Claude Skills by HolobiomicsLab

Use when you have peak/feature tables from one or more of MZmine, XCMS,

Use when when processing MS spectral data from multiple open mass spectra

Use when when preparing metabolomics data (feature tables, sample metadata)

Use when when you have raw outputs from LipidSearch or LIQUID identification

Use when when raw MS files are uploaded to MSConnect via the Raw File

Use when after writing parsed spectra to a new MSP file using mssearchr's

Use when after completing an Environment simulation or replay with scan-level

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

Use when you need to open an mzML file in pymzML and must automatically

Use when you have mass spectrometry data stored in a non-standard format

Use when you have MZmine-exported LC-MS/MS data (MGF spectra and CSV

Use when you have a raw NV (NMRViewJ) binary file and need to confirm

Use when when you need to parse mzML data stored in a format beyond the

Use when when designing or integrating a file parser for mass spectrometry

Use when a Shiny application or R package is confirmed to work on one

Use when when preparing to read Thermo Fisher Scientific .raw files using

Use when when initializing a SmartPeak session from a sequence file,

Use when after invoking the saveAnnotations function on a MetaboAnnotatoR

Use when you are preparing to reuse public tandem MS data from MassIVE

Use when you need to confirm that a software API or tool correctly implements

Use when after applying one or more mpactr filters (mispicked, group,

Use when after applying a filter function (filter_mispicked_ions(), filter_group(),

Use when reconstructing or modifying dashboard filters (e.

Use when after applying a sequence of mpactr filters (filter_mispicked_ions,

Use when when you need to apply domain-specific or novel filtering logic

Use when when expanding a compound set through multi-generation Pickaxe

Use when when you have a set of chemical compounds (as SMILES, mol, SDF,

Use when when you have a collection of small molecules with known chemical

Use when you have a pretrained deep learning model (e.

Use when you have molecule IDs from PubChem or HMDB that have been converted

Use when you have parsed molecular structures from the SMRT dataset or

Use when when implementing a similarity-based filter for Pickaxe compound

Use when when you have deposited or archived biosynfoni fingerprint vectors

Use when you have a list of metabolites or lipids with associated p-values

Use when you have partitioned genomic-metabolomic links into discrete

Use when after loading a specXplore session data object file from the

Use when you have a long-format metabolomics dataset with one row per

Use when your search engine output (PSM file) omits fixed modifications

Use when you have aligned and baseline-corrected GC-IMS data with detected

Use when when you have published LOTUS flat files (TSV or compressed

'Use when when implementing or validating a lossy numeric codec for mass-spectrometry

Use when you have sampled 10,000+ steady-state flux solutions for each

Use when you have sampled feasible flux distributions from multiple constraint-based

Use when when you have (1) LC-MS normalized intracellular metabolite

Use when you have a constraint-based metabolic model and need to establish

Use when when you have sampled the feasible flux solution space of constraint-based

Use when after performing differential abundance testing (via limma or

Use when when you have a quantified peak table (LC-MS feature intensities)

Use when you have a feature-by-sample metabolomic intensity matrix (finalData)

Use when after completing statistical tests (t-test, Mann–Whitney U,