Use when you have an untargeted metabolomics feature table (with m/z, retention time, and statistical significance values) and want to predict which metabolic pathways and…
Use when when you have multiple batches of metabolomics data in SummarizedExperiment
Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign…
Use when when preparing to run Over-representation Analysis (ORA) on metabolomics pathway data, after you have loaded both a metabolomics pathway database (e.g., KEGG, MetExplore)…
Use when you have a set of candidate metabolites for an unknown compound detected in a liquid chromatography–mass spectrometry (LC-MS) experiment, predicted RTs from a trained DNN…
Use when you have peak-abundance data (after molecular formula assignment, peak filtering by m/z, isotope, ppm error, and sample presence thresholds) and you need to quantify and…
Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to…
Use when after running do.findmain on a RAMClustR-clustered object to infer molecular weights and assign features to compound clusters, when you need to conduct structural…
Use when after preprocessing, imputation, and batch correction of LC-MS peak tables when you need to group redundant or related feature measurements (e.g., [M+H]+ and [M+Na]+…
Use when designing or validating a metabolomics pathway analysis experiment, especially when you have uncertainty about how many metabolites your detection platform will reliably…
Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment.
Use when you have simulated or experimental mzML data from two or more fragmentation controllers (e.
Use when you have a measured m/z value from spatially-resolved metabolomics or mass spectrometry imaging and need to assign a molecular formula with high confidence.
Use when you have XCMS-processed LC/MS peak data from dual-labeled (e.g., 13C) and unlabeled (12C) metabolomics samples and need to distinguish features genuinely enriched by…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological — from…
Use when you have (1) peak-picked LC-MS AIF features in a feature table with m/z and retention time, (2) corresponding xcmsSet and RAMClustR pseudo-MS/MS spectral objects from…
Use when you have an annotated list of metabolite compounds (with associated m/z features or compound IDs) and want to determine which KEGG metabolic pathways are significantly…
Use when when beginning an untargeted LC-MS annotation workflow, before attempting to match experimental m/z peaks to metabolite identities.
Use when you have a SummarizedExperiment object containing NMR or MS metabolomic data with aligned phenotype information (BMI, disease status, age, gender), and you need to…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its metabolic fate across one or more biological systems.
Use when when you have generated a set of candidate metabolites for a given experimental MS/MS spectrum and need to determine which candidate is most likely to be the true…
Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with…
Use when you have defined one or more proton NMR spectral regions-of-interest (ROIs) with lower and upper chemical-shift bounds (in ppm) from an experimental NMR spectrum of a…
Use when after constructing a background set for ORA in metabolomics: you have loaded an experimental detection list and a metabolomics pathway database, applied background-set…
Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or…
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…
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…
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…
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 setting product North Star metrics, decomposing high-level business metrics into actionable sub-metrics and leading indicators, mapping strategy to measurable outcomes,…
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 /…