Claude Skills by HolobiomicsLab

'Use when you need to set up a cloned or downloaded scientific Python

Use when you need to confirm that a Python package (especially one distributed

Use when a Python package has been relocated to a new repository location,

Use when after installing ChemDistiller or similar Python-based command-line

Use when you need to verify that a Python package (or similar installable

Use when when you need to establish a working installation of a Python

Use when when a package README or publication claims to install a large,

Use when releasing a new version of a Python package to public repositories,

Use when after creating a fresh conda environment from a pinned dependency

Use when when a multi-language analysis pipeline (R + Python) has been

Use when when you have a paired omics project document (JSON format)

Use when when processing LC-MS metabolomics datasets with 10 or fewer

Use when after peak m/z values and molecular formulas have been extracted

Use when after loading preprocessed MSI intensity data (via msimat from

Use when when you have a cleaned MS/MS dataset with chemical structure

Use when after XCMS feature detection and retention time correction,

Use when after anchor selection and RT mapping spline fitting, when you

Use when you have a collection of preprocessed mass spectra (in mzML,

Use when you have a collection of cleaned mass spectrometry spectra (in

Use when you have mass-spectrometry data in a Pandas DataFrame and need

Use when when you have mass spectrometry data in a Pandas DataFrame with

Use when when you have raw mass spectrometry data (from mzML, Bruker

Use when you have mass spectrometry data (retention time, m/z, intensity,

Use when your input consists of multiple large MSP files (hundreds of

Use when when compiling EI or MS/MS spectral libraries from multiple

Use when when you have a Spectra object backed by an on-disk MS data

Use when when a post-processing step (such as dereplication) risks removing

Use when setting up a LipidMatch analysis run and you need to select

Use when you have converted mass spectrometry data in mzXML or mzML format

Use when when integrating edited Modular.r scripts into the LipidMatch-4.2

Use when you have raw MS data in instrument-native or mzML format (Agilent

Use when when beginning an untargeted LC-MS analysis and either (1) the

Use when when processing paired augmented versions of the same input

Use when designing a contrastive learning pipeline for ion images or

Use when you have at least 3 raw mass spectrometry samples in open formats

Use when you have preprocessed, log₂-scaled metabolomics data in CSV

Use when after ISF features have been identified in Part 4 of the ISFrag

Use when after ISF features have been identified and annotated in Part

Use when you have predicted biotransformation products from BioTransformer's

Use when when you have applied biotransformation rules to generate candidate

Use when you have generated a TP object (from generateTPs) with structural

Use when after feature clustering has grouped LC-MS peaks by MS-DIAL

Use when you have evaluated a parametric denoising strategy (e.g., frequency-based

Use when apply Pareto scaling when preparing normalized metabolomics

Use when you have peak intensity vectors from LC/GC-MS experiments with

Use when when implementing or extending a DSL parser (lexer + recursive

Use when you have a log2-transformed, standardized peak intensity matrix

Use when when you have a metabolite intensity matrix (samples × metabolites)

Use when when you have an untargeted metabolomics feature table (m/z

Use when after marker identification or metabolite annotation has produced