Claude Skills by HolobiomicsLab

Use when after computing a scoring function over all possible genomic-metabolomic

Use when after computing link scores (e.g., strain correlation, IOKR,

Use when when comparing raw link scores (strain correlation or IOKR)

Use when you have two or more complementary scoring functions (e.g.,

Use when after implementing or modifying the scoring module that computes

Use when after running inference with a pre-trained or fine-tuned NaFM

Use when you have a set of gallery or example scripts that must run consistently

Use when you have edited core algorithm scripts in the Core-Match GitHub

Use when you have cloned or downloaded scripts from a development repository

Use when when you have access to a repository containing simulation scripts

Use when when you have fragment records (experimental or predicted) with

Use when you have molecular structures (from databases, design tools,

Use when when you have downloaded an SDF-formatted compound database

Use when you have PSM output files from one or more search engines (e.g.,

Use when when you have a calibrated FT-ICR mass spectrum (e.g., ESI-NEG

Use when when you have two or more implementations of a spectral search

Use when you have executed batch searches across two or more domain-specific

Use when when you have completed a DIA-MS proteomics search (e.

Use when you have executed batch searches of MS/MS spectra against multiple

Use when you have loaded DIA mass spectrometry search results containing

Use when you have search result files from one or more DIA-MS analysis

Use when when applying biotransformation rules to seed metabolites to

Use when after peak detection on composite mass tracks when you need

Use when when you have metabolomics datasets (loaded as SummarizedExperiment

Use when you have an unknown metabolite with unknown mass spectrum and

Use when you have uploaded a delimited data file (comma-, semicolon-,

Use when before executing a bioinformatics pipeline that depends on multiple

Use when when you need to confirm that a generated or retrieved release

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

'Use when you have labeled MS/MS spectra from replicate measurements

Use when you have extracted retention times from MS1 spectra for top

Use when you have extracted retention times from top MS1 features across

Use when when evaluating whether an MS data processing platform (such

Use when you maintain or curate a specialized sequence repository (such

Use when when you maintain a repository with local sequence files and

Use when you have differentially expressed isoform or exon FASTA sequences

Use when when you have a list of polypeptide sequences (plain text, CSV,

Use when when you have encoder-produced fixed-size embeddings and need

Use when you have paired multimodal scientific data (e.

Use when after receiving raw FASTQ files from SRA or local sequencing

Use when when parsing mzML or other blockwise-structured scientific data

Use when when you need to support custom data storage backends (e.g.,

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

'Use when when deploying a multi-service microarchitecture (such as MAGMa''s

Use when after you have processed raw LC-MS/MS spectral data through

Use when after computing activity scores for a collection of metabolite

Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing

Use when when you need to verify that a GitHub Actions workflow (e.g.,

Use when a scientific application (such as QCxMS2) requires multiple

Use when matching query mass spectra to a spectral library in the presence