683 skills · sorted by relevance
Für Beziehungsmatrix Personen/Taten: ordnet Norm, Beweislast und Gegenargument; Ergebnis: Prüfprodukt mit Risiko und nächstem Schritt.
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Build, refresh, report, or probe an accessibility coverage matrix across criteria, surfaces, and evidence methods. Use when assessing coverage with the accessibility runtime harness and generated evidence bundle.
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Use this skill when producing a polished, Commonly-branded deliverable (.docx brief / memo, .xlsx data matrix, .pptx deck) and you do not have specific brand guidance from the user. Trigger on: 'write me a brief', 'one-pager', 'memo', 'data sheet', 'status matrix', 'short deck', 'summary deck', 'closing slide', 'final deliverable'. Routes to `officecli merge` with one of three pre-built starter templates that already carry the Commonly palette, fonts, and structure — so you populate content with one merge call instead of 30 individual `officecli set` commands. DO NOT use for fundraising decks (use `officecli-pitch-deck`), academic papers (use `officecli-academic-paper`), or financial models (use `officecli-financial-model`).
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Compare two or more companies, products, or platforms across pricing, features, positioning, and docs. Use this skill whenever the user says "compare X vs Y", "how does X stack up against Y", "alternatives to X", "competitive landscape of …", "X vs Y vs Z", or asks for a competitor matrix. Uses search to discover competitors when the user only names a category, then scrape for each competitor's homepage, pricing page, and features/docs. Returns a normalized comparison matrix as JSON.
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Quality control for IMC/MIBI data across pixel, channel, image, slide, and batch levels, covering Poisson-count SNR (cell-level Gaussian-mixture and empty-channel comparison), spillover-matrix QC (the three physical sources), drift and the missing EQ-bead analog, acquisition artifacts, and sample-of-origin batch effects. Use when deciding whether to keep or drop a channel, ROI, or slide, distinguishing a dim antibody from a failed one, reading a spillover matrix, or diagnosing batch-driven clustering before analysis.
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Balances Hi-C contact matrices (ICE via cooler.balance_cooler, KR/SCALE/VC context), computes distance-decay expected with cooltools (expected_cis per-diagonal P(s), expected_trans scalar), builds observed/expected (O/E) matrices, and diagnoses polymer state from the P(s) log-derivative. Covers the within-matrix-vs-cross-sample distinction (balancing is NOT a normalizer), the equal-visibility assumption that CNV/aneuploidy violates (use raw counts for copy-number), cis-only balancing, mad_max/blacklist masking before balancing, multiplicative cooler weights vs divisive juicer weights, and the resolution-vs-depth budget. Use when balancing a .cool/.mcool, computing expected or P(s), making O/E matrices for compartments/loops, deciding ICE vs KR vs SCALE, choosing a resolution for a given depth, or troubleshooting NaN/all-NaN balanced matrices; route cross-sample comparison to hic-differential.
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Corrects fluorophore spillover (conventional compensation) or spectral overlap (spectral unmixing) and applies variance-stabilizing transforms (logicle/biexponential, arcsinh, log) for flow and mass cytometry. Covers spillover-matrix estimation from single-stain controls, AutoSpill, the spillover spreading matrix and why panel design (not compensation) bounds resolution, compensate-then-transform ordering, and arcsinh cofactor choice (5 for CyTOF, ~150 for fluorescence, per-channel via flowVS). Use when correcting spectral overlap, preparing data for gating/clustering, choosing logicle vs arcsinh, deciding a cofactor, or distinguishing compensation from spectral unmixing.
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Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or tximeta, RSEM, 10X Genomics MTX/H5, AnnData H5AD, and RDS. Handles silent-miscounting traps (featureCounts -p v2.0.2 API break, STAR strandedness column choice, salmon NumReads-sum without tximport, RSEM non-integer expected_count, GENCODE _PAR_Y suffix, zero-length-transcript TPM divide-by-zero), and encodes the tximport countsFromAbundance decision tree with the "lengthScaledTPM is not TPM" warning. Use when assembling a gene-by-sample count matrix from aligner or quantifier output, importing salmon/kallisto for DESeq2 vs limma-voom, choosing strandedness column for STAR, debugging zero-count panics, or building tx2gene mapping.
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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.
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Analyzes pooled CRISPR screens with MAGeCK (Li et al 2014), covering count generation (mageck count), the RRA two-condition workflow (mageck test using alpha-RRA over per-sgRNA negative-binomial p-values), the MLE multi-condition workflow (mageck mle with explicit design matrix and beta-score output), normalization choice (median vs total vs control-sgRNA vs spike-in), sgRNA efficiency injection, paired-sample testing, time-course design, drug-screen versus dropout-screen design matrices, MAGeCKFlute and MAGeCK-VISPR downstream visualization, and decision logic for when to use MAGeCK vs JACKS / BAGEL2 / drugZ / Chronos. Use when running a fresh CRISPR screen analysis, picking RRA vs MLE for the experimental design, choosing a normalization method from QC signatures, debugging MLE convergence failure or NaN beta scores, comparing MAGeCK output across tools, or building a batch-aware multi-cell-line / multi-condition MLE design matrix.
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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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Generate correct MATLAB code using the Symbolic Math Toolbox. Use when the user asks for symbolic computations, analytical solutions, symbolic differentiation/integration, equation solving, or converting symbolic results to numeric MATLAB functions. Also use when converting differential equations to transfer functions or state-space form, extracting PDE coefficients (pdeCoefficients), symbolic-to-C code generation (matlabFunction + codegen), symbolic matrix variables (symmatrix), physical units and constants (symunit, newUnit), or rewriting/combining algebraic expressions (rewrite, combine).
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Exchange data between Excel and MATLAB using Spreadsheet Link VBA macros and worksheet functions. Use when writing Excel VBA macros that call MLPutMatrix, MLGetMatrix, MLPutVar, MLGetVar, MLPutRanges, MLEvalString, MLGetFigure, or MatlabRequest.
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Extract structured data from multiple documents into comparison matrix with citations. Use for bulk document review.
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Structured legal risk assessment with 5x5 Severity x Likelihood matrix. Use for risk scoring, risk registers, escalation decisions, and risk memos.
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Run cohort analysis: retention matrix and LTV by cohort. Churn scoring → churn-risk. "build a retention matrix"
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Synthesise completed KUD charts into a developmental progression matrix and per-competency narrative sections. Use when you need a programme-level view of how knowledge, understanding, and performance develop across bands.
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Guide to analyze multiple documents (PDF, DOCX) against user-defined columns and produce a structured Excel output with citations. Use when the user wants to: (1) Extract specific information from multiple documents into a table, (2) Compare clauses or provisions across contracts, (3) Create a document review matrix with source citations. Triggers on: 'tabular review', 'document matrix', 'extract from documents', 'compare across documents', 'review multiple contracts'.
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An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.
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Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.
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Conduct full competitor strategy breakdowns across SEO, ads, social, email, pricing, and positioning. Use when the user asks to analyze competitors, benchmark against rivals, understand competitive landscape, find competitor weaknesses, or build a competitive matrix. Trigger phrases include "competitor analysis", "competitive analysis", "who are my competitors", "competitor research", "competitive landscape", "benchmark competitors", "competitor ads", "competitor SEO", "competitor pricing", "SWOT analysis", "competitive matrix".
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Rewrite `outline/claim_evidence_matrix.md` as a projection/index of evidence packs (NO PROSE), so claims/axes are driven by `outline/evidence_drafts.jsonl` rather than outline placeholders.
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Deterministic palette/matrix pixel art (not AI). Use for procedural tile art, color-quantized output, matrix sprites.
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Estimate a covariance / correlation / precision matrix incrementally with precise. Use when data arrives as a stream and you want the matrix updated per observation, or when you want an online (partial_fit) drop-in for sklearn.covariance, which is batch-only.
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