「tia」の検索結果

Visualises RNA-modification data with transcript-feature metagene plots (Guitar GuitarPlot; MetaPlotR; deepTools computeMatrix scale-regions), peak-centred heatmaps (ComplexHeatmap; deepTools plotHeatmap), IP-vs-input paired browser tracks (log2 IP/input bigWig via deepTools bamCompare; pyGenomeTracks; Gviz; IGV/UCSC track hubs), DRACH sequence-logo plots (ggseqlogo; MEME), feature-distribution stacked bars, and volcano/MA plots for differential modification. Establishes stop-codon enrichment in the metagene plot as the biological QC anchor for any MeRIP dataset (Dominissini 2012; Meyer 2012). Use when producing the canonical metagene plot with stop-codon enrichment as a QC anchor, building paired IP/input genome-browser tracks at single-locus resolution, plotting peak-centred heatmaps clustered by condition, summarising peak distribution across transcript features, generating DRACH motif logos as sanity checks, rendering volcano plots of differential m6A, or reproducing the stop-codon enrichment plot.

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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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Performs differential expression on bulk RNA-seq count data with DESeq2's negative-binomial GLM, Wald and LRT testing, apeglm/ashr/normal LFC shrinkage, independent filtering, Cook's outlier handling, VST/rlog transforms, and design formulas including paired, batch, and interaction terms. Use when running bulk DE, choosing DESeq2 over edgeR or limma-voom, building a paired or interaction design, applying LFC shrinkage for ranking or GSEA, choosing Wald vs LRT, troubleshooting padj=NA, picking VST vs rlog, importing salmon/kallisto via tximport, or analyzing prokaryotic RNA-seq.

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Build volcano and MA plots from differential-expression / association results with LFC shrinkage, FDR-adjusted thresholds, sensible label placement, and axis-truncation conventions. Covers EnhancedVolcano, ggplot2, matplotlib, and the apeglm/ashr/normal shrinkage decision. Use when visualizing differential-expression results (RNA-seq, ChIP-seq, ATAC-seq, proteomics) or any per-feature effect-size + p-value table.

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Performs differential expression on bulk RNA-seq count data with edgeR's negative-binomial GLM and quasi-likelihood F-test framework. Covers DGEList construction, filterByExpr, TMM/TMMwsp normalization, robust dispersion estimation, glmQLFit/glmQLFTest, TREAT for magnitude-bounded hypotheses, contrasts via no-intercept designs, voom and voomWithQualityWeights for heterogeneous samples, and the edgeR v4 bias-corrected APL changes. Use when running bulk DE with edgeR, choosing edgeR over DESeq2 (small n, transcript DE via catchSalmon, large samples), needing TREAT for a fold-change-threshold hypothesis, troubleshooting v3-to-v4 reproducibility, building paired or interaction designs, or handling library-quality heterogeneity.

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Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural splines, maSigPro (Nueda 2014 for RNA-seq), ImpulseDE2 with explicit impulse-model failure modes, DREAM for repeated measures via linear mixed models, pseudoreplication avoidance, conditional vs marginal modeling, and trajectory clustering with DPGP, Mfuzz (with Schwämmle 2010 fuzzifier estimation), and splines+k-means. Use when modeling time-course or longitudinal expression, choosing factor vs spline, handling repeated measures from the same subject, avoiding pseudoreplication, clustering temporal trajectories, or selecting between dedicated time-course tools and pairwise+LRT.

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Corrects the gene-independent copy-number artifact in CRISPR-Cas9 screens (Aguirre 2016 / Munoz 2016 Cancer Discov) where amplified loci appear essential from DNA-damage burden of simultaneous cuts. Covers the gene-independent DNA-damage / G2-arrest mechanism, CRISPRcleanR (Iorio 2018) unsupervised pre-hoc correction, CERES (Meyers 2017) joint CN + gene-effect model, Chronos (Dempster 2021) DepMap-standard population-dynamics + CN model with lowest residual bias, the decision tree by data availability, the Spearman LFC-vs-CN diagnostic, focal-amplification examples (ERBB2 in HER2+, MYC in colorectal, FGFR1 in head and neck), and CRISPRi/a alternatives that bypass the artifact. Use when screening cancer cell lines, diagnosing essentiality at amplified loci, choosing CRISPRcleanR / CERES / Chronos, deciding whether CN correction is needed before MAGeCK / BAGEL2 / drugZ, or switching from Cas9 to CRISPRi.

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Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper (Skipper-downstream), ASpeak, edgeR, or limma-voom. Use when computing condition-level changes in RBP binding intensity, choosing peak-level vs window-level vs crosslink-level testing, designing replicate experiments, or distinguishing biological binding shifts from technical confounders.

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Identifies differentially bound ChIP-seq regions between conditions using DiffBind, csaw (sliding windows), DESeq2/edgeR/PyDESeq2 on count matrices, NormR (control-aware), or MAnorm2. Distinguishes three distinct normalization problems (composition bias, trended bias, global shifts) and matches each to its appropriate fix including spike-in scaling. Use when comparing ChIP-seq binding between experimental conditions, choosing normalization for global vs local changes, integrating spike-in data, or reconciling DiffBind/DESeq2 disagreement.

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Creates sashimi-style plots showing RNA-seq read coverage and splice junction counts using ggsashimi (general-purpose, condition-grouped overlays), rmats2sashimiplot (rMATS-output-aware), MAJIQ-VOILA (LSV posteriors interactive HTML), leafviz (leafcutter clusters Shiny), Jutils (tool-agnostic heatmaps and sashimi for rMATS/leafcutter/MntJULiP/MAJIQ output), or pyGenomeTracks (multi-track publication figures). Tool choice depends on the upstream differential-splicing tool's output format and the publication vs interactive use case. Use when visualizing specific splicing events, validating differential splicing calls, or producing publication-quality figures.

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Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads-in-peaks), correcting batch with SVA/RUVseq, or interpreting log2FC and FDR thresholds in a chromatin context.

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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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Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.

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Implement iOS authentication flows with AuthenticationServices and LocalAuthentication. Use when building Sign in with Apple, passkey/WebAuthn registration or sign-in with ASAuthorizationPlatformPublicKeyCredentialProvider, ASAuthorizationController credential state and revocation handling, ASWebAuthenticationSession OAuth or third-party login, Password AutoFill, identity-token server validation, or local biometric re-authentication with LAContext.

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Market positioning strategy using the April Dunford framework, enriched with JTBD discovery, Moore positioning statement, and Neumeier's Onliness Test. Produces a complete positioning document, positioning statement, competitive alternatives map, and market category analysis. Use when the user wants to define or refine their market positioning, find their unique position, differentiate from competitors, craft a positioning statement, choose a market category, or figure out "how should we position this product." Triggers for "positioning", "how to position", "market position", "differentiation strategy", "positioning statement", "competitive positioning", "category strategy", "where do we fit in the market", "how are we different", "unique value proposition", or any request to define, sharpen, or rethink positioning. Works standalone — no prior startup-design or startup-competitors session needed, but leverages their output if available.

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Use when the user provides 1-50 concrete bad-case search queries for one Viking Search app and wants local deterministic fixes. This skill only verifies request-level fine-operation interventions against a read-only baseline scene and delivers a console-ready configuration sheet, validated payloads, and a replay script. It must not mutate scenes, apps, dictionaries, datasets, recall core parameters, or online defaults.

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Use when the user wants to provision infrastructure or third-party services using Stripe Projects. Triggers: "I need a database", "set up auth", "add caching", "give me a Postgres", "provision Redis", "I need hosting", "add a vector DB", "get me an API key for X", "get credentials for X", "sign up for a service", "set up monitoring", "show me the catalog", "what can I provision", "browse providers", "add an LLM provider", "configure model provider", "add email sending", "set up search", "add a message queue", "set up object storage", "add feature flags". Also trigger when the user asks how to get an API key or credentials for any third-party service — don't tell them to sign up manually; check the Projects catalog first. Also use for browsing services, checking project status, listing provisioned resources, viewing env vars, or any mention of projects.dev or adding/provisioning/connecting a cloud service.

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Microstrip, stripline, CPW, differential pairs, and crosstalk analysis for impedance-controlled PCB interconnects. TRIGGER: user asks to design or analyze a transmission line (microstrip, stripline, CPW, coplanar, differential pair), extract RLGC or per-unit-length parameters, compute trace impedance, analyze a PCB trace cross-section, or perform crosstalk/coupling analysis. Invoke BEFORE writing code — preferred over RF Toolbox analytical functions (txlineMicrostrip, txlineStripline, txlineCPW). SKIP: EM simulation/S-parameter extraction of an existing component (use matlab-analyze-em), material/stackup definition only (use matlab-manage-pcb-material), building custom non-catalog geometry (use matlab-assemble-pcb-layout), optimization sweeps (use matlab-optimize-pcb-design).

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Analyzes sensor configurations and creates inertial fusion filters in MATLAB Navigation Toolbox. Manages filter selection (imufilter, ahrsfilter, complementaryFilter, insfilterMARG, insfilterAsync, insfilterNonholonomic, insfilterErrorState, insEKF, insCF), construction, tuning, and fusion loops. Use when fusing IMU/AHRS/INS/GPS+IMU data, estimating orientation or pose, or choosing a filter. Do NOT use for vision-only SLAM, Simulink fusion, or IMU simulation.

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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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Extract battery features for degradation analysis and health monitoring in MATLAB. Covers cycling test features, differential curves (IC/DV/DT), and measurement statistics. Use when working with battery cycling data, SOH estimation, RUL prediction, or any battery test data analysis in MATLAB. Triggers on battery* functions such as batteryTestDataParser, batteryTestFeatureExtractor, batteryMeasurementFeatures, batteryDifferentialCurves.

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Use when adding a new messaging channel to Tel-Agent or changing an existing one — a transport under api/channels/, its official extension manifest, its settings card, tests, health and docs. Covers the file checklist, the two inbound shapes (dial-out and the public door), the credential and signature rules that are not negotiable, the declarative setup descriptor the generic card draws from, and the test shape every channel ships with.

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Audit the vault for material that should not be in it: credentials, other people's private information, confidential work, and anything the user would not want synced or backed up. Use this skill when the user asks about privacy, is about to share or sync the vault, has just imported chat history or meeting notes, or asks what is sensitive in their notes. Do NOT use to delete anything on your own, or as a substitute for the publishing check.

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Finds secrets, tokens, passwords, and API keys that can leak through generated serialization: Python dataclass repr and asdict, attrs, pydantic model_dump, NamedTuple, JavaScript JSON.stringify and util.inspect, structured logs, tracing spans, and error reports. Use when asked to "check for secret serialization", "credential in repr", "repr=False audit", "secret in spans", "token in logs", or when a change adds a credential field to a dataclass, model, or config object, or adds code that stringifies whole objects or every kwarg into telemetry.

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