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Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.

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Quality control for flow, spectral, and mass cytometry - time-based anomaly cleaning (flowAI, flowCut, PeacoQC, flowClean), margin/boundary event removal, signal-drift detection, dead-cell exclusion, CyTOF Gaussian/DNA/event-length checks, instrument calibration/standardization (MESF, CS&T, peak-2), and batch-level outlier flagging. Use when assessing acquisition quality, choosing a cleaning tool, ordering QC relative to compensation, deciding margin removal before density-based steps, or flagging problematic samples before clustering or differential analysis.

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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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Assesses the quality and completeness of a genome annotation with BUSCO (conserved single-copy ortholog recovery), OMArk (proteome completeness, consistency, and contamination), CheckM2 (prokaryotic completeness/contamination), and a gene-set sanity panel (gene count, mono-exonic fraction, protein-length distribution, mRNA:gene ratio, coding density). Covers the assembly-BUSCO-vs-proteome-BUSCO diagnostic, what BUSCO-Duplicated really means, why gene count is a vanity metric, and the QC of transferred annotations. Use when judging whether an annotation is good enough to publish or submit, diagnosing a suspect annotation, or comparing annotation completeness across pipelines.

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Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM. Use when subsetting a FASTA/FASTQ file, removing unwanted or low-quality records, or selecting records by specific criteria. Use the paired-end-fastq skill instead whenever the input is paired R1/R2 reads.

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Assesses genetic health of populations for conservation with Ne estimation across time horizons (LDNe NeEstimator V2 option-file API + SNeP physical-linkage correction; recent trajectory via GONE/GONE2; deep history via Stairway Plot 2 / dadi / fastsimcoal2 / PSMC), F-statistics, runs of homozygosity binned by length class to date inbreeding, genetic-load decomposition (Bertorelle 2022 realized vs masked), the modern 100/1000 Ne rule (Frankham 2014), Ne/Nc 2-6 orders of magnitude in marine fish (Hauser & Carvalho 2008), tree-sequence forward simulations (SLiM 4 + pyslim + tskit), and the Sukumaran-Knowles caveat against MSC methods for management-unit definition. Use when estimating Ne by time horizon, detecting inbreeding via F_ROH, decomposing genetic load, justifying conservation thresholds, distinguishing ESU/MU/DPS, configuring NeEstimator V2, or correcting LDNe physical linkage.

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Comprehensive quality control for CLIP-seq libraries (eCLIP, iCLIP, iCLIP2, PAR-CLIP) covering library complexity (preseq), FRiP, IDR replicate reproducibility, read-distribution metagene, SMInput vs IgG control rationale, rRNA / snoRNA contamination, fragment-length distribution, and ENCODE-compliance thresholds. Use when assessing whether a CLIP library passed, deciding lenient vs stringent peak thresholds, comparing replicates with IDR rescue and self-consistency ratios, or distinguishing failed IP from over-amplified library.

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Annotates ChIP-seq peaks to genomic features, nearest genes, ENCODE candidate cis-regulatory elements (cCREs), and regulatory domains. Uses ChIPseeker (R), HOMER annotatePeaks.pl (CLI), pyranges (Python), GREAT/rGREAT (regulatory domain gene-set enrichment), ChIP-Enrich (locus-length-adjusted), ENCODE SCREEN cCRE classification (PLS/pELS/dELS/CA-CTCF/CA-H3K4me3), and ENCODE-rE2G for cell-type-specific enhancer-gene linking. Handles nearest-TSS vs host-gene ambiguity, promoter window definition, and feature priority. Use when assigning genomic context to peaks, linking enhancer peaks to target genes, classifying peaks against ENCODE cCRE registry, or running gene-set enrichment on peak-associated genes.

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Bring documentation prose down to a high-school reading level without losing precision. Runs after the content is written and before humanizer. Targets grade 9 on four measures — sentence length, vocabulary, clause load and jargon density — and carries the rewriting moves that actually shift them.

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A workflow skill that lets Codex keep coding for 60 hours on medium and large projects: Claude Code CLI plans through an interactive requirements questionnaire, PRD, specs, and roadmap; Codex implements verified vertical slices, with resumable Long-Run Execution for lengthy work; Trellis maintains project memory. Use when the user mentions 大项目工作流, Codex 连续开发 60 小时, Codex 长任务, long-running or resumable Codex implementation, large/medium project, new SaaS, multi-module system, requirements questionnaire, Claude Code CLI planning, Codex implementation handoff, Trellis bootstrap, non-system-drive project, or vertical slice. Skip for: single-file edits, casual Q&A, copy polish, throwaway prototypes, or tasks the user explicitly wants done fast without process.

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Use when wrangler deploys silently fail or produce wrong artifacts, secrets upload as empty strings, custom domain DNS is not resolving, route assignment broke after rename, observability/tail logs are needed, D1/KV/R2 bindings are missing, OAuth scope errors block a command, cookies on a redirect are not attaching, or the worker exceeds CPU time. Triggers: "Tenant or user not found", "Authentication error" on wrangler d1 push, secret length is 0 after upload, route returns origin not worker, "compatibility_date too old", 1101 errors, custom_domain assignment lost on script rename. NOT for AWS Lambda / Vercel Edge / Deno Deploy (different runtimes), Cloudflare Zero Trust, or R2-specific tuning.

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Transition insulin pump to scheduled subcutaneous basal bolus insulin when anticipated hospital length of stay exceeds 1 to 2 days and pump expertise is unavailable. Triggers include: "Patient expected to stay >2 days, should we switch pump to scheduled insulin?

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Recommends continuing insulin pump therapy in hospitals with pump expertise; otherwise transitioning to scheduled subcutaneous basal bolus insulin if anticipated length of stay exceeds 1–2 days before pump discontinuation. Consider this when anticipating a hospital stay >2 days, lacking pump expertise, or needing to conserve supplies.

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。

Expert-level astrophysics covering stellar physics, galaxy formation, high-energy astrophysics, observational techniques, and the electromagnetic spectrum across wavelengths.

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。

Expert-level plasma physics knowledge. Use when working with plasma state, Debye shielding, plasma oscillations, magnetohydrodynamics, plasma confinement, fusion plasmas, space plasmas, plasma waves, or plasma instabilities. Also use when the user mentions 'plasma', 'Debye length', 'plasma frequency', 'MHD', 'magnetic confinement', 'tokamak', 'plasma instability', 'Alfven wave', 'Langmuir probe', 'ionosphere', or 'solar wind'.

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Adaption AI SDK for synthetic data augmentation and dataset adaptation. Use when building data pipelines with the Adaption Python SDK, uploading datasets (local files, Hugging Face, Kaggle), running augmentation/adaptation jobs, configuring brand controls (hallucination mitigation, safety categories, length), recipe specifications (reasoning traces, deduplication, preference pairs, prompt rephrase), evaluating dataset quality, downloading results, or any workflow involving `pip install adaption`, `from adaption import Adaption`, Adaptive Data, or the adaptionlabs.ai API. Also trigger when the user mentions synthetic data generation for fine-tuning, dataset augmentation pipelines, DPO preference pair generation, or grounding-based hallucination reduction on training data.

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Use when you need this project's coding standards (line length, quotes, import order, naming, commit format) — derive them from the REAL tooling config as a pointer + digest, never a guessed claim.

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Research-grounded typography for any text-bearing surface — web, PDF, email, documents. GENERATIVE: apply correct line length, font sizing, contrast, dark mode, mobile, and Japanese rules from the start when building any UI, page, layout, or document. REVIEW: audit existing CSS/HTML/templates for typography violations. Use this skill whenever you are writing CSS that touches font-size, line-height, max-width, color, or font-family. Use it when building any frontend component, page, or layout — even if the user doesn't mention typography. Use it when reviewing any rendered output for readability. Use it when generating PDFs, emails, or any formatted document. If text will be read by a human, this skill applies.

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Detect data exfiltration through DNS tunneling by analyzing query entropy, subdomain length, query volume, TXT record abuse, and response payload sizes using passive DNS monitoring.

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Analyzes DNS query logs to detect data exfiltration via DNS tunneling, DGA domain communication, and covert C2 channels using entropy analysis, query volume anomalies, and subdomain length detection in SIEM platforms. Use when SOC teams need to identify DNS-based threats that bypass traditional network security controls.

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Maintain a support docs pack — dedup, length budgets, and no splintering — and land changes as a reviewed pull request. Use when a support thread, or a hand-off from Support assist, surfaces a new resolution, a correction to an existing one, or a deployment quirk worth recording. Not for ordinary code changes.

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Use when the user explicitly invokes the `if` skill or asks for a concise, laconic, no-fluff, or to-the-point answer. Do not trigger on the ordinary word or programming keyword `if`. Detailed, step-by-step, exhaustive, educational, or fixed-length requests activate only when they also include an explicit invocation or brevity request.

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Two-phase code quality skill: (1) review codebase for structural smells — file LOC, method LOC, accidental complexity, test readability — producing a structured report, then (2) fix all smells via provable refactorings with ACN micro commits and green-bar-at-all-times discipline. Use this skill when the user says 'sweep', 'code review', 'find code smells', 'check method lengths', 'review for complexity', 'tidy up the codebase', 'refactor smells', or asks about long methods, test readability, or accidental complexity. Also trigger when users ask to 'clean up' or 'improve code quality' across multiple files.

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Publish a vetted post to an X (Twitter) account through the owner's real logged-in Chrome tab, rate-guarded and draft-first. Counts length the way X does, treating every link as 23 characters, and refuses over-limit text instead of silently truncating. Triggers: "/x-post", "tweet this", "post to X".

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。