Claude Skills by HolobiomicsLab

Use when when you have a collection of MS/MS spectra (in mzML or MGF

Use when when designing a Siamese or multi-branch neural architecture

Use when after training a deep learning model (e.g. MSBERT) on mass spectra

Use when you have pairs or triplets of MS/MS spectra with associated

Use when after training or loading a pre-trained deep learning model

Use when when you have tokenized mass spectra (peak-mass and peak-intensity

Use when you have a query mass spectrum and need to retrieve the most

Use when after instantiating and invoking a sinusoidal formula embedding

Use when you have an NMR mixture spectrum and a library of single-compound

Use when you have a tab-delimited feature table (m/z, retention time,

Use when after generating a feature table from mzML data (via Asari)

Use when after feature detection and quality control have produced a

Use when after feature table normalization and imputation are complete,

Use when after feature detection from mzML files (e.g., via Asari) when

Use when you have a pretrained encoder that produces fixed-size embeddings

'Use when you have 512-dimensional representation vectors output from

Use when when reading a binary file format with a magic integer or fixed

Use when you have an unknown MS/MS spectrum (precursor m/z and fragment

Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs)

Use when you have parsed GO enrichment results (CSV with GO term identifiers,

Use when after generating combined or alternative scores for a set of

Use when after you have normalized metabolite abundances across samples

Use when after differential expression analysis has produced gene lists

Use when after performing two-group or multi-group differential analysis

Use when after running Enrichment() on a configured EnrichParam object

Use when you have completed Fisher's exact test enrichment analysis on

Use when after pathway enrichment analysis has been executed by clusterProfiler

Use when you have a set of compounds (as SMILES strings or molecular

Use when you have pre-trained MLP and GNN models that generate different

Use when when you have retention order predictions from multiple independently

Use when when comparing two preprocessed MS/MS spectra for compound identification

Use when you need to search one or more query MS/MS spectra against large

Use when you need to quantify the degree of match between two MS/MS spectra—either

Use when after installing a Python package or cloning its repository,

Use when you need to assess the overall curation coverage and quality

Use when you need to assess the curation completeness and status distribution

Use when when you have obtained a Python package from a repository (e.g.,

Use when when deploying Galaxy-M or similar multi-component metabolomics

Use when after installing ENPKG or any component of the workflow via

Use when you have a multi-fold cross-validation training workflow that

Use when when extending a multi-service project (like MAGMa with its

Use when you have a target compound (in SMILES or structure format) and

Use when you have a small-molecule structure (in SMILES, MOL, or SDF

Use when you have a small molecule structure (SMILES, MOL, or SDF format)

Use when you have biotransformation reaction data from a curated source

Use when when implementing or auditing a data replacement method (e.g.,

Use when building a file format dispatcher or initialization routine

Use when you have predicted retention times from one or more machine

Use when when a user uploads a JSON project document to the Pairing Omics

Use when building or maintaining a system that fetches metadata from