Claude Skills by HolobiomicsLab

Use when after loading spatial metabolomics data (from CSV, imzML, or

Use when after GNPS spectral library matching has been completed on a

'Use when after training a DeepMSProfiler deep learning model and generating

Use when you have normalized peak intensity tables from FT-ICR MS data

Use when you have a measured m/z value from spatially-resolved metabolomics

Use when you have ion-mobility mass spectrometry metabolomics data with

Use when after selecting statistically significant features from multi-assay

Use when after importing raw metabolomics data (e.g., from Metabolon,

'Use when after MS1 feature extraction from mzXML files when you have:

Use when you have normalized abundance data from LC-MS/MS for multiple

Use when after PuInc_seeker has identified putative incorporations (m/z

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

Use when you have peak-picked LC-MS metabolomics data in a tabular format

Use when after m/z grouping and pairwise alignment detection when you

Use when when metabolomics data contains both QC control samples and

Use when after retention-time correction and data alignment have been

Use when you have one or multiple raw mzXML/mzML files from DDA, DIA,

Use when you have a raw metabolite abundance matrix (e.g., from MSPrep

Use when after drift correction and before imputation, when you have

Use when immediately after generating a feature table (m/z, retention

Use when after XCMS feature detection and retention time correction,

Use when after imputation and batch-effect correction (OUKS steps 3–4)

Use when you have (1) a benchmark dataset of known molecules with accurate

Use when you have two independent LC-MS untargeted metabolomic feature

Use when you have raw metabolomics peak intensity or concentration data

Use when after data merging and cleanup (blank removal) and before univariate

Use when you have loaded two or more nontargeted LCMS feature tables

Use when you have raw imzML and ibd (ion binary data) files from spatial

Use when you have a metabolomic SummarizedExperiment object with replicate

Use when when you have completed feature detection in MZmine3 or similar

Use when you have an imputed, long-format metabolomics dataset with repeated

Use when after loading raw metabolomics measurement data (samples × metabolites

Use when immediately after executing the MetaboAnalystR 4.0 unified LC-MS

Use when you have selected a subset of ReDU public tandem MS files with

Use when after applying mpactr's filter suite (filter_mispicked_ions,

Use when after applying batch-effect correction methods (parametric ComBat,

Use when after chaining one or more mpactr filter operations (mispicked,

Use when you have paired count data and metadata from a two-group metabolomics

Use when you have XCMS-processed LC/MS peak data from dual-labeled (e.g.,

Use when when you have a known drug's chemical formula and need to generate

Use when when you have access to the MAGMa source code and need to understand

Use when you have independent metabolomic GWAS results (metabolite p-values,

Use when you have metabolite identifiers sourced from or annotated against

Use when when you have a small-molecule structure (SMILES, MOL, or SDF

Use when you have extended a metabolite identification tool (such as

Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other

Use when your metabolomics dataset contains metabolite identifiers in

Use when when you have metabolite identifiers from one or more metabolome

Use when you have (1) peak-picked LC-MS AIF features in a feature table

Use when after peak detection and MS1 feature picking from merged FIA-MS