinsic vs point-mutation resistance, calling rpoB / katG / pncA / gyrA / mgrB mutations, reconciling AMRFinderPlus vs RGI vs ResFinder disagreement, contextualising carbapenemases or mcr alleles on plasmids, predicting susceptibility from genotype against the WHO Mtb 2nd-edition catalogue, or building a hAMRonized multi-lab AMR surveillance pipeline.
日本語の概要は準備中です。原文の説明を表示しています。
Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetical-reference-level trap (relevel BEFORE DESeq), LRT reduced-model rules, the interaction-term resultsNames trap, continuous-covariate scaling and splines, repeated measures via duplicateCorrelation or dream, high-cardinality categorical pseudo-singular designs, sample swap detection via XIST/RPS4Y1 expression and somalier/NGSCheckMate genotypes, SABV (sex-as-biological-variable) mandate, Simpson's-paradox collapsing of technical replicates, and the `~ 0 + group` parameterization for clean contrasts. Use when building a design matrix, troubleshooting reversed fold-change direction, encoding paired or repeated-measures designs, detecting sample swaps, deciding sex-as-covariate, or aggregating technical replicates.
日本語の概要は準備中です。原文の説明を表示しています。
Build OncoPrint and co-mutation matrix plots from somatic-variant cohorts using ComplexHeatmap, maftools, and comut.py with alteration-type stacking, sample ordering by mutational burden, mutual-exclusivity overlays, and clinical annotation tracks. Use when visualizing per-sample mutation patterns across recurrent driver genes, comparing alteration classes, or identifying mutually-exclusive / co-occurring driver pairs.
日本語の概要は準備中です。原文の説明を表示しています。
Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.
日本語の概要は準備中です。原文の説明を表示しています。
Detect somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
日本語の概要は準備中です。原文の説明を表示しています。
Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.
日本語の概要は準備中です。原文の説明を表示しています。
Use this skill when the user asks about cybersecurity for a trucking carrier — protecting ELD data, customer information, financial systems, EDI integrations, fleet telematics, ransomware risk, vendor / shipper data sharing, incident response, and FMCSA cyber-recommendations. Reference NIST + CISA cybersecurity frameworks.
日本語の概要は準備中です。原文の説明を表示しています。
Enter explore mode - a thinking partner for exploring ideas, investigating problems, and clarifying requirements. Use when the user wants to think through something before or during a change.
日本語の概要は準備中です。原文の説明を表示しています。
Dense UI posture — maximum information density with clear hierarchy. Use when building or reworking admin dashboards, data tables and grids, ops or monitoring views, settings-heavy panels, debug inspectors, state or log viewers, and multi-pane tool UIs someone drives all day.
日本語の概要は準備中です。原文の説明を表示しています。
The Platform List: Arman's own register of large platform-level work he chose not to start yet. Use when the reminder hook says a row is due, when Arman says to add, snooze, kill, or finish a row, when you own a row, or when you think something belongs there. NOT for ordinary tasks, defects, or handoffs.
日本語の概要は準備中です。原文の説明を表示しています。
Retired pointer for chat message-action docs. Use when something references message-actions-overlay-system; read the overlay-system skill's 'Message actions (chat)' section instead.
日本語の概要は準備中です。原文の説明を表示しています。
Retired pointer for Next.js SSR doctrine. Use when something references nextjs-ssr-architecture; read the ssr-zero-layout-shift skill instead.
日本語の概要は準備中です。原文の説明を表示しています。
The agent.review_queue register for work Arman must see or test in the UI. Use at the end of any task that produced something reviewable, at the start of a task to check prior feedback, and when reviewing, claiming, routing, or repairing a queue row.
日本語の概要は準備中です。原文の説明を表示しています。
Diagnostic method for any bug, failure, regression, flake, or slowdown. Use before proposing a fix: something is broken, throwing, not saving, not showing, or 'worked yesterday'; on 'debug this' or 'find the root cause'; and immediately after a fix attempt did not work.
日本語の概要は準備中です。原文の説明を表示しています。
Safe removal of a duplicate component in favor of the one being kept. Use when asked to remove a component in favor of another, eliminate duplicates, reduce two versions of something to one, or clean up redundant UI components.
日本語の概要は準備中です。原文の説明を表示しています。
Recipe for an agent building a small custom web app (an Applet) for one person or business on THEIR OWN store tables, live at aimatrx.com/applets/<slug>. Use when asked to build an app, portal, calendar, tracker, dashboard screen or client view on someone's tables/data in AI Matrx. NOT for platform features (use build-sub-feature) or tables the platform keeps for itself (defineTypedTable).
日本語の概要は準備中です。原文の説明を表示しています。
Analyze an idea, proposal, change, claim, or decision from facts through problem, value, mechanism, consequences, evidence, alternatives, and action. Use when the user asks what something is for, why it matters, whether it is worth doing, what impact it has, or how to decide. Do not use for simple factual lookup or straightforward execution.
日本語の概要は準備中です。原文の説明を表示しています。
Pushes interfaces past conventional limits with technically ambitious implementations — shaders, spring physics, scroll-driven reveals, 60fps animations. Use when the user wants to wow, impress, go all-out, or make something that feels extraordinary.
日本語の概要は準備中です。原文の説明を表示しています。
Performs a final quality pass fixing alignment, spacing, consistency, and micro-detail issues before shipping. Use when the user mentions polish, finishing touches, pre-launch review, something looks off, or wants to go from good to great.
日本語の概要は準備中です。原文の説明を表示しています。