Claude Skills by HolobiomicsLab

Use when you have a peak-abundance matrix from FT-ICR MS (peaks as rows,

Use when you have intracellular metabolomics data paired with constraint-based

Use when you have annotated mass-difference peaks with known adduct identities

Use when you have extracted a large feature set of m/z values (hundreds

Use when when you have an untargeted metabolomics dataset from HPLC–MS

Use when you have a feature intensity table with feature metadata (m/z,

Use when you have ESI/LC-MS test spectra requiring candidate metabolite

Use when you have MZmine-aligned features with m/z and retention time,

Use when you have a MultiAssayExperiment object with metabolite measurements

Use when you have ESI/LC-MS test spectra requiring metabolite annotation

Use when when annotating large-scale untargeted metabolomics datasets

Use when after running the annotateRC function on LC-MS All-ion fragmentation

Use when you have a feature table with candidate metabolite annotations

Use when you have paired metabolomics data (MS/MS spectra and feature

Use when after running in silico annotation tools (SIRIUS, ISDB) or spectral

Use when when preparing to run Over-representation Analysis (ORA) on

Use when after mzRAPP has exported a benchmark CSV file from processing

Use when you have LC-HRMS mzML files processed by a non-targeted peak-detection

Use when you have a preprocessed metabolomics dataset with a binary outcome

Use when after preprocessing GCxGC-MS chromatograms (smoothing, baseline

'Use when you have: (1) a set of predicted candidate metabolites with

Use when you have a set of candidate metabolites for an unknown compound

Use when after running annotateRC() on LC-MS AIF features, when you need

Use when you have a query mass spectrum matched to multiple candidate

Use when you have an untargeted mass spectrometry spectrum (MS/MS data)

Use when when you have omu_summary output containing log2FoldChange values

Use when you have peak-abundance data (after molecular formula assignment,

Use when when you have an omu_summary output dataframe with Class metadata

Use when after running omu_summary statistical comparison on count data

Use when after running RAMClustR clustering on XCMS-detected LC-MS features

Use when after running do.findmain on a RAMClustR-clustered object to

Use when after preprocessing, imputation, and batch correction of LC-MS

Use when apply this filter when raw metabolomics data contains metabolite

Use when you have normalized peak intensity tables from FT-ICR MS data

Use when when you have mzML files from targeted or untargeted metabolomics

Use when you have intracellular metabolomics abundance data (absolute

Use when when you have a list of known metabolite concentrations and

Use when after variance-stabilizing normalization and imputation of metabolomic

Use when you have a raw metabolite count data frame (e.g., c57_nos2KO_mouse_countDF)

Use when designing or validating a metabolomics pathway analysis experiment,

Use when after normalizing a metabolomic feature matrix when you have

Use when you have raw or baseline-corrected metabolite abundance measurements

Use when when performing untargeted metabolomics annotation at scale

Use when when you have paired tandem MS spectra and known molecular structures

Use when after generating or filtering transformation products using

Use when you have metabolomics metadata in mwTab or tabular format with

Use when you need to construct a reference metabolomics database from

Use when after peak networks have been identified and clustered from

Use when you have raw NMR metabolomics measurements paired with pre-analytical

Use when you have simulated or experimental mzML data from two or more