Claude Skills by HolobiomicsLab

Use when after calling a data import function (such as read_chrom on

Use when when you have metabolomics data (tab-delimited text or SummarizedExperiment

Use when you have raw Bruker NMR spectral data files (1D 1H format) stored

Use when you have built a reusable workflow function (e.g., a Shiny app

Use when you have a published predictive model with known coefficients

Use when you have a working R package (e.g., IonFlow for ionomics analysis)

Use when when you have a new or updated R package available via a non-CRAN

Use when before running any R function that wraps compiled C# methods

Use when when you have a functional R package with core statistical or

Use when when deploying an R package from a non-CRAN repository (e.g.,

Use when when preparing to preprocess Salmon-derived count matrices or

Use when before launching the DaDIA metabolomics pipeline or any analysis

Use when you have raw unnormalized metabolomics intensity data organized

Use when you have multiple MSP (mass spectrum) library files to read

Use when when you have a metabolomics dataset loaded into a SummarizedExperiment

Use when when your analysis requires functionality from both R (statistical

Use when you have a Spectra object in R and need to apply a specialized

Use when you have constructed or received a SummarizedExperiment object

Use when you need to switch between Modular and Flow execution modes

Use when when you have pre-written R functions organized across multiple

Use when you have located example R scripts in a version-controlled repository

Use when when you have obtained an R-based bioinformatic program (such

Use when you have a merged and batch-corrected non-targeted LC-MS/MS

Use when after training a customized R statistical or machine learning

Use when after editing R configuration scripts (e.g., Modular.r) that

Use when when you have raw metabolomics results from multiple studies

Use when you have raw mass spectrometry data in mzXML, mzML, or netCDF

Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp

Use when when you have multiple imputation methods with different function

Use when when applying a series of mpactr filter functions (filter_mispicked_ions,

Use when when working with large metabolomics peak tables (e.

Use when you need to understand or validate whether calling filter_mispicked_ions()

Use when when you need to support fast, non-sequential lookups (e.

Use when you have a large compressed scientific data file (e.g., indexed

Use when you have a large mzML file or text corpus (e.g., Moby Dick,

Use when you have a metabolomics count table (rows=metabolites, columns=samples)

Use when your MetaboSet object contains missing values (marked as NA)

Use when preparing ion image data for contrastive learning in mass spectrometry

Use when you have generated multiple random partitions (e.g., 10-fold

'Use when you have: (1) a set of spectral library matches (seed identities)

Use when when you have run a pathway ranking method (such as PALS/PLAGE)

Use when when you have predictions from one or more metabolite annotation

Use when you have completed cluster-based filtering of KEGG candidate

Use when you have a feature quantification table (m/z, retention time,

Use when you have identified significant differential metabolites (DAMs)

Use when after running annotateRC on LC–MS AIF data when you need to

Use when after completing differential analysis (e.g., via run_de())

Use when after generating ranked predictions of chemical formulas or

Use when after running retention-order prediction experiments on a test

Use when you have multiple pre-trained neural network models (e.g., MLP