Claude Skills by HolobiomicsLab

Use when you have a GNPS molecular network (in GML or GraphML format)

Use when you need to create a new backend to integrate MS data from a

Use when when you have vendor-format LC-MS acquisition files (Thermo

Use when you have acquired raw mass spectrometry data from ThermoFisher,

Use when you have vendor-specific raw mass spectrometry data files (e.g.,

Use when when you need to convert vendor-specific raw mass spectrometry

Use when training embeddings from multi-modal spectral data (peak information

Use when you have multiple centroided .mzML LC-MS files that need to

Use when after MS-DIAL has completed feature detection and peak alignment

Use when you have imported raw imzML or Analyze 7.5 imaging data and

Use when your MSI data is stored in a Cardinal imaging experiment object

Use when you have MSI intensity data exported from MSiReader or SCiLS

Use when you have MSI intensity data exported from MSiReader, SCiLS,

Use when when you need to validate that MSI software (e.g., LipidQMap)

Use when after calculating mean intensity values across all spectra in

Use when when you have imzML-format MSI data and need to identify biochemical

Use when you are converting a processed Cardinal MSImagingExperiment

Use when when loading mass spectrometry imaging data from imzML or Analyze

Use when you have loaded a feature-by-pixel intensity matrix (HDF5 format

Use when after isotope correction when you have extracted intensity matrices

Use when after generating a 3D pixel array (shape n+1, y, x) from raw

Use when you have processed and quantified MSI data from one or more

Use when you have processed MSI data (peak matrix and spatial coordinates)

Use when you have MSI intensity data exported from commercial software

Use when you have raw line-scan MSI data (from Bruker .d/.baf, converted

Use when use this skill at the start of any MSI analysis workflow when

Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays

Use when after reading an imzML file (continuous or processed format)

Use when after peak alignment with peakAlign(), when you have an MSImagingExperiment

Use when when you have a target compound (modified or unmodified) and

Use when you have raw or downloaded MSMS spectra (from online resources

Use when removing invalid or malformed entries (e.g., SMILES validation,

Use when when you have successfully resolved a USI string to extract

Use when you have acquired EI or MS2 library files in MSP format (e.g.,

Use when you have raw .msp files containing mass spectra records and

Use when you have one or more .msp spectral library files (NIST format)

Use when you are parsing mass spectrometry spectral library files in

Use when you have a Mass Spectrum Point (MSP) file containing electron

Use when you have a .msp format MS/MS spectrum library (e.g., from MassBank

Use when when you have prepared metabolomics data (e.g., covid_data)

Use when you have statistically significant features from multiple LC-MS

Use when you have independent LC-MS assays (e.g., positive and negative

Use when when you have a suite of Sphinx gallery example scripts targeting

Use when when building a mass spectrometry visualization library that

Use when you have a SummarizedExperiment object containing both a raw/imputed

Use when your metabolomics experiment includes samples acquired across

Use when when building an end-to-end deep learning model that predicts

Use when when you have LC-MS normalized intracellular metabolite abundance

Use when after importing and manually aligning two element channels in

Use when your TWIM-MS dataset contains ions with multiple charge states