Claude Skills by HolobiomicsLab

Use when adding a new converter class to MSMetaEnhancer or when modifying

Use when you have pairs of augmented ion images from mass spectrometry

Use when you have 1H NMR spectral tensors as input and need to extract

Use when when exporting quantified ion images and pixel metadata from

Use when you have a directed metabolic network (digraph) with node perturbation

Use when when implementing a custom MsBackend class for the Spectra package,

Use when when you have raw LC-MS/MS data in MGF format and need to prepare

Use when when you have raw LC-MS-MS fragmentation spectra in MGF format

Use when when deploying a Word2Vec-based spectral similarity model (such

Use when after applying one or more intensity drift correction strategies

Use when after preprocessing and log-transformation of metabolomics feature

Use when you have paired experimental and computational predictions for

Use when after identifying structural clusters (isotopologue groups,

Use when after XCMS feature detection and retention time correction,

Use when you have an aligned LCMS feature table (output from Eclipse

Use when after obtaining per-sample model predictions and metabolite

Use when after computing a correlation matrix (e.g., Pearson correlation

Use when after constructing a correlation-based network (adjacency matrix,

Use when when you have a feature abundance table (rows=features, columns=samples)

Use when after computing pairwise correlations across all features in

Use when when training a heavily regularized deep neural network on large

Use when when training a regularized deep neural network for molecular

Use when you have pre-computed BGC feature vectors (e.g., from HMM domain

Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned)

Use when when comparing two MS/MS spectra (query and reference) to quantify

Use when after generating normalized dense embeddings for both query

Use when when you have pre-computed spectral embeddings (vectors) for

Use when when you have imported and filtered mass spectrometry spectral

Use when you have a collection of deconvolved mass spectra (in MGF or

Use when when you have two or more co-registered LA-ICP-MS element channel

'Use when after count matrix quantification (e.g., from Salmon) and before

Use when after count matrix preprocessing (normalization, batch correction,

Use when when you have access to a curated dataset (such as LOTUS) with

Use when you have grouped unique 2D chemical structures by organism prevalence

Use when after normalization (Step 7) is complete and you have a clean

Use when after generating a covariance matrix from normalized metabolite

Use when you have two sets of lipid annotations—one from baseline spectral

Use when you have expression or metabolomic feature matrices, paired

Use when you have implemented both CPU and GPU versions of a spectral

Use when after identifying statistically significant features within

Use when when you have structural clusters from multiple LC-MS assays

Use when you have multiple SummarizedExperiment objects representing

Use when you have chemical entity records scattered across two or more

Use when when you have lipid abbreviations or names from different databases

Use when when you have antiSMASH-predicted BGCs and wish to link them

Use when you have received MSBERT-preprocessed spectral data from GNPS,

Use when you have two or more nontargeted LCMS feature tables from the

Use when you have two or more feature tables in HDF5 format with detected

Use when you have a pre-trained MS/MS spectral embedding model evaluated

Use when you have trained a neural network or regression model on one