Claude Skills by HolobiomicsLab

Use when you have mzML/mzXML chromatogram files from Thermo, Waters,

'Use when you have acquired LC-MS data and need to verify run quality

Use when you have a complete TIC (total ion current) table indexed by

Use when when you have generated embeddings for query and reference MS/MS

Use when you have LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData

Use when you have a normalized peak-abundance matrix from FT-ICR MS data

Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format)

Use when when you have genomic sequences (assembled contigs or antiSMASH/BOA

Use when after identifying precursor peptides from genome assemblies

'Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or

Use when when you have paired survival data (event indicator and follow-up

Use when when you have raw FASTQ files (from SRA or local storage) and

Use when metabolomics intensity data exhibits systematic signal drift

Use when after drift correction of LC-MS peak intensity data, when you

Use when you have completed pathway analysis using multiple competing

Use when when you have applied multiple normalization methods (e.g.,

Use when you have constructed consensus-clustered microbe and metabolite

Use when after training a NeatMS CNN model on labeled MS1 peaks and generating

Use when you have paired columns of predicted probabilities (or decision

Use when when you have loaded imzML MSI data into napari and need to

Use when you have raw or converted mass spectrometry data (CE-MS or LC-MS

Use when after segmenting raw profile LC-MS data into candidate ROIs

Use when raw LA-ICP-MS image data contains isolated spike artifacts—pixels

Use when you have CDF-format mass spectrometry imaging files from plant

Use when when you have paired predictions and ground-truth structural

Use when when evaluating a regression or similarity prediction model

Use when you have a trained regression model (e.g., a neural network

Use when you have implemented or are validating a reader/writer library

Use when when you have implemented conditional routing logic in the GNPS_MASST

Use when when preparing XCMS peak tables for quality classification and

Use when you have centroided mzML or mzXML LC-MS files from a single

Use when you have a set of metabolite candidates with observed retention

Use when when you have a large set of generalized reaction rules (e.

Use when metabolomics featuredata exhibits run-order-dependent signal

Use when your feature table includes QC (quality control) sample replicates

Use when you have metabolomics data structured as a SummarizedExperiment

Use when when a new version or variant of a tool claims performance improvements

Use when after invoking a Nextflow workflow via `make run` or equivalent

Use when when you have implemented or adopted a new clustering or analysis

'Use when when you need to empirically validate that one mass spectrometry

Use when when you have Rust source code (such as the mzPeak format implementation

Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping)

Use when when you have access to Rust source code in a repository with

Use when you have metabolomics data distributed across multiple experimental

Use when your metabolomics data frame has inherited or assigned class

Use when you are designing a new backend or data container that must

'Use when you are extending the MsBackend virtual class to create a new

Use when you need to create a new backend for the Spectra package that

Use when you are building a new data representation or storage strategy

Use when you need to verify that an S4 replacement method (e.g., `mz<-`)