Claude Skills by HolobiomicsLab

'Use when you have a preprocessed peak table (feature matrix: samples

Use when you have integrated, normalized lipidomic and metabolomic feature

Use when when you have a metabolite-pathway association table and per-sample

Use when after WGCNA-derived metabolic modules have been identified and

Use when after peak filtering and normalization, when you have a peak-abundance

Use when when you have normalized peak intensities from FT-ICR MS metabolomic

Use when you have a collection of tandem MS/MS samples (stored in MassIVE)

Use when you have paired microbiome and metabolomic (or similar compositional)

Use when when you have preprocessed non-targeted LC-MS/MS feature tables

Use when after data normalization (Step 7) when you have a preprocessed

Use when after preprocessing and aligning 2D chromatogram data (baseline

Use when you have mwTab format files (Mass Spectrometry or Nuclear Magnetic

Use when you have mwTab-formatted files from the Metabolomics Workbench

Use when immediately after parsing mzML files into (m/z, scan_number,

Use when after loading a feature table with m/z values from MS-Dial output

Use when when invoking Asari to process centroid mzML files for the first

Use when you have raw metabolomics data in mzML or mzXML format and need

Use when you have LC–MS/MS data processed through MZmine2 or MZmine3

Use when when building or extending a mass spectrometry data parser that

Use when you have mzML-format mass spectrometry data files and need to

Use when you have raw LCMS data in mzML format and a feature table (CSV)

Use when when you need to generate reproducible synthetic LC/GC-MS raw

Use when when you have mass spectrometry raw data in mzML format and

Use when you have mass spectrometry raw data in mzML format (including

Use when you have peak properties (mass, intensity, retention time) for

Use when after frequency-based denoising and sample-level aggregation

Use when you have raw mzML files from a mass spectrometry instrument

Use when you have raw profile LC-MS data in .mzML format and need to

Use when when you have centroided mzML format LC–MS files from multiple

Use when when you have a real mzML file from an untargeted metabolomics

Use when you have raw LC- or GC-HRMS data from vendor instruments (ESI

Use when you have a compressed mzML file (mzML.gz or indexed gzip format)

Use when after running an Environment simulation in ViMMS that has generated

Use when after completing a virtual LC-MS/MS acquisition simulation using

Use when after running a ViMMS simulation loop with a fragmentation controller

Use when after executing smiter.synthetic_mzml.write_mzml to generate

Use when after downloading an mzML file from a remote repository (e.g.,

'Use when you have raw LC-HRMS metabolomics data in mzML or ABF format

Use when your raw LC-MS data are in vendor-specific binary formats (e.g.,

Use when you have raw LC-MS/MS data in mzML or mzXML format and need

Use when when you have raw mzML or mzXML files containing uncompressed

Use when after running AirdPro's CLI conversion pipeline (run-cli.sh

Use when you have mzML-format raw data files (from any mass spectrometry

Use when when beginning a metabolomics annotation workflow with raw MS2

Use when you have an indexed gzip–compressed mzML file (mzML.gz with

Use when you have mzML files generated from raw vendor mass spectrometry

Use when you have one or more mzML files (XML-based mass spectrometry

Use when your input is an mzML file (XML-based mass spectrometry data

Use when when you have mass spectrometry data stored in mzPeak format

'Use when you have raw mass spectrometry data (vendor formats, mzML,