Claude Skills by HolobiomicsLab

Use when after XCMS peak picking, alignment, and grouping when you have

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

Use when after completing Part 4 (Identification of ISF Features) in

Use when when XCMS-aligned LC-MS data shows coefficient of variation

Use when you have raw LC-MS spectral peak data (in the format provided

Use when after loading centroided .mzML LC–MS runs and before executing

Use when starting from raw LC-MS spectral files (mzML or mzXML format)

Use when after configuring LDA hyperparameters (alpha, beta, number of

Use when you have a preprocessed bag-of-fragments corpus derived from

Use when after running gensim LDA on a corpus of MS2 fragmentation features,

Use when when you have a 1D signal array (e.g., extracted ion chromatogram,

Use when after GCMSFormer has predicted the pure mass spectral matrix

Use when you have a metabolomics dataset (LC/MS or GC/MS) with missing

Use when when you have a complete metabolomics abundance table (e.g.,

Use when after khipu has grouped LC-MS features into empirical compounds

Use when when you need to parse a domain-specific query language (like

Use when you have a mass-spectrometry query string written in MassQL

Use when you need to enable users to express complex domain-specific

Use when when you need to reconstruct or validate the control-flow architecture

Use when you have raw .msp spectral library files (e.g., from MassBank

Use when you have custom lipid entries (e.g., synthetic lipids, rare

Use when after applying mspcompiler pipeline transformation steps (e.g.,

Use when you have experimental MS/MS spectra (from mzML, mzXML, or raw

Use when you have an unknown electron ionization (EI) mass spectrum and

Use when after a Transformer model (e.g. GCMSFormer) has predicted the

Use when you have deposited mass spectrometry imaging datasets in NetCDF

Use when when preparing to perform differential abundance analysis on

Use when when you have metabolomic feature intensities (dependent variables)

Use when you have a set of calibration samples (spiked compounds) with

Use when your metabolomics experiment includes calibration line samples

Use when after log-transformation and missing-value imputation of featuredata

Use when you have extracted retention times at peak maxima (rtFittedAPEX)

Use when when you have a targeted metabolomics dataset with known concentration

Use when when you have 1H-NMR metabolite measurements from Nightingale

Use when after generating theoretical spin multiplets for individual

Use when after running a scoring algorithm (e.g., MetcalfScoring) on

Use when you have loaded GCFs (from AntiSMASH via BigScape clustering),

Use when you have vendor-specific raw mass spectrometry data (ThermoFisher

Use when when you have high-resolution tandem mass spectrometry (MS2)

Use when you have a preprocessed and normalized lipid abundance matrix

Use when after lipid matching is complete and you have a table of normalized

Use when when processing mass spectrometry imaging data with multiple

Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL,

Use when a spatial metabolomics dataset contains semicolon-delimited

Use when constructing a de novo or expanded lipid spectral library that

'Use when you have a LipidomicsExperiment object with logged and normalized

Use when immediately after loading raw lipid identifiers from LipidSearch

Use when when you have acquired a CCS reference library (such as DTCCSN2

Use when you have a lipid identification or library-generation task that

Use when when loading lipidomics data (from Skyline CSV, numerical matrix,