Claude Skills by HolobiomicsLab

Use when you have imported a raw LA-ICP-MS raster image (line-by-line,

Use when when you have preprocessed MS/MS spectral data (filtered, noise-reduced,

Use when you have a preprocessed corpus of mass spectrometry spectra

Use when you have imaging mass spectrometry (IMS) data preprocessed into

Use when you have a preprocessed metabolomics feature matrix and sample

Use when you have imaging mass spectrometry (IMS) datasets where peak

Use when when preparing LC gradient configurations for Bayesian optimization,

Use when after detecting local-maxima in LC-HRMS profile mode datasets

Use when you have raw LC-HRMS metabolomics data in .mzML or .abf format

Use when you have processed the same set of untargeted LC/HRMS files

Use when you have LC-HRMS raw data files (.mzML or .abf format) from

Use when when you have statistically significant features from multi-assay

Use when when you have paired LC-MS measurements from labeled and unlabeled

Use when you have vendor-format LC-MS acquisition files (.raw, .d, .ms)

'Use when you have raw mzML files and corresponding feature tables (CSV

Use when before launching TARDIS peak detection on a new LC–MS dataset

Use when when beginning an untargeted LC-MS metabolomics study and need

Use when after executing TARDIS in screening_mode = TRUE on centroided

Use when you have two peak-picked, conventionally aligned LC-MS metabolomics

Use when you have centroid mzML files from LC-MS experiments (converted

Use when after chromatographic peak detection on preprocessed LC-MS data,

Use when immediately after chromatographic peak detection (findChromPeaks)

Use when you have preprocessed LC-MS intensity data (e.

Use when you have generated feature tables from LC-MS data using different

Use when immediately after peak detection and feature table generation

Use when when you have a set of candidate LC gradients (parameter combinations)

Use when at the start of an untargeted LC-MS annotation pipeline when

Use when after executing a Nextflow-based LC-HRMS metabolomics workflow

Use when you have LC-MS feature tables with m/z and retention time coordinates

Use when after a CNN-Transformer peak detection model has been run on

Use when you have raw profile (not centroided) LC-MS data in .mzML format

Use when after performing peak detection on centroided .mzML LC-MS data

Use when you have centroided .mzML LC–MS data with multiple sample runs

Use when when you have extracted LC-MS ROI windows (m/z × retention time

Use when when you have a curated list of chemical compounds (real or

Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific

Use when you have a set of target molecules with known molecular formula,

Use when you have loaded mzML.gz or HDF5-formatted raw LC-IMS-MS/MS data

Use when you have raw LC-MS data from a vendor instrument or in netCDF

Use when when you have raw LC/MS data in mzML format and need to execute

Use when you have an LCMS feature table annotated with MS2 spectral data

Use when you have raw LC-MS data (mzML or equivalent format) from a metabolomics

Use when when you have raw LC-MS chromatographic data (mzML or vendor

Use when you have an untargeted LC/MS feature table (m/z, retention time,

Use when after ISFrag has completed identification of in-source fragment

Use when you have centroided, single-polarity mzML files from DDA LC-MS

Use when you have raw nontargeted LCMS feature tables from one or more

Use when you have raw LC-HRMS metabolomics data in .mzML or .

Use when you have an XCMS-processed feature set (XCMSet object) from

Use when you have one or more raw mzXML or mzML LCMS data files (from