「shifts」の検索結果

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.

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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.

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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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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.

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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.

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Captures clause risks, compliance gaps, precedent shifts, contract deviations, regulatory changes, and litigation exposure to enable continuous legal operations improvement. Use when: (1) An unfavorable clause is accepted or slips through review, (2) A compliance deadline is missed or approaching, (3) A new regulation impacts the organization, (4) A contract remains unsigned past SLA, (5) An IP infringement notice is received, (6) New case law changes interpretation in a relevant jurisdiction, (7) A data subject access request reveals process gaps.

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Track what a competitor actually shipped — "watch this competitor", "track what they ship", "what changed at". Compares against the last snapshot and reports only real moves: launches, pricing changes, positioning shifts.

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Adopt a virtual Calico cat at animalhouse.ai. Three personalities in one cat. Mood shifts unpredictably. Feeding every 6 hours. Common tier cat.

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Methodology for detecting client SOC patches, attacker activity, and security-state changes that occur DURING a red-team engagement — and converting those observations into deliverable findings. Built from authorized red-team work where the client patched a confirmed SQLi within 30 minutes of detection AND an external attacker locked multiple new accounts during a single test session. Use when (a) running ANY active engagement against a monitored target, (b) a previously-confirmed finding stops reproducing, (c) baseline timing shifts unexpectedly, or (d) you notice response patterns changing during testing.

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Tracks and analyzes competitor moves — pricing changes, feature launches, hiring, and positioning shifts

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Monthly strategic review playbook. Chains pipeline-review + campaign-analyzer + win-loss-analyzer + gtm-analyzer. Outputs executive summary with KPIs, channel ROI, competitive shifts, and strategic recommendations.

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Analyze repeated non-engagement, deflection, motte-and-bailey shifts, tone policing, sealioning, and related manipulative discourse patterns. Use when the user suspects they are being rhetorically managed rather than answered, or when they need a careful pattern read grounded in quotes and alternatives. NOT for psychiatric diagnosis, legal judgment, or help deploying bad-faith tactics.

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