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Describe patterns that may indicate bad-faith or manipulative communication including gish gallop, whataboutism, tone policing, motte-and-bailey, sealioning, lying by omission, deflection, and strategic evasion. Use when the user suspects manipulation, notices repeated non-engagement, wants to analyze debate tactics, or mentions 'bad faith', 'deflection', 'manipulation', 'dodging the question', 'avoiding the issue', 'gaslighting', 'moving goalposts'. Describes behavioral patterns without making psychological diagnoses.

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Read-only audit of .codex/ structural overhead: 'remove X save Y tokens' vs the context window. NOT for cost tracking (budget skill); NOT for runtime read/compact decisions (mk:context-engineering).

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Bulk Confluence ops (10+ pages): bulk-label/move/delete via confluence-as; dry-run mandatory. NOT single-page (mk:confluence-page) or comments/attachments (mk:confluence-collaborate).

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Turn a raw idea into ONE honest recommendation: interview one question at a time until the problem, requirements, goals, non-goals, and constraints are CONFIRMED, then deliver a single verdict — do, don't, cheaper alternatives, trade-offs, ordered checklist, success metrics. Required: the user wants exactly ONE recommendation — not options, not a debate — and their framing is open to challenge (advise may answer a different question than the one asked). Triggers on "what should I do about X", "advise me on X", "am I approaching this right", "is this the right move". Do NOT use to be interrogated with no recommendation (→ mk:grill) — advise also interviews one question at a time, but only to reach a verdict. Do NOT use when the framing is settled and only the options are open (→ mk:brainstorming). Do NOT use to decide whether something is worth building (→ mk:office-hours). Do NOT use when you want several perspectives to argue it out (→ mk:party).

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Confluence page CRUD via the confluence-as wrapper. Triggers: 'create page in SPACE', 'show me page 12345', 'update title of page 12345', 'delete page 12345', 'page hierarchy under 12345', 'copy page 12345 to SPACE'. NOT for bulk ops on 10+ pages (mk:confluence-bulk); NOT for spec analysis (mk:confluence-spec-analyst); NOT for comments/attachments/labels (mk:confluence-collaborate).

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Read-only audit of `.claude/` structural overhead. Reports prioritized "remove X save Y tokens" recommendations against the model context window. NOT for monetary cost tracking — that's /mk:budget. NOT for transcript size monitoring — long-session continuity defers to Claude Code native compaction. NOT for runtime context decisions (what to read, when to compact) — see mk:context-engineering. Use when planning to add context capacity, diagnosing perceived slowdowns, or auditing health.

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Connect business positioning to a concrete visual language. Maps strategic positioning (category, differentiator, who-it's-for, who-it's-against) onto visual decisions — palette, type, imagery, tone — so the look reinforces the strategy. Use when the user says "positioning into visuals", "what should the brand look like given our strategy", "align visuals with positioning", or is moving from strategy to brand expression. Part of the Creative Production set.

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Rework a change as if the intended UX and architecture had existed from day one — deleting compatibility cruft, dead branches, and accidental complexity instead of patching around them. Use when refactoring, cleaning up after a feature lands, removing flags, collapsing legacy paths, or when the user says the code "should look like X from scratch".

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Migrates React projects and components from Radix UI to Base UI. Use when asked to migrate from radix, move to base-ui, convert radix primitives, or switch a shadcn project's base library. Handles single components ("migrate accordion") and whole projects.

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Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM. Use when subsetting a FASTA/FASTQ file, removing unwanted or low-quality records, or selecting records by specific criteria. Use the paired-end-fastq skill instead whenever the input is paired R1/R2 reads.

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Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.

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Build Sankey, alluvial, river, and CONSORT-style flow diagrams to visualize cohort transitions, cell-state changes, or pipeline filtering using ggalluvial, networkD3, plotly, and consort. Use when showing how entities move between categories across timepoints (cell states, drug response classes, patient flow through a trial) or filtering pipelines (variants filtered through QC stages).

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Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias analysis.

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Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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Computes and interprets treatment effect measures (OR, RR, RD, HR, NNT) with calibrated confidence intervals (Wilson, Newcombe, Miettinen-Nurminen, MOVER, profile likelihood, Bender NNT) and reports marginal vs conditional estimands per FDA 2023 covariate adjustment guidance. Use when reporting treatment effects in confirmatory trials, comparing effect sizes across studies, or constructing forest plots.

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Call accessible chromatin regions from ATAC-seq BAM files using MACS3, MACS2, Genrich, or HMMRATAC. Use when identifying open chromatin from aligned ATAC-seq, choosing between point-source vs HMM peak callers, applying ENCODE-style pseudoreplicate IDR, removing blacklist regions, or fixing 501bp consensus peaks for downstream differential analysis.

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Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.

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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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Create and manage database migrations with reversible changes, proper naming conventions, and zero-downtime deployment strategies. Use this skill when creating database migration files, modifying schema, adding or removing tables/columns, managing indexes, or handling data migrations. Apply when working with migration files (e.g., db/migrate/, migrations/, alembic/, sequelize migrations), schema changes, database versioning, rollback implementations, or when you need to ensure backwards compatibility during deployments. Use for any task involving database structure changes, index creation, constraint modifications, or data transformation scripts.

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Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.

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If CGM fails or is removed, revert the insulin pump to manual mode provided basic criteria for pump use in hospital are still met. Trigger phrase: "CGM failed, should we switch pump to manual mode?

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Remove signs of AI-generated writing from text. Use when editing or reviewing text to make it sound more natural and human-written. Based on Wikipedia's comprehensive "Signs of AI writing" guide. Detects and fixes patterns including: inflated symbolism, promotional language, superficial -ing analyses, vague attributions, em dash overuse, rule of three, AI vocabulary words, negative parallelisms, and excessive conjunctive phrases. Credits: Original skill by @blader - https://github.com/blader/humanizer

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。