Claude Skills by HolobiomicsLab

Use when after you have detected and assigned molecular formulas to peaks

Use when you have identified a package available in the Bioconda channel

'Use when you are building a new mass spectrometry data backend or storage

Use when you have CE-MS test files archived in the msdata Bioconductor

Use when after constructing a SummarizedExperiment object from raw metabolomics

'Use when after successfully reading and validating a tab-delimited metabolomics

Use when you have a small-molecule chemical structure (as SMILES, MOL,

Use when when you have processed Cardinal MSI data (normalized peak intensities,

Use when constructing or enriching a chemical formula database that must

Use when after normalizing a log-transformed metabolomics featuredata

Use when you have raw or processed TWIM-MS data with arrival time and

Use when after biomolecular class labels have been assigned to features

Use when you have raw or processed TWIM-MS data with arrival time and

Use when after data transformation (e.g., log2 normalization) but before

Use when after running iMd-ANOVA or G-test statistical analysis on normalized

'Use when initiating a proteomics or panomics analysis with peptide-

Use when when you have a natural product structure (as a molecule object,

Use when you have a natural product molecule structure in SMILES, InChI,

Use when when you have BGC sequences in FASTA or GenBank format and need

Use when you have assembled microbial genomes (nucleotide FASTA files)

Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format)

Use when you have GenBank-formatted BGC records and need to prepare them

Use when you have output from a biotransformation rules module (candidate

Use when you have a known parent drug chemical formula and aim to predict

Use when you have one or more small-molecule chemical structures (as

Use when you have untargeted metabolomics data with unknown or ambiguous

Use when when you have a small-molecule structure (SMILES, MOL, or SDF

Use when you have untargeted metabolomics data with unknown metabolite

Use when you need to populate or reconstruct a biotransformation prediction

Use when after constructing a bipartite network graph with metabolites

'Use when you have two MS/MS fragmentation spectra with fragment ion

Use when after completing dereplication and cosine similarity clustering

Use when you need to represent natural product molecules as fixed-length

Use when you have normalized and imputed metabolite abundance measurements

Use when when you need to audit whether Python source files in a repository

Use when your peak table includes features flagged in blank control samples

Use when you have a feature intensity matrix with both blank and QC (quality

Use when apply this filter after feature detection and before downstream

Use when after MS1 feature detection and accurate mass annotation, when

Use when you have a feature quantification table exported from MZmine3

Use when you have a trained sequence-to-sequence model (such as GCMSFormer)

Use when when you have tandem mass spectra from ribosomally synthesized

Use when when preparing NMR datasets for processing in NMRFx and the

Use when when you need random access into a large text or XML file that

Use when you are planning a blood sampling campaign and need to verify

Use when when you have peripheral blood sample cohorts (plasma/serum)

Use when you have predicted or partially assembled molecular fragments

Use when when you have performed many pairwise correlation tests between

Use when when you have a trained CNN binary classifier for peak detection

'Use when you have raw LC-MS feature-intensity tables (rows: samples,