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HolobiomicsLab

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1. ▌
   Assay Matrix Formatting · holobiomicslab

   Use when after generating a feature table via mzrtsim() containing simulated peak abundances across samples with condition and batch effects, and you need to expose the abundance data through Bioconductor's SummarizedExperiment interface for use with standard accessor functions (assay(), colData()).
   12 installs
2. ▌
   Module Coverage Mapping · holobiomicslab

   Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation techniques.
   8 installs
3. ▌
   Msp File Format Parsing · holobiomicslab

   Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign SMILES, retention indices, or combine multiple libraries into a single consolidated MSP file for MS-DIAL.
   11 installs
4. ▌
   Smiles Notation Parsing · holobiomicslab

   Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields rather than a dedicated SMILES field, or when assigning SMILES from external structure databases (SDF files) to library.
   14 installs
5. ▌
   Xcms Workflow Execution · holobiomicslab

   Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the cohort.
   7 installs
6. ▌
   Cosine Distance Scoring · holobiomicslab

   Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of spectra to identify similar compounds, search spectral libraries, or build a similarity network for spectral clustering or.
   6 installs
7. ▌
   Dia File Format Parsing · holobiomicslab

   Use when you have raw DIA mass spectrometry files in timsTOF (.d), TripleTOF (.wiff), or Orbitrap (.raw) format and need to extract precursor ion chromatogram (PIC) data as input for quality metric computation or machine learning-based file quality prediction.
   7 installs
8. ▌
   Error Report Generation · holobiomicslab

   Use when when a user uploads a JSON project document to the Pairing Omics Data Platform and you need to determine whether it satisfies the platform's data structure requirements, including all mandatory fields, proper data types, and constraint satisfaction for paired omics metadata (e.
   7 installs
9. ▌
   Gnps Network Processing · holobiomicslab

   Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or chemical class information.
   15 installs
10. ▌
    Hdf5 File Io Operations · holobiomicslab

    Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS calibration), or when you need to export annotated feature tables with isotopologue metadata back to HDF5 for archival.
    12 installs
11. ▌
    Lc Ms Output Validation · holobiomicslab

    Use when after executing a Nextflow-based LC-HRMS metabolomics workflow with Docker or Singularity containerization on .mzML LC-MS data, before proceeding to downstream statistical or visualization analyses.
    10 installs
12. ▌
    Lcms Feature Extraction · holobiomicslab

    Use when when you have raw LC-MS chromatographic data (mzML or vendor format) and need to identify and characterize all detectable peaks across the full retention time range for untargeted metabolomics or discovery workflows.
    10 installs
13. ▌
    Lipid Class Enumeration · holobiomicslab

    Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine, triglyceride) and fatty acid composition ranges (e.g., C14–C22 with 0–6 degrees of unsaturation).
    10 installs
14. ▌
    M Z Rt Feature Matching · holobiomicslab

    Use when you have extracted peaks from multiple LC/HRMS batches (n > 1) with their m/z and RT values, and you need to identify and align peaks representing the same compound across batches to build a consensus feature matrix.
    13 installs
15. ▌
    Mass Accuracy Alignment · holobiomicslab

    Use when after parsing MRM transition tables (m/z values, retention times, transition parameters) from mzML data, before statistical analysis or visualization. Use this skill when you have detected but unannotated transitions and need to map them to lipid species with quantified confidence.
    8 installs
16. ▌
    Mass Defect Calculation · holobiomicslab

    Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS candidates.
    11 installs
17. ▌
    Massql Query Generation · holobiomicslab

    Use when you have trained a shallow decision tree on ChemEcho feature vectors (representing unique peak or neutral loss formulas from tandem MS spectra) and need to deploy the learned splitting logic as a queryable, inspectable artifact.
    9 installs
18. ▌
    Metabolite Set Analysis · holobiomicslab

    Use when you have a metabolite intensity matrix (rows=metabolites or peaks, columns=samples) paired with metabolite-to-pathway or metabolite-to-feature-group annotations, and you want to score activity levels across pathways or metabolite groupings in a way that tolerates missing peaks and.
    7 installs
19. ▌
    Ms Finder Format Export · holobiomicslab

    Use when after completing MS-CleanR filtering (blank subtraction, background removal, RSD/RMD thresholding) and feature clustering steps, when you have a consolidated set of representative features and need structural identification via MS/MS spectral matching.
    10 installs
20. ▌
    Ms1 Spectrum Simulation · holobiomicslab

    Use when when you need to generate synthetic LC-MS/MS data to test fragmentation strategies, validate acquisition controllers, or benchmark peak-picking and spectral matching algorithms before deployment on real mass spectrometers.
    12 installs
21. ▌
    Ms1 Spectrum Subsetting · holobiomicslab

    Use when after generating a scan index from a Thermo Fisher Orbitrap raw file using readIndex(), apply this skill when your analysis goal requires working exclusively with MS1 (precursor) scans rather than tandem MS (MS2/MS3) spectra.
    8 installs
22. ▌
    Mse Reconstruction Loss · holobiomicslab

    Use when training embeddings from multi-modal spectral data (peak information + metadata) where you need to ensure both contrastive discriminability AND reconstruction fidelity. Specifically use it in transformer-based architectures that produce embeddings from heterogeneous inputs (e.
    13 installs
23. ▌
    Mztab Format Generation · holobiomicslab

    Use when after completing peak detection, MS1 feature picking, and accurate mass database search (e.g., against HMDB) on FIA-MS or LC-MS(/MS) data.
    8 installs
24. ▌
    Neutral Loss Prediction · holobiomicslab

    Use when you have LC-HRMS features with fragmentation data (observed m/z shifts, mass deficits, or tandem MS spectra) and a suspect compound database with known or predictable neutral loss fragments (e.g., H₂O, CO₂, CH₄, or structure-specific losses).
    13 installs
25. ▌
    Peaklist Format Parsing · holobiomicslab

    Use when you have raw or semi-processed m/z peak detection output from LC-MS/MS instruments (typically from XCMS, MSnbase, or other peak-picking tools) in one of several known formats (MetaboAnalyst-like, MetaboShiny native, or Metabolights) and need to ingest them into MetaboShiny for compound.
    10 installs
26. ▌
    Pfas Feature Annotation · holobiomicslab

    Use when when you have a feature list (m/z, retention time, intensity) from LC- or GC-HRMS non-target screening and need to identify PFAS-like homologous series characterized by CF₂ (14 Da) repeating units.
    9 installs
27. ▌
    Query Result Tabulation · holobiomicslab

    Use when after executing MassQL queries against mzML mass spectrometry files when you need to organize heterogeneous scan-level results (MS1 and MS2 data) into consistent tabular schemas for batch analysis, statistical comparison across files/queries, or visual summary generation.
    12 installs
28. ▌
    R Statistical Computing · holobiomicslab

    Use when you have a merged and batch-corrected non-targeted LC-MS/MS feature table with sample metadata and need to perform statistical testing to identify significant features, compare groups (e.g., disease vs. control), or explore multivariate patterns.
    15 installs
29. ▌
    Raw File Format Parsing · holobiomicslab

    Use when you have native Thermo Fisher RAW files and need to recover file-level metadata (instrument details, run statistics), scan headers (retention time, total ion current, scan mode for MS1 or MS2), or peak lists (m/z and intensity arrays) in tabular or array form suitable for computational.
    11 installs
30. ▌
    Realtime Alert Dispatch · holobiomicslab

    Use when a QC check fails during an active LC-MS instrument run and you need to immediately notify configured users (via Slack channel or email address) of the failure event, including timestamp, check type, and severity metadata.
    9 installs
31. ▌
    Spectral Data Alignment · holobiomicslab

    Use when you have quantification tables (with feature IDs and abundance values), metadata tables (with sample annotations), and separate spectral data files (e.g., MS/MS spectra or fragmentation patterns), and you need to integrate them into a unified input for msFeaST.
    8 installs
32. ▌
    Spectral Data Filtering · holobiomicslab

    Use when you have loaded a full set of MS scans (e.g., all MS1 scans from readAllScanMS1 in Aerith) and need to restrict analysis to a specific retention-time window (e.g., 9–10 min with 0.
    11 installs
33. ▌
    Spectral Data Retrieval · holobiomicslab

    Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/... or mzspec:MSV000084951:AH22) and need to extract the corresponding mass spectrum peak list (m/z and intensity pairs) for downstream analysis, visualization, or cross-repository comparison.
    7 installs
34. ▌
    Chemical Shift Annotation · holobiomicslab

    Use when when you have preprocessed 1H NMR spectral data with unidentified peaks and need to determine metabolite identity by exploiting the correlation structure of NMR signals.
    10 installs
35. ▌
    Diffusion Model Inference · holobiomicslab

    Use when when you have multi-modal spectroscopic data (IR, Raman, UV-Vis, mass spectra, or NMR) and need to recover the underlying molecular structure without relying on finite spectral libraries or autoregressive SMILES generation.
    10 installs
36. ▌
    File Integrity Validation · holobiomicslab

    Use when you have a raw NV (NMRViewJ) binary file and need to confirm it is well-formed before parsing or processing.
    13 installs