Claude Skills by HolobiomicsLab

Use when you have vendor raw files (e.g., .raw from Thermo, .d from Agilent,

Use when when building a mass-spectrometry analysis pipeline that must

Use when after loading peptide or protein-level quantification matrices

Use when after the Proteomics_Data_Processor tool has completed analysis

Use when you have experimental protocol information scattered across

Use when you have SMILES-encoded molecular structures and need to model

Use when when you have a raw list of SMILES strings but lack sufficient

Use when after executing annotateRC to match six or more lipidomics/metabolomics

Use when when you have an MS2 scan with observed peak data (m/z, intensity,

Use when you have a PSM file from a proteomics search engine containing

Use when your PSM input file (e.g., from MaxQuant or other search engines

Use when when you have grouped PSMs by spectrum identifier and need to

Use when when you have PSM identifications from a search engine (e.

Use when when you have PSM files from a proteomics search engine (e.g.,

Use when when you have raw chemical structures in diverse input formats

Use when you need to supply candidate metabolite structures for mass

'Use when you have metabolite or compound identifiers in mixed formats

Use when after compound database dereplication (via SIRIUS or MetFrag)

Use when your metadata table contains compound names but lacks structure

Use when you have an experimental tandem mass spectrum and chemical formula

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

Use when after annotating a mass spectrometry spectrum with fragment

Use when after generating initial visualizations (volcano plots, heatmaps,

Use when you have a mass spectrometry spectrum from a supported repository

Use when you have resolved a USI string pointing to a spectrum in a supported

Use when you have Nightingale Health 1H-NMR metabolomics measurements

'Use when investigating how a specific pull request (e.g., PR #72 introducing

Use when analyzing GC-MS data containing overlapped peaks where two or

Use when you have an mzML file (e.g. Manuels_customs_ids.mzML) with non-standard

Use when when you have mzML spectrum XML already parsed (either from

Use when when you have polypeptide sequences and need to compute their

Use when after running `pytest tests/` on a Python package (especially

Use when after installing a package in development mode (e.g., via `pip

Use when when extending MSMetaEnhancer with a new local chemical transformation

Use when when contributing code changes to a Python project (fork, feature

Use when when you have mzPeak files (Parquet-based archives in uncompressed

Use when when you have a C++ library (such as OpenMS) with nanobind binding

Use when you have a blockwise-indexed compressed file (e.g., indexed

Use when when you need to enable bracket notation (e.g., handler[5])

Use when when building an extensible converter framework where new converter

Use when you have mzML spectral data stored in a non-standard format

'Use when when building a machine learning library for scientific workflows

Use when preparing Python code for contribution to a project that documents

Use when you need to represent structured scientific data (e.g., molecular

Use when when setting up a multi-language data analysis pipeline that

Use when you have raw mass spectrometry quantification tables (feature

Use when when you have a pre-trained deep learning model checkpoint (saved

Use when you have a requirements file (e.g., jestr_requirements.

Use when when initializing a new Python project environment, reproducing

Use when when setting up a multi-stage bioinformatics workflow (e.g.,