Claude Skills by HolobiomicsLab

Use when you have generated a lipid spectral library (lipid identities,

'Use when you have an unknown MS/MS query spectrum with a known or measured

Use when when you have a compound's SMILES string or molecular formula

Use when when comparing two MS/MS spectra using modified cosine similarity

Use when after retrieving top-scoring library candidates from a full

Use when when analyzing tandem mass spectra (MS/MS data) and you want

Use when after cosine similarity or dot-product scoring of experimental

Use when when preparing augmented training data for Siamese or contrastive

Use when after loading an MsmsSpectrum object but before intensity filtering

Use when you have assembled genome FASTA sequences (from SPAdes, metaSPAdes,

Use when you have centroided MS2 spectra from data-dependent acquisition

Use when you have raw MRM sample files from a LC-MS/MS instrument and

Use when when computing entropy_similarity() between experimental (noisy

Use when you have retention order predictions from multiple trained ROASMI

Use when when you have trained multiple machine learning regressors on

Use when you have a trained predictor (like BitterPredict) that accepts

Use when when a GUI widget (e.g., isotopes display, compound list, or

Use when valueMatcher.series_match has detected database-ID values (HMDB

Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d)

Use when you have multi-class or time-course metabolomic peak table data

Use when you have a pretrained PyTorch model checkpoint (e.g., JESTR

Use when you are developing a standalone Perl application for Windows

'Use when after loading a Metaboprep object containing metabolomic abundance

Use when when you have normalized MS1 ion intensity features from multiple

Use when after normalizing and log-transforming lipidomics abundance

Use when you have a log2-transformed metabolite abundance matrix and

Use when you have a log2-normalized, zero-mean and unit-variance standardized

Use when when you have computed pairwise distances between MS2 fingerprint

Use when you have per-sample metabolite abundance data and a metabolite-pathway

Use when you have a Thermo Fisher Scientific .raw file containing PRM

Use when when you have raw mass spectrometry imaging data tensors and

Use when during the LDA training phase when you need to decide whether

Use when you have preprocessed tandem mass spectrometry spectra converted

Use when when you need to reduce a large compound set generated by reaction

Use when after running ModiFinder's probability generation on a known

Use when you have raw MS2 spectra (m/z and intensity pairs) that you

Use when after training or loading a NeatMS neural network model, apply

Use when you have a trained NeatMS neural network model (.h5 format)

Use when you have a ProForma 2.0 peptidoform string (e.

Use when you have peptide sequences with chemical modifications encoded

Use when when peptide identifications from a search engine (MaxQuant,

Use when when you have a ProForma 2.0–formatted peptide string with PSI-MOD

Use when a paired omics project record contains a genome identifier (e.g.,

Use when when a user uploads a JSON project document to the Pairing Omics

Use when you have 3D optimized molecular conformers (RDKit mol objects

Use when after initial peak detection on composite mass tracks via local

Use when you have received raw mass spectrometry data in one of four

Use when after predicting coding potential (via CPAT) on differentially

Use when you have co-fractionation/mass-spectrometry (CF-MS) elution

'Use when you have a collection of MS/MS spectra in MGF format and need