Claude Skills by HolobiomicsLab

Use when after pre-annotation grouping (e.g., via khipu) has assigned

Use when you have parsed a MassQL query string into an AST representation

Use when you have raw or semi-curated mass spectrometry spectral data

Use when when you have raw mass spectrometry spectral data in JSON format

Use when after serializing empirical compound collections to JSON format

Use when after Mass2Motif annotation candidates have been ranked and

Use when you need to persist and communicate the health status of multiple

Use when you have extracted tabular data (e.g., from experimental spreadsheets)

Use when after enriching a project JSON document with external metadata

Use when when building reproducible Python-based computational workflows

Use when when you have three coordinated mass spectrometry data tables

Use when when you have raw LC-MS/MS spectral data in .

Use when you have a curated training dataset of molecular structures

Use when when you have obtained source code for a Maven-based Java project

Use when when deploying the ipbhalle/metfragweb Docker container and

Use when when fitting a multi-block PLS discriminant model on multi-assay

Use when your raw metabolomics dataset contains missing values scattered

Use when when a Shiny application currently uses orca for static plot

Use when after metabolite KEGG identifiers and hierarchy metadata have

Use when after cluster-based filtering has produced a set of candidate

Use when when you have selected one or more organisms to analyze and

Use when you have identified two or more organisms (via their KEGG organism

Use when you have raw LC-MS peak intensity data with mass-to-charge ratios

Use when you have untargeted MS2 spectral data (in MS2MP-compatible format)

Use when you have uploaded m/z values from a high-resolution mass spectrometry

Use when you have a feature list from LC- or GC-HRMS analysis (with m/z,

Use when you have pre-trained Keras models from the NP-Classifier repository

Use when you have downloaded Keras-format pre-trained models (e.g., via

Use when you have downloaded pre-trained Keras model files (via get_models.sh

Use when when extending an existing neural network class (e.g., SiameseModel)

Use when you have defined a Keras model architecture (convolutional and

Use when when you have a training set of MS2 spectra with known chemical

Use when you have a set of ions detected in LC-MS data that are suspected

Use when you have raw LC-MS data (mzML, NetCDF) from multiple runs that

'Use when after deciding to use KNN imputation on a metabolomic assay

Use when when integrating two spatial omics modalities (ST and SM) measured

Use when you have untargeted metabolomics data (MS/MS spectra) and need

Use when after completing all per-sample annotation steps (molecular

Use when designing a metabolite annotation workflow that must simultaneously

Use when you have compiled a multi-source EI library (NIST, RIKEN, MoNA,

Use when raw LA-ICP-MS images contain isolated spike pixels (hot spots

Use when you have multi-isotope LA-ICP-MS data (e.

Use when you have a ranked list of seed genes or metabolites (e.g., from

Use when when preparing mass tracks for retention-time (RT) alignment

Use when you have (1) genomic data from a Streptomyces or other RiPP-producing

Use when you have two or more MS/MS fragmentation spectra (with precursor

Use when you have multiple competing spectral similarity scoring methods

Use when you have a query mass spectrum (or a metabolite reference spectrum

Use when you have a collection of molecular structures (as SMILES or

Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned)