Claude Skills by HolobiomicsLab

Use when after loading log-transformed, pre-processed metabolomics feature

Use when you have a collection of 100+ molecules in SMILES, SDF, MOL,

Use when when evaluating whether a new or candidate mass spectrometry

Use when you have a metabolomics dataset with samples collected across

Use when when processing a SummarizedExperiment containing metabolomics

Use when you have LC/MS feature data (m/z, retention time, intensity)

Use when your input is a filtered metabolite abundance matrix with remaining

Use when you have experimental retention times (RTs) for a small set

Use when you have a pre-trained DNN RT predictor (e.g., trained on METLIN

Use when you need to transfer retention time predictions from one chromatographic

Use when you have completed one or more LC-MS gradient runs, extracted

Use when after fitting a Gaussian Process regression model to prior LC-MS

Use when using Casanovo for de novo peptide sequencing on high-stakes

Use when you have a set of centroided mzML files from LC-HRMS analysis,

Use when you have post-processed clustering results from multiple tools

Use when when you need to quantify and document the computational cost

Use when you have trained a new machine learning model for chemical formula

Use when when you have a pathway-metabolite bipartite network and a filtered

Use when you have completed a BiG-SLiCE v2 clustering analysis and need

Use when when you have pre-computed BGC feature vectors (from domain

Use when you have assembled genome sequences (contigs or scaffolds in

Use when you have computed raw strain correlation scores and IOKR scores

Use when you have preprocessed GCF-MF link pairs from paired genomics–metabolomics

Use when you have BGC sequences (in FASTA or GenBank format) from antiSMASH

Use when when you have a collection of microbial genomes with predicted

'Use when you have: (1) a trained IOKR model mapping from spectrum kernels

Use when you have GenBank-format BGC sequences annotated with Pfam domain

Use when you have paired spectrum-compound reference data and need to

Use when you have a normalized matrix of feature attribution scores (microbes

Use when you have a collection of antiSMASH-processed GenBank files (or

'Use when when preparing NPLinker input data and the BigScape directory

Use when constructing HPLC column feature vectors from raw metadata that

Use when you have raw LC-MS data in .mzML (XML-based) or Thermo .raw

Use when you have curated a labeled dataset of MS/MS spectra annotated

Use when you have executed a binary classifier (such as BitterPredict.m)

Use when you have a trained binary molecular classifier (like BitterPredict)

Use when when you have a pretrained spectrum encoder (TCN) and need to

Use when when converting simulated or real LC/GC-MS spectral data (m/z–retention-time

Use when after implementing a lossless compression–decompression cycle

Use when you encounter a proprietary or undocumented binary file (e.

Use when you have a compressed file format (e.g., igzip) with a custom

Use when you have imported a laser ablation ICP-MS image into pew² and

Use when you have raw mass spectra data (MGF format with m/z/intensity

Use when you have parsed imzML XML metadata and loaded the corresponding

Use when you have a large gzip-compressed file (e.g., mzML.gz) with an

Use when when you have both (1) a molecular network graph from GNPS with

Use when when you have (1) a molecular network graph from GNPS with node

Use when when you have raw peak table data from mass spectrometry or

Use when you have loaded MSI data into napari, defined one or more ROIs

Use when when you have LC/MS feature data (m/z, retention time, intensity)