Claude Skills by HolobiomicsLab

Use when after integratePeaks has been executed with a chosen integration

Use when after peak detection in GC-IMS preprocessing, when you need

Use when after autoQ has extracted isotopologue peak area measurements

Use when when working with raw GC-MS data in NetCDF (ANDI) format that

Use when you have raw GC-MS data (aroma, breath, or other volatile analyte

Use when after auto-deconvolution of GC-MS data has produced a table

Use when you have raw GC-MS data (in netCDF or vendor format) containing

Use when when you have GC-MS data with detected peaks that require structural

Use when you have raw GC-MS data files containing overlapped peaks (unresolved

Use when when you have deconvolved GC-MS spectra (post-deconvolution

Use when when you have pre-computed BGC feature vectors (from domain

Use when when you have predicted BGC-spectrum IOKR scores or other pairwise

Use when you have paired GCF and MF datasets with strain membership information

Use when after BGC detection and clustering (producing GCFs) and metabolomics

Use when when you have integrated genomic data (GCFs from AntiSMASH via

Use when you have completed a BiG-SLiCE v2 clustering run and need to

Use when you have raw GCIMS sample files (from a GC–IMS instrument) and

Use when input GC-MS data (netCDF or mzML format) exhibits overlapping

Use when you have raw GCxGC-MS data in NetCDF format that contains instrumental

Use when after preprocessing a set of aligned 2D-TIC (two-dimensional

Use when you have preprocessed individual GCxGC-MS chromatograms (each

Use when you have a collection of sequence files (e.g., in a `genbanks`

Use when you have BGC sequences in GenBank format and need to extract

Use when you have antiSMASH v5.0.0 BGC predictions from a set of microbial

Use when you have a collection of BGCs tokenised as Pfam domain / subPfam

Use when when you have a generic constraint-based metabolic model, RNA-seq

Use when when you have differential expression results from genes, miRNAs,

Use when after completing differential expression analysis (edgeR, DESeq2,

Use when when you have metabolomic enrichment scores for genes (e.g.,

Use when you have completed a GO enrichment analysis (e.g., via hypergeometric

Use when you have a constraint-based metabolic model with embedded GPR

Use when when you have GenBank-format BGC sequences with Pfam domain

Use when when a feature table from LC-MS metabolomic profiling contains

Use when when fitting a nonlinear retention time (RT) mapping spline

Use when when you have converted multidimensional MS data to MZA HDF5

Use when when running metabologenomic RiPP detection pipelines (MetaMiner)

Use when you have pre-processed AntiSMASH BGC annotations (optionally

Use when a paired omics project JSON document contains genome identifiers

Use when a paired omics project record contains a genome identifier field

Use when you have multiple draft genome-scale metabolic reconstructions

Use when you have assembled genomic DNA sequences (contigs in FASTA format,

Use when when you have genomic DNA sequences (from isolates or metagenomes)

Use when after sub-clusters have been detected by PRESTO-STAT or PRESTO-TOP

Use when you have paired genomic (BGCs clustered into GCFs via BiG-SCAPE)

Use when when you have raw genotype and phenotype data files (e.g., from

Use when you have an MS2 spectral file (MGF format) from LC-MS/MS metabolomics

Use when when a statistical analysis function (e.g., random_forest or

Use when after running qc_summary() on a filtered mpactr object and aggregating

Use when after performing PCA (or other dimensionality reduction) on

Use when you have a frequency table (generated by count_fold_changes