Claude Skills by HolobiomicsLab

Use when you have an mzPeak file (uncompressed ZIP archive containing

Use when you have mass spectrometry run data (spectra, chromatograms,

Use when after Casanovo has generated ranked peptide sequence predictions

Use when after completing peak detection, MS1 feature picking, and accurate

Use when when constructing derived elemental ratio images via Calculator

Use when when processing mass spectrometry imaging (MSI) data in positive

Use when you have LC-MS fractional abundances of measured isotopologues

Use when you have a set of natural product molecules (or suspected natural

Use when you have molecular structures encoded as SMILES strings and

Use when gNPS has ceased supplying ClassyFire ontology information for

Use when you need to update your local LOTUS natural-product database

Use when you have a chemical structure (as SMILES string or identifier)

Use when when ingesting raw data from multiple external natural-product

Use when after curating and integrating structure-organism pairs from

Use when you have (1) a collection of natural product or drug candidate

Use when you have a natural product dataset with taxonomy labels (Class,

Use when when you need to represent natural product molecules as numerical

Use when you have natural product molecules in SMILES, InChI, or SDF

Use when you have separately cleaned and validated tables for organisms

Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative

Use when you have raw fractional abundances of measured isotopologues

Use when you have parsed a collection of sequence files with associated

Use when you have a collection of sequence files (e.g., GenBank format

Use when when you have a large spectral library (thousands to millions

Use when processing LC-MS metabolomics studies with >10 samples where

Use when you have extracted mass tracks (EICs) from individual samples

Use when when you have millions of high-resolution MS/MS spectra converted

Use when you have millions of MS/MS spectra to cluster and have already

Use when you have negative-mode MS/MS spectra with annotated molecular

Use when when XCMS or other DTW-based aligners have produced misaligned

Use when after library-matching has produced ranked candidate spectra

Use when you have loaded raw Agilent Unknowns Analysis CSV output with

Use when when applying str directives during JSON-to-JSON conversion

Use when you have an untargeted metabolomics feature table with m/z values,

Use when when you have m/z values from spatially-resolved mass spectrometry

Use when you have a GNPS GraphML molecular network and need to isolate

Use when after clustering and filtering KEGG candidates for LC-MS features,

Use when after completing dereplication and cosine similarity clustering

Use when your network contains multiple edge types between the same pair

Use when you have a molecular network graph exported from GNPS (as GraphML,

Use when you have a sparse network graph generated by GLASSO and corresponding

Use when when you have completed an initial ModiFinder analysis on a

Use when you have applied graphical lasso (GLASSO) to estimate a sparse

Use when you have a network object (nodes and edges) loaded in MetaNet

Use when after biclustering a normalized microbe-metabolite feature attribution

Use when you have constructed a NetworkX graph with LC-MS features as

Use when you have a GLASSO-generated network graph and corresponding

Use when you have an untargeted metabolomics dataset with a two-layer

Use when you have (1) metabolomic hits (DAMs or enriched metabolites)

Use when you have constructed a network object (from correlation data,