Claude Skills by HolobiomicsLab

Use when when you have loaded a raw or processed Cardinal MSImagingExperiment

Use when when you have loaded an unprocessed Cardinal object from MS

Use when after completing Cardinal-based preprocessing (feature summarization,

Use when when searching high-resolution mass spectra against spectral

Use when use this strategy when analyzing tandem mass spectrometry data

Use when when performing open modification spectral library searches

'Use when you have a flat table of structure-organism pairs or entity

Use when after running qc_summary() on a filtered mpactr object when

'Use when when preparing heterogeneous column-metadata inputs for a graph

Use when you have IM-MS lipidomics data acquired on samples spiked with

Use when you have acquired tunemix or reference standard data in ion

Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5)

Use when when you have received or cloned a CCS reference library (such

Use when you have structural input data (SMILES or molecular geometry

Use when you have a dataset of molecules with known or reference CCS

Use when you have a dataset of SMILES strings with corresponding experimental

Use when you have obtained or need to prepare a DTCCS_N2 reference library

Use when you have TWIM-MS experimental data with arrival/drift times

'Use when when you have multiple CDF files from mass spectrometry imaging

Use when you have raw CE-MS instrument output in mzML or netCDF format

Use when when processing CE-MS test files and you need to identify and

Use when when processing raw CE-MS data and need to establish a baseline

Use when your CE-MS dataset exhibits migration time drift between runs

Use when you have co-registered IMC (protein imaging mass cytometry)

Use when apply CLR normalization when you have count-based microbiome

Use when apply CLR transformation when working with microbiome or metabolomic

Use when after computing raw betweenness centrality scores for metabolites

Use when you have vendor-independent centroided mzML files from data-dependent

Use when you have centroided data-dependent acquisition (DDA/ddMS2) mzML

Use when when downloading a lipidomics dataset from Metabolomics Workbench

Use when you have added or modified user-facing parameters to a model

Use when when analyzing high-resolution mass spectrometry data from natural-abundance

Use when you have peak-picked features with m/z, drift_time, retention_time,

Use when training neural networks on MS/MS spectra (or similar scientific

Use when after completing a full training loop on preprocessed molecular

Use when when you have received chemical annotations from GNPS spectral

Use when after training a tandem mass spectrometry embedding model (such

Use when you have selected a subset of public tandem MS files from ReDU/MassIVE

Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates)

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

Use when you have generated a GNPS molecular network (classical or feature-based

Use when you have a GNPS mass spectral molecular network (in graphml

Use when when you have CANOPUS chemical class predictions for your samples

Use when you have a collection of standardized molecular structures (SMILES

Use when you have structural annotations from in silico tools (SIRIUS,

Use when your LC-MS feature table is incomplete or has low chemical coverage

Use when when you have mass-to-charge (m/z) values from mass spectrometry

Use when you have BioTransformer-predicted metabolite structures (in

Use when you have standardized molecular structures (SMILES or SDF format)

Use when after harmonizing compound identifiers to PubChem IDs (e.g.,