Claude Skills by HolobiomicsLab

Use when you have built a Shiny application (global.R, ui.R, server.

Use when you have developed an R-based workflow (e.g., data processing,

Use when when a Shiny application is documented or observed to run only

Use when you have a complete R package (e.g., pmartR) implementing a

Use when when building or maintaining a Shiny GUI for omics data analysis

Use when you have an R package with analytical functions (e.g., meta-analysis,

Use when you have an existing R package with statistical or data-processing

Use when when refactoring a mass-spectrometry formula-prediction codebase

Use when after a TCN-based formula prediction model has generated initial

Use when when you need to reduce overfitting in a Siamese neural network

Use when you have preprocessed MS/MS spectra binned into 10,000 equally-sized

Use when you have a collection of preprocessed tandem mass spectra (binned

Use when you have a collection of cleaned MS/MS spectra (in formats like

Use when when you have pairs of mass spectrometry spectra and need to

Use when working with natural product molecules where conventional synthetic-molecule

Use when you have processed the same GC–MS dataset (m/z vs retention

Use when you have raw total ion current (TIC) traces extracted from mass

Use when when processing raw Bruker Solarix transient files (.d format)

Use when after loading raw LC-MS data from multiple disease groups when

Use when after executing multidimensional smoothing, spike removal, or

'Use when after generating consensus spectra with fragment recurrence

Use when you have differentially expressed isoform or exon FASTA sequences

Use when apply this preprocessing chain when you have loaded raw or continuous

Use when when you have a 1D intensity array from a mass spectrum (m/z

Use when you have imported raw MSI spectral data in imzML format and

Use when you observe jagged or noisy peak profiles in low-abundance ions

Use when analyzing 1D signal arrays (e.g., extracted ion chromatograms,

Use when when working with raw LC-HRMS profile-mode data containing noisy

Use when immediately after peak detection in the IDSL.IPA workflow, when

Use when when preparing a 1D 1H NMR spectral peak list for input to the

Use when after elution peaks have been detected on composite mass tracks

Use when after peak detection in nontargeted LC-MS workflows when you

Use when you have QCpool (pooled quality control) samples measured at

Use when when you have a pre-computed hierarchical dendrogram from structural

Use when after computing pairwise similarity scores across a collection

Use when when you have cleaned and filtered mass spectrometry spectral

Use when you have a collection of cleaned spectra in supported formats

Use when you have a collection of tokenized BGCs (each gene represented

Use when after training contrastive embeddings that unify MS/MS spectra

Use when you have a preprocessed unknown sample spectrum (m/z peaks and

Use when when you have a query electron ionization mass spectrum (m/z

Use when after a deep-learning model has predicted structural similarity

Use when you have LC-MS/MS query spectra in mgf format that you need

Use when when you have computed Spec2Vec similarity scores (typically

Use when you have a set of metabolites or chemical formulas to analyze

Use when when you have simulated DDA (data-dependent acquisition) scans

Use when after a ViMMS Environment.run() simulation completes with save_eval

Use when after executing a multi-stage simulation workflow in R and/or

Use when when you have a computational simulation framework (e.

Use when when you have access to a study's source repository containing