Claude Skills by HolobiomicsLab

Use when when you have preprocessed ST and SM AnnData objects with spatial

Use when you are developing or comparing new data-dependent acquisition

Use when after completing an Environment simulation run with save_eval

Use when when building or fine-tuning a molecular representation model

Use when you have feature pairs identified by temporal correlation in

Use when after feature detection and alignment on raw MS data, when you

Use when after loading raw Agilent Unknowns Analysis CSV output and when

Use when you have a GC-MS dataset in CSV format with retention times,

'Use when you have a preprocessed LC-MS peak table exported from peak-picking

Use when when you have an Excel file downloaded from InjectionDesign's

Use when when preparing to run QCxMS2 or similar multi-tool orchestration

Use when your R package wraps a compiled .NET assembly or binary executable

'Use when you have measured execution times from multiple scripts that

Use when you have computation-time metrics from a gallery or benchmark

Use when you have a CSV feature table from XCMS or other MS feature detection

Use when before initiating raw file conversion or feature extraction,

Use when when you have LC-MS raw data and need to process it through

Use when when you have downloaded or retrieved fragment records from

Use when you are in the Bayesian optimization loop after fitting a Gaussian

Use when you have a tabular file (CSV or Excel) that has been manually

Use when when you have a raw count matrix derived from Salmon or similar

Use when you have raw omics expression data in CSV format (rows=genes/features,

Use when you have loaded raw expression data (linear-scale peptide or

Use when after validating a peak table (either standardized format or

Use when you have acquired targeted mass spectrometry data with measured

Use when your project JSON document contains genome identifiers but lacks

Use when you have constraint-based metabolic models of multiple cell

Use when after running MS1 extraction and prescreening on mzML files

Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .

Use when after running tardisPeaks() in screening mode or peak detection

Use when after isolating TIC peak regions via sliding window analysis

Use when after features have been grouped by retention time similarity

Use when you have Thermo Fisher Orbitrap .raw files and need to locate

Use when you have CE-MS raw data (mzML or netCDF format) containing a

Use when you are reconstructing targeted ion chromatograms (XIC) and

Use when you have a LipidomicsExperiment object with samples grouped

Use when after performing spectral library matching (whether unmodified

Use when you have generated candidate peptide-spectrum matches from a

Use when performing untargeted metabolomics annotation (i.e., matching

Use when when you have executed database search pipelines (Dereplicator,

Use when after high-scoring spectral library matching (e.g., EQ module

Use when you have implemented an automated feature annotation or adduct

Use when after running Paramounter's peak-height optimization on XCMS

Use when when reconstructing or validating the ColumnFinder component

Use when you have run ORA on simulated metabolite sets with known null

Use when immediately after FASTQ file acquisition (whether from SRA download

Use when you need to systematically enumerate all possible lipid species

Use when when a metabolite feature has been assigned a top-rank lipid

Use when you have completed NMR data quality control analysis and possess

'Use when rescoring PSMs with machine learning or statistical models