Claude Skills by HolobiomicsLab

Use when after completing feature m/z grouping and pairwise alignment

Use when when you have preprocessed metabolomics peak tables (feature

Use when after loading or merging spatial metabolomics data into an AnnData

Use when when you have imzML and accompanying ibd (ion binary data) files

Use when you have preprocessed and filtered ST and SM AnnData objects

Use when you have LC–MS all-ion fragmentation chromatograms already processed

Use when after executing an end-to-end structure annotation pipeline

Use when after running an end-to-end annotation workflow (matching, clustering,

Use when you have pseudo-MS/MS spectra from LC-MS all-ion fragmentation

Use when after generating TP candidates from annotation algorithms (ann_comp

Use when you have MS imaging or LC-MS data with pre-annotated m/z values

Use when after MS-FINDER in silico annotation has been executed on exported

Use when after recursive annotation propagation has assigned metabolite

Use when you have run MSMetaEnhancer's annotate_spectra() method on a

Use when after completing metabolite annotation of LC-MS AIF features

Use when when you have raw PubChem compound records or other public chemical

Use when you have in silico annotations (e.g. from GNPS, timaR, or SIRIUS)

Use when you have experimental mass spectra from untargeted metabolomics

Use when when you have access to multiple public metabolomics databases

Use when after obtaining in silico annotations from SIRIUS (Zodiac/Cosmic

Use when you have a normalized LC-MS/MS metabolite abundance matrix (e.g.,

Use when you have completed ANOVA or G-test statistical testing across

Use when when preparing genomic data for NPLinker analysis and you have

Use when you have mzPeak files stored as Parquet tables within a ZIP

Use when when you have multiple mass spectrometry data formats (mzML,

Use when integrating with an external API (such as TensorFlow Serving)

Use when you need to obtain all project JSON documents currently deposited

Use when when you have a Python package with docstrings in the source

Use when you have fingerprint or spectrum data that requires compound-class

Use when when enriching mass spectra metadata by querying multiple external

Use when when you have a chemical structure query (as a SMILES string

Use when you have nuclear magnetic resonance (NMR) peak data (proton

Use when when building asynchronous metadata enrichment workflows that

Use when when annotating .msp files with metadata from multiple external

Use when after submitting a POST request to the /api/smart3/search endpoint

Use when you have access to the source code of a webservice component

Use when when deploying a Java web application (such as CEU Mass Mediator)

Use when when you have a large collection of reference MS/MS spectra

Use when when you have a large spectral library (hundreds of thousands

Use when when you have a large spectral library (hundreds of thousands

Use when when you have pre-computed spectrum embeddings (e.g., Word2vec

Use when you are building a Qt5-based desktop application with cross-platform

'Use when when you have downloaded a GNPS molecular networking job archive

Use when you have region-of-interest (ROI) LC-MS data and a pre-trained

Use when after molecular formula assignment from FT-ICR MS peaks and

Use when you have tabular experimental data (e.g., sample metadata, mass

Use when you have raw or processed TWIM-MS data with arrival time and

Use when when you have raw TWIM-MS arrival-time data and need to transform

Use when when processing raw TWIM-MS experimental data that contains

Use when when reading mzPeak files or other Parquet-backed mass spectrometry