Claude Skills by HolobiomicsLab

Use when you have generated a ggplot2 object from a domain-specific function

Use when your metabolomics dataset contains missing values below a known

Use when when preparing to create a release branch in a Maven-based multi-module

Use when when contributing a new feature, bug fix, or documentation update

Use when when you need to reproduce a computational workflow described

Use when you need to obtain source code or computational workflows from

Use when when you need to reproduce or validate a specific historical

Use when when you need to verify that a GitHub Actions workflow (such

Use when you need to verify that a GitHub Actions workflow (such as a

Use when when you have a Python package repository on GitHub and need

Use when you have a GitHub repository containing scientific records (e.

Use when a GitHub repository displays a CI workflow badge (e.g., passing/failing

Use when you have reproduced a release artifact locally (e.g., via Semantic

Use when when you need to verify that a software package (such as MassQL)

Use when when estimating a sparse network graph from a feature matrix

Use when after computing pairwise cosine similarities between all spectra

Use when when you have preprocessed molecular graph data (node and edge

Use when you have a pre-trained GNN model checkpoint, a test dataset

Use when you have GNPS molecular networking output (from GNPS1 at https://gnps.ucsd.edu

Use when after extracting a GNPS molecular networking job archive using

Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format)

Use when you have mass spectrometry MS/MS spectral data in GNPS-style

Use when you have computed frequent fragmentation patterns from a collection

Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu)

Use when you have a GNPS molecular network job and need to programmatically

Use when you have generated a GNPS mass spectral molecular network (in

Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-...

Use when your input is raw or semi-processed MS/MS spectra fetched from

Use when you have GNPS library accession IDs (e.g. CCMSLIB00011906190)

Use when you have downloaded a GNPS molecular networking job archive

Use when when you have a GNPS molecular networking task ID and need to

Use when when you have run a spectral networking job on GNPS (e.g. ProteoSAFe-METABOLOMICS-SNETS-V2)

Use when when deploying a Perl-based GUI application (such as LipidOne)

'Use when when processing large-scale mass spectrometry datasets (>1

Use when when searching unknown mass spectra against large high-resolution

Use when when you have a trainable neural network model (e.g., MSNovelist),

Use when you have a large spectral library and many query spectra to

Use when you have a large collection of tandem mass spectra (≥100k spectra)

Use when when clustering or encoding large MS/MS spectra datasets (>1

Use when after setting up a conda/pip environment with PyTorch and CUDA,

Use when you need to run a PyTorch model that was trained on GPU (e.g.,

Use when you have a trained graph neural network model for CCS prediction

Use when after implementing a multi-task fusion module (such as FuseBlock)

Use when after implementing a composite loss function that combines multiple

Use when when you have extracted retention times from the top detected

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

Use when after dereplication and cosine similarity clustering have been

Use when you have a GNPS molecular network (in GML or GraphML format)

Use when when you have spectral library matches (seed identities with

Use when annotating metabolites in untargeted metabolomics experiments