Claude Skills by HolobiomicsLab

Use when after NPLinker computes scored links between genomic and metabolomic

Use when you have a collection of MS/MS spectra (stored as Spectrum2

Use when when you have 1D NMR spectra (¹H and/or ¹³C) as input and need

Use when after constructing a network (adjacency matrix, edge list, or

Use when after constructing a spectral similarity network from pairwise

Use when you have a sparse inverse covariance graph (GLASSO output) and

Use when you have retrieved and deduplicated chemical formulae and metadata

Use when you have a network object (loaded as igraph or MetaNet format

Use when you have a GNPS mass spectral molecular network and wish to

Use when when comparing two or more lipid structures and you need to

Use when you have trained ML models that predict pairwise relationships

'Use when when you have: (1) a collection of molecules represented as

Use when you have molecular structures that need to be represented as

Use when you have a baseline GNN model trained on a molecular property

Use when you have 1D or 2D NMR spectra (1H and/or 13C) and need to predict

Use when when you need to compare spectrum prediction models fairly across

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

Use when when you have a pre-trained GNN checkpoint and a smaller, task-specific

Use when when your input includes molecular structures (SMILES, conformers)

Use when you have a trained GNN model (stored as .h5 weights) and molecular

Use when when you need to evaluate GNN performance on collision cross

Use when when you have a molecular dataset (e.g., SMRT retention-time

Use when you have statistically significant LC-MS features grouped into

Use when you have KEGG metabolic data for one or more organisms and need

Use when after constructing a network graph where nodes represent Mass2Motifs

Use when after constructing feature tensors encoding atom adjacency matrices,

Use when you have (1) a set of input metabolites (e.

Use when after constructing a NetworkX graph object from structural clusters

'Use when when building a standalone desktop application with a graphical

Use when your XCMS-processed LC-MS dataset exhibits retention-time drift

Use when you have a fitted alignment model (e.g., metabCombiner object

Use when when generating synthetic LC/GC-MS .mzML files with companion

Use when after running retention-order prediction on a test or evaluation

Use when you have an expression matrix (e.g., heatmap_test.csv with genes

Use when after data integration, batch correction, and sample separation

Use when when implementing a fold-change filter or similar feature-level

Use when you have omics data with group labels (e.g., treatment vs. control,

Use when when comparing GNPS chemical annotations across two or more

Use when you have constraint-based metabolic models with integrated transcriptomics

Use when a GUI widget (e.g., isotopes display, compound list, or metabolite

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

Use when you have a large text or structured file (mzML, XML, plain text)

Use when when you have an indexed gzip-compressed mzML file (mzML.gz

Use when releasing or evaluating scientific software with claimed performance

Use when you have imported mass spectrometry spectra from multiple file

Use when when processing open mass spectrometry library (OMSL) data that

Use when when you have normalized or vectorized mass spectrometry spectral

Use when after performing isotopic correction, quantitation, or other

Use when you have mass spectrometry feature data stored in HDF5 format

'Use when you have isotope-corrected or raw ion-image intensity matrices