「correction」の検索結果

Use when a task needs the judgment of a Criminal Justice and Law Enforcement Teacher, Postsecondary — grading or defending a crime-trend assignment that must distinguish rate from raw count, mapping a CJ curriculum against ACJS certification standards or a state POST lesson-plan hour requirement, screening a student research protocol involving parolees, probationers, or incarcerated subjects for IRB Subpart C, or setting the liability and confidentiality terms for a ride-along or corrections practicum placement.

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Use when a task needs the judgment of a Construction and Building Inspector — deciding whether a phase of work passes a hold-point inspection (foundation, framing, rough-in, insulation, final) or gets red-tagged, writing a correction notice that will hold up on appeal, resolving a conflict between the approved plans and field conditions, applying a specific IRC/IBC section to a borderline condition (egress, smoke/CO detector placement, GFCI/AFCI locations), or deciding whether schedule pressure from a contractor changes the call.

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Use when a task needs the judgment of an Automotive Engineering Technician — setting up and instrumenting test equipment (strain-gauge bridges, thermocouples, load/torque sensors) to an engineer's written test plan, selecting DAQ sample rate and an SAE J211 CFC filter class for a vehicle test channel, verifying instrument calibration (torque wrench, thermocouple, load cell, shunt-cal check on a strain bridge) against a traceable standard before a test run, reducing dyno or road-load test data (SAE J1349 power correction, rainflow-counted durability damage fraction) into engineering units, and documenting test results against the engineer's target with stated margin. Distinct from an automotive engineer (owns the system-level design decisions — structure, powertrain sizing, suspension geometry, NVH) — this role installs the sensors, configures the DAQ, executes the instrumented test, and reduces the data under a design and test plan the engineer specified.

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Use when a task needs the judgment of a Bioinformatics Scientist — designing a differential-expression or GWAS analysis with correct multiple-testing correction, calling and triaging variants from NGS data using genotype-likelihood confidence rather than raw allele counts, interpreting a BLAST/DIAMOND homology search, choosing or building a genomics pipeline (aligner, caller, normalization method) for a specific data-generating process, or judging whether a computational-biology analysis's statistical design actually supports the biological claim being made. Distinct from a bioinformatics-technician (executes and QC-gates an established pipeline someone else designed) and a data-scientist (general product/experimentation judgment, not genomics-specific statistics) — this role owns which method and statistical model a genomics question requires, and why.

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Use when a task needs the judgment of an Aviation Inspector — determining whether an air carrier's fleet is in compliance with an Airworthiness Directive across a maintenance-records sample, deciding where the FAA's compliance-and-enforcement ladder places a finding (compliance action vs. Letter of Correction vs. civil penalty vs. certificate action), auditing a Safety Management System for a functioning safety-assurance loop rather than paperwork completeness, scoping a records-sampling strategy across a fleet under surveillance, or deciding whether to ground an aircraft pending an AD compliance finding.

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Conduct rigorous cross-study meta-analysis of scRNA-seq data from ENCODE, integrating multiple single-cell transcriptomic datasets for a tissue/cell type. Use when the user wants to answer "what cell types exist in my tissue and what genes define them?" by combining scRNA-seq data across donors, labs, and platforms. Follows the Mawla et al. 2019 framework for assessing cross-study reproducibility, TIN-based quality filtering, and detection-limit-aware interpretation. Handles batch correction (Harmony/Seurat), dropout awareness, cross-contamination artifacts, and platform-specific biases. Use this skill for ANY scRNA-seq integration task, cross-dataset comparison, cell atlas construction, or reproducibility assessment involving ENCODE single-cell data.

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Execute ENCODE ATAC-seq processing pipeline from FASTQ to peaks and signal tracks. Child of pipeline-guide. Provides stage-by-stage Nextflow execution with Docker containers and cloud deployment. Handles Tn5 transposase offset correction, mitochondrial read removal, and nucleosome-free fragment selection. Use when users need to process ATAC-seq data following ENCODE standards. Trigger on: ATAC-seq pipeline, run ATAC-seq, process ATAC-seq, chromatin accessibility, open chromatin, Tn5 shift, TSS enrichment.

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Assess the scientific integrity and trustworthiness of publications before relying on their findings. Use this skill whenever evaluating a paper for a workflow, citing a study, building an analysis on published methods, or when a user asks about the reliability of a study. Checks for formal retractions, corrections, expressions of concern, and — critically — informal contradictions where subsequent studies failed to reproduce key findings. Integrates with PubMed, bioRxiv, and Consensus to provide a trust assessment. Use this skill for ANY publication evaluation, retraction checking, author reliability assessment, or when a user says "can I trust this paper", "is this study reliable", "has this been refuted", or "check this publication".

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Translating coarse global climate projections to local scales — dynamical vs statistical downscaling, bias correction, and added value.

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Build agents that work toward goals with minimal supervision — goal decomposition, self-correction loops, safe autonomy levels, and long-horizon task management. Use when an agent must run for hours or complete open-ended tasks.

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Evaluate survey data pipelines and research methodology. Analyzes response bias detection (speeders, straight-liners, bots), statistical significance testing (t-test, chi-square, ANOVA with Bonferroni correction), sentiment and theme extraction from open-ended responses.

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**WORKFLOW SKILL** — Register and generalize agent errors into reusable lessons. USE FOR: when the user corrects the agent, capturing what went wrong, analyzing root cause, generalizing the error into a lesson that prevents recurrence. Use to register errors, analyze mistakes, create lessons, generalize corrections. DO NOT USE FOR: general debugging, writing tests, code review.

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Curate the project's knowledge base and memory in .unikit/memory/ — the indexed reference library of coding standards and framework usage patterns. ALWAYS use this skill whenever the user adds knowledge from a source: a URL, a file, a folder path, a PDF, an article, or a book — any path/link/document is a strong signal for the knowledge base, not a quick rule. Also use it to research or document how the project uses a framework, or to add a researched core/stack knowledge entry. Sub-commands by phrasing: "migrate the rules" or "promote rules" runs migrate-rules; "optimize the knowledge base" or "optimize the rules" runs optimise (extract large sections into references); "validate" re-syncs RULES_INDEX.md; "--module <id>" targets a module. For a quick one-line convention or correction typed as a prompt ("always do X", "never use Y", "remember this") with no source, use /unikit-rules; for architecture decisions use ARCHITECTURE.md.

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Add a short, project-specific rule, convention, or override to .unikit/RULES.md — the quick-capture inbox for this project's rules (common rules always load; topic files in .unikit/rules/ load when the work matches), automatically loaded by /unikit-implement (later promotable via /unikit-memory migrate-rules). Works only with a rule typed as a prompt — it does NOT read files, folders, URLs, or PDFs. Cross-checks against the knowledge base (RULES_INDEX.md) to avoid duplicating core/stack entries. Use for fast, one-line conventions and corrections: "add a rule", "remember this", "convention", "always do X", "never use Y", "from now on do Z", or when the user corrects agent behavior and wants it remembered; also "split the rules into topics" (optimise), "clean up the rules" (prune), "shorten RULES.md" (compact). If the user points to a source (file, folder, URL, PDF, article, book) or wants to research/document framework usage, use /unikit-memory; for architecture decisions use ARCHITECTURE.md.

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ครูสอนภาษาต่างประเทศ (Eng/Chi/Jpn/Kor) — ประเมิน CEFR + lesson plan + conversation practice + error correction + คำศัพท์เป็น chunk

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Error pattern tracking for AI agents. Detects corrections, escalates recurring mistakes, learns mitigations. The 'something's off' detector from the AI Brain series.

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Use for insight, reframing, contradiction, impasse, and anomaly-driven problem solving when execution effort no longer helps. NOT for routine optimization, error correction, or well-specified tasks with known solution paths.

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Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML. Covers between-sample (TMM, TMMwsp, RLE/median-of-ratios, upper quartile), within-sample (TPM, FPKM/RPKM), variance-stabilizing (VST, rlog, log-CPM), GC-content correction (cqn, EDASeq), and single-cell (scran deconvolution, scanpy normalize_total). Encodes the composition-bias rationale, the "most genes not DE" assumption and its catastrophic failure modes (MYC amplification, apoptosis, viral host shutoff, prokaryotic stress), the "lengthScaledTPM is not TPM" naming trap, the "TPM is not for DE" rule, the blind=TRUE vs FALSE decision, ERCC spike-in normalization (SBN), and the single-cell zero-inflation breakdown of TMM/RLE. Use when choosing or applying normalization, debugging shifted-MA-plot diagnostics, handling zero-heavy single-cell data, or correcting GC bias.

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Extracts cfDNA fragmentomics features (DELFI genome-wide short/long ratios, WPS nucleosome positioning, Griffin GC-corrected accessibility profiles, end-motifs/MDS, OCF) for cancer detection and tissue-of-origin from plasma WGS. Centers on the nuclease-footprint reframe (every feature re-reads one nucleosome object), the mandatory GC correction, and the cross-protocol non-comparability that breaks naive classifiers. Runs FinaleToolkit (real CLI/Python, MIT) and the Griffin Snakemake pipeline; DELFI is a method, not a package. Use when deriving fragment-based signal from cfDNA, choosing a feature family for detection vs subtyping, or diagnosing why a fragmentomic model failed validation.

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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.

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Differential abundance (DA) and differential state (DS) analysis for flow and mass cytometry - tests which cell populations change in frequency or marker expression between conditions using diffcyt (edgeR/voom/GLMM for DA, limma/LMM for DS), with cydar, CITRUS, and compositional methods (sccomp, scCODA, DCATS) as alternatives. Covers the sample-is-the-experimental-unit principle, design/contrast and mixed-model formulas, compositionality of cluster proportions, and FDR across clusters. Use when comparing populations between groups, choosing a DA method, handling paired/batch designs, or deciding whether compositional correction is needed.

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Estimates time-scaled phylogenies, molecular-clock rates, effective reproduction number R_e, and population dynamics from dated pathogen genomes using TreeTime (maximum-likelihood) and BEAST2 (Bayesian; strict/relaxed clocks; coalescent, Bayesian-Skyline, Skygrid, Birth-Death-Skyline, and sampled-ancestor priors; structured coalescent via MASCOT). Covers root-to-tip clock QC via TempEst, date-randomisation tests, recombination masking via Gubbins/ClonalFrameML before clock inference for recombining bacteria, BDSKY origin-vs-rootHeight pitfalls, sampling-bias correction, multi-chain convergence diagnostics, and reconciling phylodynamic R_e with case-based R_t. Use when dating outbreak origins, estimating substitution rates, inferring R_e through time, building time-calibrated Nextstrain Augur trees, choosing between strict and relaxed clocks, fitting Birth-Death-Skyline models, diagnosing temporal-signal failure, running MASCOT for structured-population analyses, or using UShER for pandemic-scale placement.

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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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Extracts, filters, annotates, and exports differential expression results from DESeq2 or edgeR with proper handling of padj=NA (independent filtering, Cook's outliers, all-zero), multiple-testing correction choice (BH vs Storey q-value vs IHW vs lfsr), TREAT vs post-hoc fold-change filtering, p-value histogram diagnostics, gene annotation via org.db/biomaRt/mygene, GSEA preranked input, ORA background construction, replication reality (Schurch 2016 small-n result), and SABV/sex-stratified reporting. Use when extracting and interpreting DE results, troubleshooting padj=NA, choosing FDR method, preparing ranked lists for pathway analysis, annotating gene IDs, or comparing DESeq2 vs edgeR outputs.

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