Claude Skills by HolobiomicsLab

Use when when comparing pathway analysis methods on metabolomics peak

Use when when you have raw LC-HRMS profile-mode data (rt × mz intensity

Use when your input is a raw two-dimensional MS map (m/z vs retention

Use when working with raw IM-MS data (Agilent MassHunter .d or UIMF format)

Use when you have metabolomics intensity data with peak annotations,

Use when you have raw LC/MS data in mzML format and your analysis goal

Use when you have LC-HRMS mzML data processed by at least one non-targeted

Use when you have high-dimensional replicate experiment data (e.

Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other

Use when you have raw LC-MS data in vendor or mzML format and need to

Use when when tabulating chemical annotation enrichment (e.g., GNPS spectral

Use when you have raw metabolomics intensity data affected by batch effects

Use when after completing intra-batch and inter-batch normalisation steps

Use when you have differential analysis results (p-values and log2 fold

Use when when you have access to a peer-reviewed manuscript with an accompanying

Use when setting up a Rapid QC-MS monitoring job and you need to define

Use when when a QC check fails during an LC-MS instrument run and you

Use when you have an unknown mass spectrum from a suspicious analyte

Use when you have a trained PS2MS deep learning model, a set of evaluation

Use when when your input biomolecule is a nucleoside or modified nucleoside

Use when you are preparing to build a .NET project (WPF, class library,

Use when after implementing or modifying a numerical compression codec

Use when implementing a backendInitialize() method for a custom MsBackend

Use when when extending the MsBackend virtual class to create a custom

Use when you have loaded a numeric column (e.g., H/C ratio, O/C ratio,

Use when you need to confirm that omitting an optional input parameter

Use when when you have reimplemented an algorithm in a new package or

Use when after computing molecular descriptors (RDKit, mordred) or featurizing

Use when a formula is documented in a system or article (e.g., resource

Use when when correcting LC-MS isotope labeling data and existing numerical

Use when you have instantiated a learned component (embedding layer,

Use when you have raw floating-point m/z and intensity arrays extracted

Use when when you have raw MS/MS peak lists that need to be loaded, analyzed

Use when you have a raw NV file from NMRViewJ or compatible NMR acquisition

Use when you have annotated LC-MS ROI snippets with ground-truth peak/non-peak

Use when when you need to create a plotting or visualization framework

Use when you need to understand or document the extensibility architecture

Use when when calling filter functions (e.g., filter_mispicked_ions(),

Use when after training multiple MLPNN models (via cross-validation)

Use when you have trained multi-layer perceptron neural networks on paired

Use when when preparing raw omics data (gene expression matrices, differential

Use when you have completed statistical analysis of omics data (proteomics,

Use when after loading peptide or protein-level quantification matrices

Use when you have tabular omics data (expression matrices, p-values,

Use when after you have built a network object (adjacency matrix, edge

Use when after constructing a correlation-based network from omics data

Use when you have raw CE-MS data and need to (1) transform migration

Use when you have raw HPLC column metadata containing categorical fields

Use when when deploying an OpenMS streamlit application that must support

Use when your analysis requires MS/MS spectra from public proteomics