Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of…
Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference…
Use when after statistical analysis (e.g., MB-PLS with permutation testing) has identified a subset of significant LC-MS features (p < 0.05 or similar threshold) that require…
Use when after MamsiStructSearch has completed structural clustering of statistically significant LC-MS features (p < 0.
Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural…
Use when when you have raw or GNPS-processed MS2 spectral data from microbial strains and need to organize spectra into molecular families (grouped by spectral similarity) while…
Use when when importing a tab-delimited or Sciex OS text export metabolomics dataset into mzQuality, before building the SummarizedExperiment object.
Use when you have raw metabolomics count data (e.g., from mass spectrometry or NMR experiments) in tabular format and associated sample metadata (e.g., treatment groups,…
Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to…
Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high…
Use when when beginning an LC-MS/MS metabolomics analysis pipeline and you have preprocessed xcms result objects (XcmsExperiment or legacy xcmsSet) that need to be loaded into…
Use when after completing outlier detection, batch correction, and quality metric calculation on a SummarizedExperiment object using mzQuality's doAnalysis function, and after…
Use when when you have LC-MS/MS acquisitions in DDA mode and need to train a customized DNMS2Purifier model to purify chimeric MS/MS spectra specific to your experimental…
Use when when you have generated a feature abundance matrix from mzrtsim() peak list simulation with known sample-level attributes (condition assignments, batch labels, sample…
Use when you need to reverse-engineer or document the architecture of a multi-component research software system where design information is embedded in repository structure,…
Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be…
Plan and implement experimental Metal neural-rendering paths with MetalFX, Metal 4 machine-learning passes, Metal tensors, and Metal Performance Primitives.
Profiles shotgun metagenomes to species/SGB relative abundance with MetaPhlAn 4's clade-specific marker genes (bowtie2 short reads, minimap2 long reads).
Metaphysical inquiry into the fundamental nature of reality. Covers ontology (what exists), substance and properties, universals vs.
Use when you have extracted clustering or classification accuracy metrics (NMI, ARI, purity scores) for two or more competing methods evaluated on multiple datasets, and need to…
Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode…
Write and revise the Methods section of research papers to ensure reproducibility; use when preparing an IMRAD manuscript or responding to journal/reporting-guideline requirements…
Audit a minimum-necessary research Question Pack for evaluation validity, leakage, confounding, statistics, reproducibility, falsification, and evidence quality.
Apply Bootstrapped AI Methodology Engineering (BAIME) to develop project-specific methodologies through systematic Observe-Codify-Automate cycles with dual-layer value functions…
Evaluate study design, identify methodological weaknesses, and assess internal and external validity.
Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs.
Build comprehensive DNA methylation maps by aggregating WGBS (Whole Genome Bisulfite Sequencing) data across multiple ENCODE experiments, donors, and labs.
Use when after calculating differential methylation across samples using calculateDiffMeth(), when you need to separately enumerate and extract hyper-methylated (increased…
Use when you have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level…
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons.
Use when when analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when…
Atmospheric analysis with MetPy and Siphon: download NWP data from THREDDS/NOMADS, plot skew-T log-P diagrams, compute CAPE/CIN parcel metrics, and build synoptic composites.
Use when investigating unexpected metric changes - systematically narrows root cause through 4D segmentation, intrinsic vs extrinsic factor analysis, hypothesis testing, and North…
Search, list, and audit GrowthBook metrics and fact tables. Use when the user asks "what metrics do we have", "find our revenue metric", "what fact tables exist", "which metrics…
Use when setting product North Star metrics, decomposing high-level business metrics into actionable sub-metrics and leading indicators, mapping strategy to measurable outcomes,…
Use when the user asks for body action, choreography, physics, object movement, movement timing, action continuity, stunt direction, or motion-reference mapping, for any…
Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL…
Search the web, crawl pages, research companies, and find people using Exa AI via n8n webhooks. Use when the user says "search for", "look up", "research company", "find person",…
Krypto-Unternehmen beantragt MiCA-Lizenz für Stablecoin (ART oder EMT) bei BaFin: MiCA VO 2023/1114 Art. 16-21 Whitepaper-Pflicht Art. 19 Eigenmittel Art. 35 Reserveaktiva Art...
Analyze DNA microarray data from GEO datasets. Use when asked to analyze microarray data, perform differential expression analysis, or when given a GEO accession (GSE*).
Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single…
Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1,…
Browser agent mã nguồn mở của Microsoft Research — agent viết Python/Playwright script thay vì click từng bước, script có thể reuse. SOTA 86.7% trên Online-Mind2Web.
Boucle d'amélioration nocturne autonome du simulateur diagnostic microsolder. Pattern autoresearch — tune engine_params.json (knob layer, préféré) ou modifies simulator.py /…
Use when working with UMI-tagged or barcoded sequencing data — extracting sample/cell/UMI barcodes from reads, demultiplexing with degenerate adapter patterns, trimming barcodes…
Migrate Exa, Tavily, Perplexity, or Firecrawl web-data integrations completely to the appropriate Parallel products while preserving application behavior.
Generate the migration RESEARCH document docs/migration/NNN-research-.md for moving any legacy component (WCF service, ASP.NET MVC/WebForms front-end, Web API, Windows…
Generate the migration TEST PLAN document docs/migration/NNN-tests-.md from an existing NNN-research-.md, for any legacy component being migrated (service,…
Apply behavioral mimicry — making an interface element behave like a familiar physical object so the user''s physical-world intuitions transfer to the digital interaction.
Mindset theory, implicit theories of intelligence, and motivation research applied to learning. Covers fixed vs.
Develop Minecraft server plugins using the Paper/Bukkit/Spigot API for Minecraft 1.21.x. Handles creating Paper plugins with JavaPlugin, event listeners with @EventHandler,…
Mingli (命理) — Multi-system daily horoscope: Western astrology (natal chart + transits), Ba-Zi / Four Pillars (Bát Tự), numerology, I Ching (Kinh Dịch).
成本可預期的輕量多來源網路研究——用「一個比較項目派一個 subagent」平行深查,15 個項目以內直接跑、超過 15 才停下來問使用者,最後彙整成一張帶來源的比較表。這是內建 /deep-research 的省成本替代:刻意砍掉「每條主張多票對抗式查證」那個會讓 agent…
Activate economy coding stance. Research-backed emotional mode from claude-temper.
[DEPRECATED] Use /research skill with Zai MCP instead - Optimal patterns for MiniMax MCP tools
Use MiniMax MCP to perform web searches and retrieve up-to-date information from the internet. Use when the user asks to search the web, find current information, look up news, or…
Use when a task needs the judgment of a Mining and Geological Engineer — running a pit-slope or underground-opening stability check (limit-equilibrium factor of safety, RMR/Q…
Guide for creating deployment scripts for the vdarkobar/lab repository on Debian 13 (Trixie) servers in Proxmox VE environments
Use when choosing and defending the research design for a MIS Quarterly manuscript — a behavioral survey/experiment, an economics-of-IS identification strategy, a design-science…
Use when shaping or stress-testing a research question for MIS Quarterly — confirming it is a genuine information-systems question, naming which of the four IS traditions…