「fts」の検索結果

Edit EcoSIM PFT-parameter NetCDF files such as ecosim_pftpar_20260303.nc with the ParEditor class from applications/notebooks/scripts/ParamEditor.py. Use when asked to modify, scale, copy, compare, or delete PFT parameter records for a plant functional type (six-character pfts code such as gr3s43 or ndlf34), update microbe parameter NetCDF values, or maintain the JSONL change log that records past parameter changes. Never modify plant_trait.*.desc files; they are read-only references.

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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.

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

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GPT Image 2 image generation workflow for this repo MCP server. Use for gpt-image-2, OpenAI image generation, concept art, UCUF reference exploration, UI icon, badge, card art, prompt drafting, transparent-background asset drafts, and saving generated images to local files under artifacts/ui-source or other workspace paths.

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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.

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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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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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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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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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Submit a blog draft to waynesutton.ai. Use when the user says "blog this", "blog to wsai", "send to wsai", "write to wsai", "post this to my blog", "write this up for the blog", "turn this session into a blog post", "turn this session into a blog post wsai", "draft a post about", "wsai draft a post about", or asks to file session notes to waynesutton.ai. Drafts go to a review inbox and are never published without approval.

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Autonomous DevSecOps & FinOps Guardrails. Orchestrates Gemini 3 Flash to audit Linux Kernel patches, Terraform cost drifts, and K8s compliance.

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Query Solana blockchain data with USD pricing — wallet balances, token portfolios with values, transaction details, NFTs, whale detection, and live network stats. Uses Solana RPC + CoinGecko. No API key required.

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Drafts formal explanation letters for Canadian Study Permit applications by structuring the argument around program attractiveness, background relevance, choice rationale, and family benefits.

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Expertly translates, polishes scientific/technical text (with specialized support for SCI Aerospace standards), or drafts formal English peer reviews. Ensures accuracy, clarity, and adherence to high academic standards.

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自动从知乎热榜选题、调用 AI 生成原创回答并保存为草稿，支持自定义话题关键词、写作风格和批量生成。 Draft Zhihu answers automatically: picks hot questions, generates original answers via AI, and saves them as drafts — with custom topic filters, writing style, and batch support. Never publishes.

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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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Publish content to X/Twitter, LinkedIn, WeChat Official Account, and Xiaohongshu with one command. Automatically adapts content format for each platform — threads for Twitter, professional articles for LinkedIn, HTML drafts for WeChat, emoji notes for Xiaohongshu. Triggers: publish content, social media, twitter post, linkedin post, wechat article, xiaohongshu note, cross-platform publish, multi-platform

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Gmail API integration with managed OAuth. Read, send, and manage emails, threads, labels, and drafts. Use this skill when users want to interact with Gmail. For other third party apps, use the api-gateway skill (https://clawhub.ai/byungkyu/api-gateway).

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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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A comprehensive guide for GitHub Copilot to craft immersive, high-performance web experiences with advanced motion, typography, and architectural craftsmanship.

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Draft and review professional emails that match your personal writing style. Analyzes your sent emails for tone, greeting, structure, and sign-off patterns via WorkIQ, then generates context-aware drafts for any recipient. USE FOR: draft email, write email, compose email, reply email, follow-up email, analyze email tone, email style.

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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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