Claude Skills by HolobiomicsLab

Use when when designing or optimizing S4-based data backends (such as

Use when after successfully parsing vendor-specific metabolomic data

Use when designing multi-batch LC/GC-MS experiments where samples belong

Use when you have tab-delimited metabolomics data with columns for aliquot

Use when when designing injection sequences for LC/GC-MS multi-omics

Use when after MZmine feature detection and molecular networking on a

Use when when you have picked and annotated MS1 features from replicate

Use when you have a preprocessed count matrix (genes, miRNAs, isoforms,

Use when when you have a validated ReDU sample-information metadata file

Use when you have a raw peak table (CSV format, from any of 12 supported

Use when you have measured metabolites or lipids from archival blood

Use when when aligning detected features across multiple LC-IMS-MS/MS

Use when when you have loaded centroided .mzML files into a Spectra object

Use when when you have an Excel file uploaded by a user following the

Use when when you have an aligned MemoMatrix (sample-by-feature occurrence

Use when when you have LC-MS peak table data in Excel format (e.g., from

Use when when you have retrieved a large, heterogeneous collection of

Use when when you have loaded (un)targeted metabolite data into a Metaboprep

Use when when you have a Marr() output object containing reproducibility

Use when you have a merged MGF file (e.g., from MZmine output) containing

Use when you have 2D NMR spectral data (HSQC, HMBC, COSY) from multiple

Use when after loading and basic filtering of (un)targeted metabolomic

Use when after generating aligned MS2 fingerprints (sample-by-fingerprint

Use when you have high-throughput replicate measurements (e.g., mass

Use when you have a GNPS task ID from a completed molecular networking

Use when when beginning mass alignment in a multi-sample LC-MS metabolomics

Use when after mass tracks have been aligned across samples into a MassGrid

Use when after feature detection but before statistical analysis, when

Use when you have unaligned MS2 spectra from multiple metabolomics samples

Use when after loading multiple LC-MS .mzML files into an MsExperiment

Use when after loading and normalizing a LipidomicsExperiment object

Use when you have access to ALISTER's web app or codebase and need to

Use when processing IM-MS data files (Agilent .d or UIMF format) that

Use when when executing peak integration on preprocessed GC-IMS data

Use when apply Savitzky-Golay smoothing when your mass spectra contain

Use when after filtering retention time and drift time ranges on raw

Use when when you have consensus metabolic reconstructions in SBML format

'Use when when pre-training or fine-tuning a molecular representation

Use when you have a new or modified LC-MS data processing tool and need

Use when when working with feature abundance tables (rows=features, columns=samples)

Use when when converting mzML files to imzML format and the source mzML

Use when when you have generated a scan index from rawrr::readIndex()

Use when you have a Thermo Orbitrap .raw file and need to (1) verify

Use when after performing LOWESS regression on landmark peak RT pairs

Use when when processing LC-MS data with multiple overlapping m/z scan

Use when when uploading or ingesting a new paired omics project JSON

Use when you have a collection of records in a standardized format (e.g.,

Use when a user uploads a JSON project file to the platform and you need

Use when you have txt files exported from Sciex MultiQuant (>v3.0.3)

Use when you have prediction arrays (model outputs) and ground-truth