Claude Skills by HolobiomicsLab

Use when a Shiny application or R package currently runs only on Windows

Use when after generating a numerical visualization (e.g., confusion

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

Use when you have a preprocessed peak table (feature matrix with samples

Use when when running NPLinker in PODP mode (as opposed to local mode),

Use when when preparing augmented variants of ion images (single-channel

Use when augmenting mass spectrometry ion images for contrastive learning,

Use when augmenting mass spectrometry ion images for contrastive learning,

Use when when performing targeted peak detection on LC-MS data where

Use when you have a multi-polarity compound target list (e.g., a .xlsx

Use when when working with targeted LC–MS metabolomics or lipidomics

Use when you have a comprehensive target list (containing compounds from

Use when after ASE-ANI has filtered conformers to remove high-energy

Use when when you have multiple file format variants (compressed indexed

Use when when building a plotting library that must support multiple

Use when after fitting a polynomial calibration model to tunemix reference

Use when you have one or more polypeptide sequences (from FASTA, CSV,

Use when when you have validated link annotations from multiple independent

Use when when you have a containerized web application with a fixed internal

Use when preparing mass spectrum input tensors for transformer encoder

Use when you need to feed discrete chemical formula representations (e.g.,

Use when you have LC-MS metabolomics data in positive ionization mode

Use when when training a formula rescoring model on MS/MS spectra where

Use when after training a GNN model on molecular structures with continuous

Use when when you have tandem mass spectrometry data (LC-MS/MS in MGF,

Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or

Use when you have metabolomics data with left-censored missing values

Use when after successful gensim LDA inference has produced a JSON result

Use when you have raw GC–MS or LC–MS data in two-dimensional m/z vs retention

Use when after molecular formula assignment has been performed on FT-ICR

Use when when annotating m/z features from Cardinal MSImagingExperiment

Use when when processing imzML/ibd Imaging Mass Spectrometry datasets

Use when when you have assigned molecular formulas to m/z peaks or computed

Use when you have extracted a list of candidate molecular formulae for

Use when a mass spectrum calibration procedure initialized with a narrow

Use when you have uploaded a pre-analytical data table containing sample

Use when when you have NMR metabolite measurements paired with documented

Use when you have identified a set of lipid or polar metabolite analytes

'Use when you have collected blood samples under specific pre-analytical

Use when after completing a hierarchical batch normalisation workflow

Use when you have a small training dataset for molecular property prediction

Use when you have a feature matrix (rows=samples, columns=features) and

Use when you have computed spectral similarity scores from multiple methods

Use when when you have computed similarity scores (e.g., MS2DeepScore,

Use when you have extracted fragmentation patterns from a collection

Use when you have loaded raw tandem MS spectra (in MGF, mzML, or similar

Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo,

Use when when designing a targeted lipidomics experiment and you have

Use when you have raw DIA mass spectrometry data files (.raw, .d, or

Use when processing SWATH-MS (Sequential Windowed Acquisition of all