Claude Skills by HolobiomicsLab

Use when you have an NMR mixture spectrum (1D or 2D) and a library of

Use when you have MS/MS spectra matched to a reference library via both

Use when you have a GC-MS dataset with multiple sample files (e.g., Std_soln_00,

Use when after compound database dereplication has produced candidate

Use when after submitting a fingerprint or spectrum query to the CANOPUS

Use when after peaks have been filtered (by m/z, isotopic presence, and

Use when you have an unknown mass spectrometry spectrum (acquired experimentally

Use when after peak picking has identified individual signals in an INADEQUATE

Use when after modifying a FIDDLE configuration file to add or remove

Use when you have a GC-MS dataset with a Match.Factor column (or equivalent

Use when after feature extraction from LC–MS raw data (via XCMS, MS-Dial,

Use when you have MS2 .mzML spectral data from untargeted metabolomics

Use when when you have pre-computed embeddings for query and reference

Use when you have raw GC-MS or LC-MS data in vendor format (NetCDF, .raw,

Use when you have LC-MS/MS data in mgf format and a custom spectral database

Use when after training a FlavorFormer model end-to-end with weighted

Use when you have preprocessed MS/MS spectra (noise-filtered, normalized)

Use when when you have an unknown MS/MS spectrum (in .

Use when you have metabolomics results from multiple studies with compound

'Use when when you have prepared raw mass spectrometry transition data

Use when when you receive a raw query string destined for the ClassyFire

Use when you have an experimental MS/MS spectrum (m/z and intensity pairs

Use when when integrating MS/MS spectra from multiple source repositories

Use when after filtering a peak table to remove mispicked ions, group

Use when ingesting compound metadata from multiple sources (PubChem,

Use when immediately after loading metabolomics measurements into a SummarizedExperiment

Use when after XCMS feature detection, retention time correction, regrouping,

Use when when you have a set of query chemicals (e.g., ethyl hexanoate,

Use when after marker identification or feature selection has produced

Use when after completing doAnalysis on a SummarizedExperiment object

Use when after peak picking on INADEQUATE NMR spectra when you have a

Use when you have a set of chemical compounds (identified by name, SMILES,

Use when apply this filter after batch correction of compound/internal-standard

Use when after batch correction and internal standard ratio calculation

Use when when you have generated spectral embeddings for a query set

Use when when running Pickaxe reaction network expansion and you need

Use when you have completed XCMS grouping on LC-MS data and suspect misaligned

Use when xCMS alignment produces suspected misaligned feature groups

Use when you have raw peak area or intensity measurements for both compounds

Use when you have a set of query chemicals and a reference library (organized

Use when you have a collection of preprocessed MS/MS spectra with structural

Use when you have two MS/MS spectra from related compounds (e.g., a reference

Use when you have a set of seed compounds (as SMILES strings) and want

Use when when you have SMILES strings or molecular structures for compounds

Use when you have a collection of DNA adduct or small-molecule compound

Use when when you have experimental MS/MS data (peak lists, precursor

Use when you have a large indexed gzip file (igz format) with metadata

Use when when consolidating multiple cleaned and validated data sources

'Use when when processing aligned LC-MS data across multiple samples

Use when at the start of any DaDIA pipeline execution, or whenever you