「summary」の検索結果

Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enrichment QC via plotFingerprint and per-transcript IP/input ratio distributions, library-complexity saturation curves via PreSeq c_curve / lc_extrap, and the explicit do-NOT-deduplicate convention for standard non-UMI MeRIP. Use when preparing paired IP and input BAM files for exomePeak2 / MeTPeak / MACS3 peak calling, evaluating MeRIP replicate concordance and IP enrichment, deciding whether to deduplicate (standard MeRIP typically NOT — see Tips), choosing genome-vs-transcriptome alignment for downstream peak vs m6Anet workflows, recording antibody clone and lot metadata for downstream cross-batch reconciliation, detecting failed IPs via saturation curves and IP/input distribution shape, or generating IP-over-Input bigWig tracks for downstream visualisation.

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Download genome assemblies, gene records, and ortholog data from NCBI using the modern Datasets v2 CLI (replaces assembly_summary.txt scraping and many EFetch workflows). Use when bulk-pulling genome assemblies, gene metadata across species, ortholog sets, or BLAST databases; when E-utilities are too slow for genome-scale work; or when automatic checksum verification, parallel download, and clean accession-driven retrieval are required. Encodes the JSON-lines output format, dataformat conversion, --dehydrated for cloud workflows, and when Datasets is/isn't the right tool.

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Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document summaries, parsing nested XML, navigating GI deprecation, choosing between rettype+retmode combinations, and parsing into Biopython SeqRecord/SwissProt objects. Covers nucleotide, protein, gene, pubmed, sra, gds, taxonomy, snp, clinvar.

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Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling, and LD-aware regional rendering. Use when visualizing association results across the genome, comparing two traits, computing genomic inflation lambda, or zooming into a locus with LD coloring.

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Build forest plots (HR, OR, RR, beta-coefficient summaries with CIs) and funnel plots (meta-analysis publication-bias diagnostics) using forestplot, metafor, ggforest, and MendelianRandomization with proper axis-scaling, summary-diamond placement, subgroup nesting, and Egger / trim-and-fill asymmetry tests. Use when summarizing effects across subgroups, trials, or instruments — meta-analysis, Mendelian randomization, subgroup HRs.

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Performs gene-level association from GWAS summary statistics via genetically predicted tissue expression using FUSION, PrediXcan, S-PrediXcan, S-MultiXcan, UTMOST, MOSTWAS, kTWAS, EpiXcan, TIGAR-V2, and probabilistic fine-mapping with FOCUS and MA-FOCUS. Use when running TWAS from GWAS sumstats, prioritising candidate causal genes from a GWAS lead locus, picking single-tissue vs cross-tissue models, identifying LD-induced TWAS false positives, choosing ancestry-matched prediction weights, fine-mapping co-regulated TWAS hits, or triangulating TWAS with cis-eQTL Mendelian randomization and colocalization to nominate a causal gene.

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Fits structural equation models to GWAS summary statistics using GenomicSEM (Grotzinger 2019), including common-factor models, confirmatory factor models, ESEM, common-factor GWAS with Q_SNP heterogeneity, multivariate Wald tests, and stratified GenomicSEM partitioned heritability. Reconciles results against MTAG multi-trait analysis. Handles sample overlap via the LDSC sampling-covariance matrix, identifies and resolves Heywood cases, and verifies model fit with CFI / RMSEA. Use when modeling latent genetic architecture across correlated traits, running multivariate GWAS on a shared factor, distinguishing factor-mediated from trait-specific SNP effects, or comparing GenomicSEM common-factor results against MTAG when both depend on accurate sampling covariance.

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Estimate causal effects of an exposure on an outcome from GWAS summary statistics using genetic instruments. Implements IVW (fixed/random), MR-Egger, weighted median/mode, MR-RAPS, CAUSE, GSMR-HEIDI, MR-PRESSO, MVMR, MR-Clust, LCV, and LHC-MR via TwoSampleMR, MendelianRandomization, MR-PRESSO, cause, and lhcMR. Use when testing causal direction between traits, evaluating drug-target effects via cis-pQTL/cis-eQTL, performing multivariable mediation MR, distinguishing causation from correlated horizontal pleiotropy, or producing STROBE-MR-compliant sensitivity batteries.

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Estimate bivariate genetic correlation (rg) between traits from GWAS summary statistics or individual-level genotypes using cross-trait LDSC, HDL, LAVA, rho-HESS, GREML-bivariate, Popcorn, and HDL-L. Use when quantifying shared genetic architecture between two traits, screening MR validity before causal inference, distinguishing global from locus-level rg, estimating trans-ancestry rg, separating partial from full causation via LCV gcp, or producing a STROBE-MR-compliant cross-trait sensitivity battery. Cross-trait LDSC intercept absorbs sample overlap and is NOT a bias; HDL is biased under sample overlap above ~5%. High rg between exposure and outcome motivates CHP-aware MR sensitivity (CAUSE, LHC-MR).

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Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro). Use when integrating GWAS with eQTL/sQTL/pQTL/mQTL, distinguishing shared causal variants from LD-driven coincidence, handling allelic heterogeneity, choosing between single-causal vs multi-causal methods, picking PP.H4 thresholds, running sensitivity over p12, or harmonising summary statistics for colocalization.

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生成图文并茂的分析报告/实验报告/质检报告（固定模版）。当用户要求"生成报告/总结报告/实验报告/质检报告/QC报告"，或分析流程收尾需要交付报告时使用。报告必须基于真实分析输出，包含固定章节结构、关键指标表格和真实结果图。

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Use this skill any time a .pptx or .potx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations as PowerPoint (.pptx) files; reading, parsing, or extracting text from any .pptx or .potx file (even if the extracted content will be used elsewhere, like in an email, summary, or creating a different type of slide deck); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates (.potx), layouts, speaker notes, or comments. Trigger whenever the user asks for a PowerPoint or .pptx file, or references a .pptx or .potx filename, regardless of what they plan to do with the content afterward. However, when the user asks for a deck, slides, a slide deck, or a presentation without naming a file format, default to using a dedicated slide-deck artifact type or a separate slides skill if this session offers one; otherwise, use this skill.

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docs (editable docs people share and comment on; the default for any document, named as a doc or not: a document, report, proposal, resume, cover letter, letter, contract, policy, form, template, worksheet, essay, handbook, guide, how-to, cheat sheet, SOP or other writing to keep, share, collaborate on, send, submit, print or sign; a doc exports to Word, PDF, Markdown or Google Docs, so needing a file to send, attach, upload, submit or print is no reason to pick Word, and a file nobody asked for is a doc, not Word; a plan, comparison, summary or notes asked in chat stays in chat; a pasted claude.ai artifact link may be a doc: check with docs tools first; Word or another file format named, tracked changes wanted, or a .docx to change or use as a template → that format's skill): making one → if no docs-connector instructions are in context, call its `guide` (topic.instructions) first; then create the doc (headings only, no body) before any search, file read or plan, even with files attached.

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Refresh the Key Metrics table in a thesis with current data from Financial Modeling Prep, with a Quartr standardized-statement tie-break for Revenue Growth / Gross Margin gaps (Step 4b-Q) and a scoped web-search fallback (Step 4b) when FMP has no data or resolved the wrong company. Use when user says "numbers", "refresh metrics", "update key metrics", or "refresh [TICKER]" with no other action implied. Surgical edit only — does NOT create research notes or propagate via /sync. Also flags (never auto-edits) stale price/valuation framing in the thesis Summary — see Step 10b.

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Earnings-season triage across ALL active theses (not just Live Portfolio holdings) — every earnings call reported inside the window gets a Quartr event summary, a Conviction-Trigger/Outstanding-Questions cross-reference, and a coverage check against existing Research notes, producing a ranked deep-read queue for /transcript. Use when user says "earnings sweep", "who reported", "triage earnings", "catch up on earnings season", or after any earnings-heavy stretch. Default window 14 days; `/earnings-sweep 90` covers a full season.

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Targeted deep research to fill a specific gap in an existing thesis. Use when user says "deepen", "flesh out", "expand on", "fill in", or specifies a thesis section to improve. Also supports --sync-metrics mode — detects stale financial metrics across every in-scope analytical section of a thesis (not just Key Metrics or Summary) and coherently updates every sentence that depends on them, using a Key-Metrics-table / FMP / web-search waterfall. Use when user says "sync metrics", "update the numbers throughout the note", or "fix stale figures across the whole thesis". The batch form `--sync-metrics --all-flagged` syncs every thesis flagged by the latest `/numbers --all-open` in one operation — detection fanned out to capped READ-ONLY agents, one consolidated confirmation gate, direct sequential writes (agents never write).

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。

Targeted deep research to fill a specific gap in an existing thesis. Use when user says "deepen", "flesh out", "expand on", "fill in", or specifies a thesis section to improve. Also supports --sync-metrics mode — detects stale financial metrics across every in-scope analytical section of a thesis (not just Key Metrics or Summary) and coherently updates every sentence that depends on them, using a Key-Metrics-table / FMP / web-search waterfall. Use when user says "sync metrics", "update the numbers throughout the note", or "fix stale figures across the whole thesis". The batch form `--sync-metrics --all-flagged` syncs every thesis flagged by the latest `$numbers --all-open` in one operation — detection fanned out to capped READ-ONLY agents, one consolidated confirmation gate, direct sequential writes (agents never write).

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。

Refresh the Key Metrics table in a thesis with current data from Financial Modeling Prep, with a scoped web-search fallback (Step 4b) when FMP has no data or resolved the wrong company. Use when user says "numbers", "refresh metrics", "update key metrics", or "refresh [TICKER]" with no other action implied. Surgical edit only — does NOT create research notes or propagate via $sync. Also flags (never auto-edits) stale price/valuation framing in the thesis Summary — see Step 10b.

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Use when the user asks about the pwdev-prd audit trail — 'auditoria do prd', 'eventos', 'decisões registradas', 'audit report', 'exportar relatório de auditoria' — querying the shared SQLite database read-only (summary, events, decisions, artifacts, stats, export, query).

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Use when the user wants to query the local pwdev audit trail — 'ver auditoria', 'relatório de auditoria', 'audit stats', 'exportar auditoria em PDF' — summary, events, decisions, artifacts, statistics, a Markdown/PDF export or a custom read-only SELECT. Do NOT use to enable the audit (feat-init) or for plan status (feat-status).

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Promote QA → production by opening a PR from peterdrier/Humans:main to nobodies-collective/Humans:main with a properly-qualified commit summary. Use when the user says "PR to production", "promote to prod", "PR from origin to upstream", "prod PR", or any variation of pushing batched fork changes upstream. Always use this skill for the two-remote promotion flow even if the user doesn't say "prod" explicitly.

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Systematically QA test a web application and fix bugs found. Runs QA testing, then iteratively fixes bugs in source code, committing each fix atomically and re-verifying. Use when asked to "qa", "QA", "test this site", "find bugs", "test and fix", or "fix what's broken". Proactively suggest when the user says a feature is ready for testing or asks "does this work?". Three tiers: Quick (critical/high only), Standard (+ medium), Exhaustive (+ cosmetic). Produces before/after health scores, fix evidence, and a ship-readiness summary. For report-only mode, use /qa-only. (gstack) Voice triggers (speech-to-text aliases): "quality check", "test the app", "run QA".

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Produces a compact KPI digest showing how key metrics changed over a period and what's driving the movement. Use this skill when someone asks for a performance summary, a weekly recap, a morning briefing, a KPI update, or any variation of "how did we do this week/month." Also trigger for "give me a performance overview," "what moved in the last 7 days," "pull our AA KPI report," or "summarize our metrics."

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。

Produces a compact KPI digest showing how key metrics changed over a period and what's driving the movement. Use this skill when someone asks for a performance summary, a weekly recap, a morning briefing, a KPI update, or any variation of "how did we do this week/month." Also trigger for requests like "give me a performance overview," "what moved in the last 7 days," "pull our KPI report," or "summarize our metrics."

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。