「shifts」の検索結果

Detect positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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。

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.

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。

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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。

Adversarial code review that breaks the self-review monoculture. Use when you want a genuinely critical review of recent changes, before merging a PR, or when you suspect Claude is being too agreeable about code quality. Forces perspective shifts through hostile reviewer personas that catch blind spots the author's mental model shares with the reviewer.

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。

Knowledge base from the DoD Digital Engineering Strategy (2018, OUSD/ODASD(SE)). Use for the Department of Defense's five digital engineering goals — (1) formalize the development, integration, and use of models; (2) provide an enduring authoritative source of truth; (3) incorporate technological innovation; (4) establish supporting infrastructure and environments; (5) transform the culture and workforce — plus their focus areas, the document-to-model and design-build-test→model-analyze-build shifts, model formalisms/provenance, governance and access control of the authoritative source of truth, and the coordinate→plan→pilot→sustain rollout. A vision-and-policy strategy, deliberately non-prescriptive. Does NOT provide a how-to method, tool tutorials, MBSE/SysML mechanics, or implementation-plan content; thin on metrics, acquisition-policy detail, and step-by-step procedure. Excludes the CAC-gated Digital Engineering Body of Knowledge (DEBoK).

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。

Optimize Core Web Vitals (LCP, INP, CLS) for better page experience and search ranking. Use when asked to "improve Core Web Vitals", "fix LCP", "reduce CLS", "optimize INP", "page experience optimization", or "fix layout shifts".

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。

When the user wants to monitor competitor apps on an ongoing basis — tracking metadata changes, keyword shifts, screenshot updates, rating trends, or new features. Use when the user mentions "competitor monitoring", "track competitors", "competitor alert", "competitor changed their title", "watch a competitor app", "competitor weekly report", "competitive intelligence", or "what changed in competitor's listing". For a one-time deep competitive analysis, see competitor-analysis. For market-wide chart movements, see market-movers.

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。

When the user wants to track App Store chart rank changes, find top gainers and losers, detect breakout apps entering the top 100, or identify apps dropping out of charts. Also use when the user mentions "chart movers", "rank changes", "who's rising", "who's falling", "new chart entries", "top gainers", or "market shifts". For broader market overview, see market-pulse. For competitive keyword analysis, see competitor-analysis.

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 when user shows signs of overwhelm or frustration — repeated failed attempts, tone shifts, sudden brevity, topic abandonment. Guides gentle check-ins without being patronizing or clinical.

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。

Focused Signals scout for PostHog projects using logs. Watches for volume bursts, severity-distribution shifts, service silence, fresh message patterns, and trace-correlated bursts via the logs ingestion pipeline. Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.

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。

Focused Signals scout for PostHog projects using feature flags. Watches the flag roster and the `$feature_flag_called` evaluation stream for contradictions between a flag's configured state and its real traffic: evaluation cliffs on healthy flags, ghost flags (code calling keys that no longer exist), response-distribution shifts with no corresponding flag edit, and flag debt (stale, fully-rolled-out, or dead flags still burning evaluations). Emits findings only when they clear the confidence bar; otherwise writes durable memory and closes out empty. Self-contained peer in the signals-scout-* fleet — no dependencies on other skills.

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。

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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 positive (diversifying / episodic / pervasive) selection using codon dN/dS frameworks. Implements PAML codeml site models (M0/M1a/M2a/M7/M8/M8a), branch models, branch-site model A (Zhang 2005), and HyPhy methods (BUSTED, BUSTED-S, BUSTED-MH, BUSTED-PH, MEME, FEL, FUBAR, aBSREL, SLAC, RELAX, GARD, FUBAR-MH). Includes McDonald-Kreitman framework (asymptotic alpha, impMKT, polyDFE, DFE-alpha, GRAPES) for within-species + divergence inference, RERconverge for trait-correlated rate shifts, CSUBST for convergent substitution, and PhyloAcc for accelerated noncoding evolution. Use when testing adaptive evolution at codons, branches, or full gene; running GARD recombination pre-screen; controlling alignment-error and gBGC false positives; reconciling PAML vs HyPhy results; or performing genome-scale selection scans.

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。

Model gene-family birth-death dynamics across a species tree using CAFE5 (Mendes et al 2020 Bioinformatics 36:5516 gamma-distributed rate categories), CAFE5-error (annotation-error-aware), Count (Csurös 2010 ancestral state reconstruction), BadiRate (Librado 2012 likelihood + parsimony), DupliPHY-Family, and ALE/AleRax (for per-family DTL; see [[gene-tree-species-tree-reconciliation]]). Test lineage-specific gene-family expansions and contractions, distinguish biological dynamics from annotation artifacts, account for assembly fragmentation, identify functional enrichment in expanded / contracted families. Use when correlating gene-family changes with phenotype evolution, ranking lineages by adaptive gene-family-rate shifts, post-WGD dosage-balance analysis, or building Birth-death models from OrthoFinder presence/absence matrices.

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 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.

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。

Calls ChIP-seq peaks with MACS3, MACS2, HOMER, or SPP across narrow (TF) and broad (histone) modes. Handles input control matching, fragment-size modeling vs --nomodel, effective genome size, ENCODE-style IDR vs naive overlap, hyper-ChIPable artifacts, and aligner-specific shifts. Use when calling peaks from ChIP-seq alignments, choosing between narrow vs broad mode for a histone mark, deciding model vs nomodel for low-depth data, applying ENCODE pseudoreplicate IDR, or reconciling MACS vs HOMER vs SPP results.

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。

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.

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。

Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.

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。

Pull an earnings call transcript from Financial Modeling Prep, extract qualitative signal (management commentary deltas, hedging shifts, Q&A tone), and produce a thesis-delta-first Research note. Use when user says "transcript", "pull earnings call", "transcript diff", or "ingest [TICKER] earnings".

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。

Pull an earnings call (or investor-event) transcript from Quartr (FMP fallback), extract qualitative signal (management commentary deltas, hedging shifts, Q&A tone), and produce a thesis-delta-first Research note. Use when user says "transcript", "pull earnings call", "transcript diff", or "ingest [TICKER] earnings".

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。

Autonomous Reforge-guided refactor workflow for the Humans repository. Use when the user wants Codex to target a section such as Shifts, Users, Teams, Tickets, Camps, or Store, create a dedicated worktree/branch from origin/main, run iterative architecture-focused improvements, score each stage with Reforge, gate commits through a score-blind read-only architecture review, append score and verdict details to commit messages after review acceptance, push progress, and open a PR when the loop reaches stasis.

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。

Route communication modes, learning workflows, retrospectives, output discipline, and perspective shifts to focused productivity skills.

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。

Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 with `bam_ip` + `bam_input` (control arm) and `bam_treated_ip` + `bam_treated_input` (treatment arm) for integrated GC-bias-aware differential calling (Liu 2022 *NAR Genom Bioinform* 4:lqac046), QNB beta-binomial test (Liu 2017 *BMC Bioinformatics* 18:387), MeTDiff HMM-based differential bundled with MeTPeak, RADAR (Zhang 2019 *Genome Biol* 20:294) with its `filterBins -> diffIP -> reportResult` workflow, and the defensible paired-symmetric case of edgeR / DESeq2 on featureCounts-on-peaks matrices when batch / lot covariates need explicit fixed-effect handling (exomePeak2's top-level API does NOT accept arbitrary covariates). Covers paired vs unpaired vs interaction designs, batch confounding (antibody lot, RNA prep, sequencing run) and the per-lot meta-analysis strategy when exomePeak2 is the primary caller, the stoichiometry-vs-expression-vs-IP-efficiency confound that all MeRIP differential methods inherit, normalisation choice (size factor on IP, on input, on per-sample IP/input ratio), the McIntyre 2020 reproducibility caveat, effect-size filtering as a guardrail against under-powered N=2 designs, and orthogonal-validation routes for absolute stoichiometry (GLORI / SAC-seq / m6Anet `mod_ratio`). Use when comparing m6A levels across two or more conditions, choosing between exomePeak2 / QNB / RADAR / MeTDiff for a given design, handling batch confounding when exomePeak2's API is too rigid, normalising against input properly, distinguishing real hyper- / hypo-methylation from expression-level shifts, applying effect-size thresholds, interpreting volcano plots of differential peaks, or planning a follow-up orthogonal stoichiometry validation.

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 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.

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。