Results for “summary”

Detects m6A modifications from Oxford Nanopore direct-RNA-sequencing (ONT DRS) signal data using m6Anet (Hendra 2022 *Nat Methods* 19:1590; multiple-instance-learning neural network over DRACH 5-mer signal). Covers the required upstream pipeline (Dorado / Guppy basecalling -> minimap2 transcriptome alignment with `-ax map-ont -uf -k14 --secondary=no` -> nanopolish eventalign with `--scale-events --signal-index` (m6Anet-required) plus `--summary` / `--threads` housekeeping -> m6anet dataprep -> m6anet inference), per-site vs per-read probability interpretation including the `mod_ratio` per-site stoichiometry column, the DRACH-only modeling constraint, minimum-coverage thresholds (20-50 reads per site for stable probability estimates), multi-condition comparison via xPore (Pratanwanich 2021 *Nat Biotechnol* 39:1394), Nanocompore (Leger 2021 *Nat Commun* 12:7198), ELIGOS (Jenjaroenpun 2021 *NAR* 49:e7), and Dorado native modification calling (RNA004 chemistry, 2024+), reference-transcriptome version pinning, the cDNA-vs-DRS chemistry distinction (cDNA-Nanopore CANNOT be used for modification detection), and orthogonal validation against MeRIP / GLORI. Use when calling m6A from ONT DRS without immunoprecipitation, choosing m6Anet vs xPore vs Nanocompore vs ELIGOS vs Dorado native, interpreting per-site `probability_modified` vs `mod_ratio` vs per-read modification probabilities, comparing methylation between conditions from ONT data, deciding between m6Anet for known DRACH sites and Dorado/Remora for genome-wide screening, pinning RNA002 vs RNA004 chemistry and basecaller model versions, or troubleshooting eventalign / dataprep failures.

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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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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 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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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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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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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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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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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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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 when the user asks about FCRA adverse action procedures — what to do when a background check (MVR, criminal, drug test) returns information that may lead to denying employment or terminating a CDL driver. Covers the 5-business-day pre-adverse-action notice, FCRA Summary of Rights, final adverse action notice, state-specific add-ons (CA, NY, etc.), and how to handle disputes. Cite 15 USC § 1681 (FCRA) and 49 CFR 391.

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Author a pull request an AI coding agent can actually get merged: a scoped, coherent diff; a Summary and Test Plan backed by real evidence; correct triage of required-and-blocking CI gates versus external/advisory checks (e.g. a Cloudflare Pages preview build); draft-while-WIP discipline; named fixup commits for real review findings; and a clean landing through a merge queue without force-pushing or bypassing branch protection. Use when opening, updating, triaging red CI on, or landing an agent-authored GitHub PR. NOT for this repo's internal release ceremony, actor embodiments, or contributor mirror-sync mechanics (use port-daddy-internal-dev), tracking backlog/issue lifecycle across a board (use agent-issue-tracker-workflow), or deciding what to build next / sequencing a roadmap (use legible-roadmap-with-sidequests).

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Analyze a Coval accent testing report from runs across different speaker accents. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or metric summary and wants evidence-backed next steps such as prompt changes, STT/confirmation adjustments, accent-robust routing, or expanded accent coverage.

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Analyze a Coval audio-quality testing report from runs across different voice, speaking-style, volume, interruption, and background-noise scenarios. Use when a user provides a Coval report URL, report export, run IDs, screenshots, or metric summary and wants evidence-backed next steps such as prompt changes, tool handling fixes, STT/TTS adjustments, trace setup, or expanded audio-scenario coverage.

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Ingest meeting transcripts from any recorder into Knowledge with attendee enrichment, timeline merge, supported decisions and commitments, and verification of substance and sequence. Summary-only input is not a verified meeting ingestion.

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Runs the end-of-day maintainer handoff for NemoClaw. Checks version target progress, bumps stragglers to the next patch version, generates a QA handoff summary, and cuts the release tag. Use at the end of the workday. Trigger keywords - evening, end of day, EOD, wrap up, ship it, cut tag, handoff, done for the day.

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Use this skill when building or debugging table usage with nuxt-ui-tools as a package consumer. Covers defineTableSchema, useTable, DataList, granular composition, columns, filters, sorting, offset or cursor loading, layouts, summary rows on phones, first-use empty states, actions, selection, accessible row names, context, and URL state with concrete examples.

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Use this skill any time a .pptx file is involved in any way — as input, output, or both. This includes: creating slide decks, pitch decks, or presentations; reading, parsing, or extracting text from any .pptx file (even if the extracted content will be used elsewhere, like in an email or summary); editing, modifying, or updating existing presentations; combining or splitting slide files; working with templates, layouts, speaker notes, or comments. Trigger whenever the user mentions "deck," "slides," "presentation," or references a .pptx filename, regardless of what they plan to do with the content afterward. If a .pptx file needs to be opened, created, or touched, use this skill.

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Generates professional infographics with 21 layout types and 20 visual styles. Analyzes content, recommends layout×style combinations, and generates publication-ready infographics. Use when user asks to create "infographic", "信息图", "visual summary", "可视化", or "高密度信息大图".

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Draft a client proposal — "write a proposal for", "draft a proposal", "turn this brief into a proposal". Produces executive summary, understanding of their problem, approach, scope, and pricing.

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Monitor Power Automate flow health, track failure rates, and inventory tenant assets using the FlowStudio MCP cached store. The live API only returns top-level run status. Store tools surface aggregated stats, per-run failure details with remediation hints, maker activity, and Power Apps inventory — all from a fast cache with no rate-limit pressure on the PA API. Load this skill when asked to: check flow health, find failing flows, get failure rates, review error trends, list all flows with monitoring enabled, check who built a flow, find inactive makers, inventory Power Apps, see environment or connection counts, get a flow summary, or any tenant-wide health overview. Requires a FlowStudio for Teams or MCP Pro+ subscription — see https://mcp.flowstudio.app

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Configure and use Honcho memory with Hermes -- cross-session user modeling, multi-profile peer isolation, observation config, dialectic reasoning, session summaries, and context budget enforcement. Use when setting up Honcho, troubleshooting memory, managing profiles with Honcho peers, or tuning observation, recall, and dialectic settings.

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Operate the Teams meeting summary pipeline via Hermes CLI — summarize meetings, inspect pipeline status, replay jobs, manage Microsoft Graph subscriptions.

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