Claude Skills by HolobiomicsLab

Use when after chromatographic peak detection, fill-in of missing peaks,

Use when raw metabolomics peak intensity data exhibits right-skewed distributions

Use when apply log-transformation immediately after loading a raw metabolomics

Use when apply log transformation when peak intensity distributions are

Use when when implementing a metadata annotation pipeline for mass spectra

Use when when computing Reaction Activity Scores (RAS) from transcriptomics

Use when when you have a wide-format feature intensity table (samples

Use when you have imputed metabolomics data in long format (with id,

Use when when you have raw mzML or mzXML mass spectrometry files with

Use when you have raw compound or natural-product metadata in spreadsheet

Use when after generating an ensemble of 3D conformers via RDKit conformation

Use when you have low-resolution GC-MS data (e.g., ANDI NetCDF format)

Use when when processing low-resolution GC-MS data in NetCDF format where

Use when you have low-resolution MS data (e.g., from quadrupole instruments)

Use when you have extracted mass tracks (EICs) from multiple LC-MS samples

Use when when processing multiple centroided mzML LC-MS files from the

Use when before committing to full-scale targeted peak integration across

Use when you have spatial metabolomics data with semi-colon-delimited

Use when when you have imported MSI data (imzML or vendor format) loaded

Use when after retention-time clustering has grouped features from multiple

Use when you have a set of observed m/z values extracted from a Cardinal

Use when you have raw or processed MS spectrum data (m/z and intensity

Use when you have imported mass spectrometry data in .raw, .d, or mzXML

'Use when when you have a spatial metabolomics or LC-MS dataset with

Use when you have two peak-picked, conventionally aligned untargeted

Use when after extracting a feature table from XCMS, MS-Dial, or similar

Use when you have extracted peaks from multiple LC/HRMS batches (n >

Use when you have uploaded peak list data containing m/z values and wish

Use when when you have detected features with m/z, drift time, and retention

Use when processing extracted peak lists from MSI data and you need to

Use when when implementing or modifying data replacement methods (e.g.,

Use when after parsing an imzML XML metadata file and loading the corresponding

Use when when you have generated multiple 3D conformations for a molecule

Use when you have a labeled dataset (e.g., mass spectra with molecular

Use when you have completed cross-validation tuning of one or more machine-learning

Use when you have MS-DIAL lipid identifications from an Orbitrap or TOF

Use when after fitting a random forest model to metabolomics count data

Use when you have a trained NeatMS neural network model and a labelled

Use when you have molecular descriptors or fingerprints for a set of

Use when when you have a preprocessed metabolomics feature matrix with

Use when your metabolomics analysis pipeline requires CCS value prediction

Use when when you have a labeled peak quality matrix (with known pass/fail

Use when you have a labeled dataset of DIA raw files (.raw, .d, .wiff)

Use when after training a binary MS/MS spectral classifier on labeled

Use when you have adapted an ML pipeline (e.g., MSNovelist) to consume

Use when you have matched multiomics data (CNV, mutations, DNA methylation,

Use when after data normalization (Box-Cox transformation) and before

Use when you have paired pre- and post-MALDI microscopy images with visible,

Use when after generating mzPeak files from prototype implementations

Use when you need to audit a bioinformatics repository (such as MIBiG)