Claude Skills by HolobiomicsLab

Use when you have a SMILES input file of small organic molecules and

Use when you have generated a TPs object (via generateTPs) containing

Use when when preparing SMILES strings as training targets for a sequence-to-sequence

Use when you have a set of anchor feature pairs (m/z and retention time

Use when you have multiple mzML or mzML.gz files from LC-IMS-MS/MS instruments

Use when after composite map peak detection has generated a full unfiltered

Use when analyzing MALDI-mass spectrometry imaging data in which sodium

Use when after computing a biweight midcorrelation similarity matrix

Use when you need to verify the scope and completeness of a software

Use when when you need to understand the modular structure of a multi-component

Use when you are preparing to run the MetaboDirect pipeline for the first

Use when you have edited one or more core algorithm scripts (Modular.r,

Use when you need to assess whether a newly developed FT-ICR MS pipeline

'Use when you are preparing to run LipidMatch or FluoroMatch and need

Use when when a tool claims to be 'scalable' or 'performance-conscious'

Use when when you have a scientific software tool (e.g., Met-ID) that

Use when after implementing code changes to MS2Query (e.g., modifying

Use when after successful compilation or artifact generation (e.g., after

Use when you need to determine the full scope of hardware and methodological

Use when after making code modifications (bug fixes, new features, or

Use when a software package claims to bundle or install a specific number

Use when when you have a small molecule (SMILES, MOL, or SDF format)

Use when when you have a GitHub-hosted Python project (or other supported

Use when when you need to reverse-engineer or formally document the computational

Use when when you need to verify that a specific data transformation

Use when you need to obtain the full source code of a scientific tool

Use when normalizing peptide or protein-level quantification matrices

Use when you have a large collection of MS/MS spectra (hundreds of thousands

Use when you have computed a sparse pairwise distance matrix from nearest

Use when when you have tandem mass spectra (mz/intensity pairs with precursor

Use when when you have a feature matrix (samples × features) and need

Use when clustering large collections of high-resolution MS/MS spectra

Use when when converting high-resolution tandem mass spectra to vectors

Use when when you have loaded a dataset of molecular fingerprint vectors

Use when after loading and preprocessing a Cardinal MSImagingExperiment

Use when after LC-MS feature detection, alignment, quantification, and

Use when you have raw imzML files (paired with .ibd binary data) from

Use when when you have preprocessed spatial transcriptomics (ST) and

Use when after annotating ion pairs with known adducts (using adductMatch

Use when after identifying candidate parent–adduct mass-difference pairs

Use when when you have paired spatial transcriptome and metabolome datasets

Use when when you have loaded MSI peak data with associated m/z values

Use when when analyzing imaging mass spectrometry datasets where you

Use when preparing raw ion image data from mass spectrometry imaging

Use when your spatial metabolomics dataset contains raw m/z features

Use when when you have paired spatial metabolomics and spatial transcriptomics

Use when when annotating matrix-related peaks in MSI datasets where candidate

Use when you have two co-registered LA-ICP-MS element channel images

Use when you have mzML files from a mass spectrometry imaging (MSI) experiment

Use when apply SSC when you have preprocessed and normalized MS imaging