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HolobiomicsLab

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1. ▌
   Metabolite Database Matching · holobiomicslab

   Use when after peak networks have been identified and clustered from INADEQUATE spectra (typically via the clustering and finding modules), use this skill when you need to assign chemical identities to unknown peak networks by comparing them against reference spectral signatures in a simulated.
   0 installs
2. ▌
   Metabolite Spectral Matching · holobiomicslab

   Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference spectra in GNPS or a local indexed repository.
   0 installs
3. ▌
   Molecular Formula Prediction · holobiomicslab

   Use when you have 1D ¹H or ¹³C NMR spectra from an unknown organic compound and need to predict its molecular formula (e.g., C₆H₁₂O₂). The compound must contain ≤19 heavy (non-hydrogen) atoms. Use this as the first stage of a structure elucidation pipeline before predicting molecular connectivity.
   0 installs
4. ▌
   R Package Function Execution · holobiomicslab

   Use when you have raw Bruker NMR spectral data files (1D 1H format) stored in a directory structure and need to prepare them for automated metabolite identification and quantification in ASICS.
   0 installs
5. ▌
   Repository Cloning And Setup · holobiomicslab

   Use when when you need to deploy a containerized scientific tool (e.g., CloMet) for the first time on a local machine or CI/CD environment, and the project provides a Dockerfile and GitHub repository.
   0 installs
6. ▌
   Spectral Feature Engineering · holobiomicslab

   Use when you have molecular structures (SMILES or graph representations) and need to predict or analyze infrared spectral properties using message passing neural networks.
   0 installs
7. ▌
   Spectral File Format Parsing · holobiomicslab

   Use when you receive raw spectral data files (jcamp, RAW, or mzML) from NMR, IR, or MS instruments and need to extract peak tables, metadata, and spectral parameters before generating visualizations, performing peak annotation, or converting to standardized output formats.
   0 installs
8. ▌
   Stocsy Metabolite Assignment · holobiomicslab

   Use when use STOCSY when you have preprocessed 1H NMR spectral data with an unidentified peak of interest (driver signal at a specific δ ppm value) and need to determine its metabolite identity by finding correlated signals across the spectrum.
   0 installs
9. ▌
   Structured Report Generation · holobiomicslab

   Use when after applying jsonschema validation to a parsed mwTab file against MS or NMR schema definitions, when you have collected validation errors, warnings, and metadata column matching results and need to communicate findings to data curators or submitters in a structured, machine-readable.
   0 installs
10. ▌
    Hic Map Format Validation · holobiomicslab

    Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.
    0 installs
11. ▌
    Juicer CLI Tool Execution · holobiomicslab

    Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating domains, or annotate other structural features without re-running the full alignment and contact matrix construction.
    0 installs
12. ▌
    Macs3 Subcommand Chaining · holobiomicslab

    Use when when you have aligned ChIP-Seq reads (BED or BEDPE format) and a corresponding control sample, and you need explicit control over peak-calling parameters—including fragment-length prediction, local bias windows (d, slocal=1kb, llocal=10kb), background scaling, and score-cutoff.
    0 installs
13. ▌
    Badge Endpoint Retrieval · holobiomicslab

    Use when when you need to verify the current operational status of a software project across multiple dimensions (CI/CD, code quality, test coverage, containerization, archival) and those status indicators are exposed as badge endpoints in the project's README.
    0 installs
14. ▌
    Build Badge Verification · holobiomicslab

    Use when you need to validate that a repository's automated build and publish pipeline is functioning correctly on a release or target branch, particularly when assessing the reliability of release artifacts or the health of a CI/CD workflow.
    0 installs
15. ▌
    Code Repository Analysis · holobiomicslab

    Use when you have a published research article describing a new FT-ICR MS analysis tool and need to verify which analytical and visualization features are actually implemented (not just claimed).
    0 installs
16. ▌
    Interoperability Testing · holobiomicslab

    Use when when a new file format specification exists as a living document (e.
    0 installs
17. ▌
    JSON Response Validation · holobiomicslab

    Use when after sending HTTP requests to API endpoints (such as /classify or /model/metadata on an NP-Classifier server) to verify that the response is parseable JSON and contains the expected output fields and metadata before attempting to extract or process the data programmatically.
    0 installs
18. ▌
    Lipid Candidate Matching · holobiomicslab

    Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
    0 installs
19. ▌
    Metabolic Model Curation · holobiomicslab

    Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
    0 installs
20. ▌
    Peak Pairwise Comparison · holobiomicslab

    Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover biochemical transformations without prior knowledge of reaction networks.
    0 installs
21. ▌
    Similarity Matrix Export · holobiomicslab

    Use when after computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular fingerprint-based, or metadata-related assessments), use this skill to persist the resulting similarity matrix to a named output file.
    0 installs
22. ▌
    Smiles String Formatting · holobiomicslab

    Use when you have a set of chemical structures (as SMILES strings or convertible to SMILES) and need to submit them programmatically to the NP Classifier /classify endpoint for batch or automated classification.
    0 installs
23. ▌
    Tabular Data Tag Parsing · holobiomicslab

    Use when you have raw tabular experimental data (CSV or Excel) with column headers annotated using MESSES tag syntax (#<table_name>.id for record identifiers, #.
    0 installs
24. ▌
    API Adapter Layer Design · holobiomicslab

    Use when when you have multiple mass spectrometry data formats (mzML, mzXML, or others) that must be ingested into a single format-agnostic processing engine (e.g., mspack compression), and you need to avoid replicating the core logic for each format.
    0 installs
25. ▌
    Batch Vector Preparation · holobiomicslab

    Use when you have a metabolomics dataset with samples collected across multiple batches (e.g., different MS runs, sample preparation rounds, or instrument configurations) and need to apply batch-aware correction methods such as CordBat.
    0 installs
26. ▌
    CI Workflow Reproduction · holobiomicslab

    Use when you have access to a GitHub repository with a Maven-based CI workflow (e.g., defined in .
    0 installs
27. ▌
    Code Artifact Inspection · holobiomicslab

    Use when use when the workflow requires code_artifact_inspection.
    0 installs
28. ▌
    Dynamic Method Discovery · holobiomicslab

    Use when you need to enumerate all supported metadata conversions in a plugin-based architecture without hard-coding converter names or method signatures.
    0 installs
29. ▌
    Feature Table Subsetting · holobiomicslab

    Use when after loading an MS-DIAL feature table when you need to separate features into two disjoint groups: one meeting a quantitative threshold (e.g., m/z decimal values outside [4, 8], coefficient of variation below a cutoff, or mass defects within acceptable bounds) and one not meeting it.
    0 installs
30. ▌
    Gc CI Ms Data Processing · holobiomicslab

    Use when you have vendor-format GC-CI-MS raw data from a stable isotope labeling experiment, a list of targeted compounds with known monoisotopic m/z, retention time, and molecular formula, and you need to extract per-isotopologue area and intensity values across multiple samples with consistent.
    0 installs
31. ▌
    Header Key Value Mapping · holobiomicslab

    Use when when you have JSON table records (arrays of field-indexed objects) and need to restructure them into dictionaries where specific table columns are mapped to new key names, and you want to control which columns appear in the output and under what names.
    0 installs
32. ▌
    Job Artifact Persistence · holobiomicslab

    Use when when deploying OpenMS workflows in online mode via RQ (Redis Queue) in a Docker container where the Streamlit frontend may restart or rerun without losing track of submitted jobs.
    0 installs
33. ▌
    Lipid Similarity Scoring · holobiomicslab

    Use when you have two or more lipid structures (represented as molecular graphs or parsed lipid names) and need to quantify their structural dissimilarity for dendrogram construction, lipidome clustering, or identification of structurally similar lipids.
    0 installs
34. ▌
    Mass Accuracy Validation · holobiomicslab

    Use when after implementing or modifying an mzML parser module that converts mzML files into MS-DIAL's internal data model, and before integrating the parser into the production analysis pipeline.
    0 installs
35. ▌
    Mass Spectrum Simulation · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution patterns to compare against experimental MS data, validate peak assignments, or generate synthetic spectra for method development.
    0 installs
36. ▌
    Msi Spectral Data Import · holobiomicslab

    Use when use this skill at the start of any MSI analysis workflow when you have raw imzML files or vendor-specific MSI data that need to be loaded into napari-MSI-Explorer for visualization, mean intensity calculation, ROI analysis, or annotation.
    0 installs
37. ▌
    Omics Data Visualization · holobiomicslab

    Use when you have tabular omics data (expression matrices, p-values, fold changes, functional annotations, or clinical outcomes) in CSV format and need to generate publication-ready visualizations that reveal distributional patterns, statistical significance thresholds, group comparisons, or.
    0 installs
38. ▌
    Open Modification Search · holobiomicslab

    Use when your query spectra contain peptides with unknown modifications (e.g., oxidation, phosphorylation, acetylation, or non-enzymatic modifications not specified in the search parameters), and you have a reference spectral library in mzML or mzXML format.
    0 installs
39. ▌
    Pathway Function Mapping · holobiomicslab

    Use when when you have reconstructed metabolic networks for two or more organisms from KEGG and need to compare them both topologically and functionally.
    0 installs
40. ▌
    Peak List Column Mapping · holobiomicslab

    Use when when uploading a new peak list or complex sample data file with delimiter-separated columns to Punc'data, especially when column headers are ambiguous or use non-standard naming conventions.
    0 installs
41. ▌
    Poisson Noise Generation · holobiomicslab

    Use when when preparing augmented variants of ion images (single-channel 2D arrays or multi-channel spectral images) for contrastive learning in mass spectrometry imaging tasks.
    0 installs
42. ▌
    R Graphics Customization · holobiomicslab

    Use when when you have completed a comprehensive ranking of preprocessing workflows (e.
    0 installs
43. ▌
    R Object Slot Inspection · holobiomicslab

    Use when after calling a data import function (such as read_chrom on a NetCDF chromatogram file) that returns a structured S4 object, inspect its slots to confirm the object was constructed correctly, validate that retention times and modulation parameters were parsed as expected, and ensure the.
    0 installs
44. ▌
    R Pipe Operator Chaining · holobiomicslab

    Use when when you have a metabolomics dataset loaded into a SummarizedExperiment and need to apply a sequence of analysis steps (data loading, annotation, statistical analysis, visualization, reporting) in a reproducible, self-contained pipeline where each function's output becomes the next.
    0 installs
45. ▌
    Retention Time Windowing · holobiomicslab

    Use when you have a complete TIC (total ion current) table indexed by retention time and need to visualize or analyze only a specific time interval—for example, when isolating a chromatographic peak region (9–10 min) before plotting or when a mass spectrometry run spans a time range wider than the.
    0 installs
46. ▌
    Smiles Molecular Parsing · holobiomicslab

    Use when when you have a list of candidate metabolite identifiers in SMILES or mol format and need to programmatically apply chemical transformations (e.g., derivatization reactions), compute molecular weights, or enumerate adduct ions for mass spectrometry matching.
    0 installs
47. ▌
    Smiles String Validation · holobiomicslab

    Use when you have MSBERT-preprocessed spectral datasets (GNPS, MoNA, or MTBLS1572 format) with SMILES annotations before training a spectral embedding or compound identification model.
    0 installs
48. ▌
    Spectral Image Filtering · holobiomicslab

    Use when when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
    0 installs
49. ▌
    Tautomer Standardization · holobiomicslab

    Use when ingesting raw SMILES strings from curated structure inventories where the same chemical may be represented in multiple tautomeric forms (e.g., keto–enol pairs, lactam–lactim forms) across different literature sources or input databases.
    0 installs
50. ▌
    Threshold Sweep Analysis · holobiomicslab

    Use when when you have predicted probabilities and binary true labels from a classifier and need to evaluate its discriminative ability across multiple operating points, or when you need to generate a publication-quality ROC curve with AUC to compare classifiers or communicate model performance to.
    0 installs
51. ▌
    Type I Error Computation · holobiomicslab

    Use when when you need to verify that reported Type I error rates from a statistical method (here, PaIRKAT) can be independently reproduced, or when you require baseline false positive rate estimates across multiple simulation conditions (sample sizes, effect configurations, significance.
    0 installs
52. ▌
    C Stream Io Debugging · holobiomicslab

    Use when when a C++ program writes records to an output stream (e.g., SAM alignment file) and the final output file contains fewer records than expected based on upstream counts (e.g., salmon's NumReads total in quant.sf exceeds SAM record count), indicating buffered data loss at stream closure.
    0 installs
53. ▌
    Salmon Output Parsing · holobiomicslab

    Use when when you have salmon quant.sf.gz output files from pseudoalignment-based transcript quantification and need to convert transcript-level abundance estimates and counts into gene-level matrices for differential expression analysis with edgeR, DESeq2, or limma-voom.
    0 installs
54. ▌
    Matlab Scientific Computing · holobiomicslab

    Use when you have mass spectrometry data in mzXML or mzML format and need to systematically extract regions of interest (ROIs) from multi-dimensional m/z-intensity-time arrays, normalize feature values, and augment datasets for untargeted metabolomics workflows.
    0 installs
55. ▌
    Msflo Metabolite Annotation · holobiomicslab

    Use when after MS-DIAL has completed feature detection and peak alignment on .mzML LC-HRMS data, producing an aligned feature table. Use MSFLO when you need to assign metabolite identities to detected features and filter results by significance criteria before downstream interpretation.
    0 installs
56. ▌
    R Data Structure Conversion · holobiomicslab

    Use when you have preprocessed MSI data in Cardinal format (post-peakBin) and need to apply mass2adduct's adduct-detection workflow, OR you have exported MSI intensity data as CSV from third-party software (SCiLS, MSiReader) and must convert it into a standardized R object for downstream analysis.
    0 installs
57. ▌
    Spectral Similarity Scoring · holobiomicslab

    Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g., PNNLMetV20191015.MSL) to identify the unknown compound.
    0 installs
58. ▌
    Spectrum Similarity Scoring · holobiomicslab

    Use when you have an unknown MS/MS spectrum (query spectrum with m/z and intensity pairs) and a reference spectral library (local or public: GNPS, MASSBANK, DrugBANK), and you need to identify the -matching compounds by ranking library entries by spectral similarity.
    0 installs
59. ▌
    Vendor Data Standardization · holobiomicslab

    Use when you have raw MS data files directly from a vendor instrument (Thermo .raw, Agilent .d, Waters .ms, etc.) and need to process them through AriumMS or any other metabolomics pipeline that accepts only .mzXML or .mzML formats.
    0 installs
60. ▌
    Binary Data Base64 Encoding · holobiomicslab

    Use when when converting simulated or real LC/GC-MS spectral data (m/z–retention-time intensity matrices) into mzML format for archival, sharing, or downstream processing.
    0 installs
61. ▌
    Ei Mass Spectrum Simulation · holobiomicslab

    Use when when you have a molecular structure (XYZ or equivalent format) and need to predict its EI mass spectrum including major fragment ions and their relative intensities, particularly for validation against experimental data or when experimental spectra are unavailable;
    0 installs
62. ▌
    Gcms Spectrum Deconvolution · holobiomicslab

    Use when input GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks where multiple analytes co-elute at the same retention time, resulting in composite mass spectra that conflate signals from distinct molecular species.
    0 installs
63. ▌
    Instrument Metadata Parsing · holobiomicslab

    Use when when you have raw or semi-processed mass spectrometry data files in mixed formats (e.g., vendor-native .raw, .d, .
    0 installs
64. ▌
    Java Source Code Inspection · holobiomicslab

    Use when when you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format types (e.
    0 installs
65. ▌
    Lipid Feature Normalization · holobiomicslab

    Use when after raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate statistical analysis to identify differential lipids and metabolites.
    0 installs
66. ▌
    Mass Chromatogram Alignment · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data, when you have detected features (peaks) in multiple samples and need to establish which peaks across samples represent the same molecular species.
    0 installs
67. ▌
    Mass Spectrum Peak Matching · holobiomicslab

    Use when when you have a query electron ionization mass spectrum (as m/z and intensity pairs) and need to identify it against a spectral library stored in msp format.
    0 installs
68. ▌
    Mzml File Format Generation · holobiomicslab

    Use when when you need to generate reproducible synthetic LC/GC-MS raw data files with known ground-truth peak properties (m/z, retention time, intensity) for benchmarking peak detection, feature extraction, normalization, or batch correction algorithms;
    0 installs
69. ▌
    Network Topology Comparison · holobiomicslab

    Use when after executing a molecular networking workflow on GC-MS data that has been processed through auto-deconvolution, and a published reference network exists from a prior analysis of the same or analogous dataset.
    0 installs
70. ▌
    Network Topology Validation · holobiomicslab

    Use when after retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra. Use this skill to confirm the network structure is sound before performing chemical similarity searches, community detection, or annotation.
    0 installs
71. ▌
    R Data Structure Processing · holobiomicslab

    Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100 s) and drift time (5–16 ms) ranges, or when you need to apply smoothing, decimation, or baseline correction to raw GCIMS.
    0 installs
72. ▌
    Reactant Ion Peak Exclusion · holobiomicslab

    Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion source) would otherwise be misidentified as an analyte peak, causing false positives in the peak list.
    0 installs
73. ▌
    Spectral Feature Annotation · holobiomicslab

    Use when after auto-deconvolution has resolved co-eluting GC-MS peaks into individual component spectra.
    0 installs
74. ▌
    Spectral Feature Extraction · holobiomicslab

    Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.
    0 installs
75. ▌
    Spectrum Metadata Filtering · holobiomicslab

    Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality. Use when you observe spectra annotated with negative adducts (e.
    0 installs
76. ▌
    Transformer Model Inference · holobiomicslab

    Use when you have electron ionization mass spectrum data (m/z and intensity pairs) and a pre-trained transformer model checkpoint, and you need to predict molecular weight directly from the spectrum without manual feature engineering or rule-based methods.
    0 installs
77. ▌
    Two Dimensional Tic Folding · holobiomicslab

    Use when immediately after acquiring raw GCxGC-MS data in NetCDF format (.cdf files) and before any signal enhancement (smoothing, baseline correction) or alignment steps.
    0 installs
78. ▌
    Unique Compound Enumeration · holobiomicslab

    Use when you have a GC-MS results table with a Match.Factor column (representing identification confidence) and you need to understand how many distinct compounds survive at different quality cutoffs (e.g., ≥65, ≥80, ≥90).
    0 installs
79. ▌
    Benchmark Harness Execution · holobiomicslab

    Use when you have post-processed clustering results from multiple tools (msCluster, Falcon, MaRaCluster) on the same tandem MS dataset and need to generate a comparative performance report with quality metrics and runtime statistics to determine which tool suits your metabolomics workflow.
    0 installs
80. ▌
    Chemical Class Node Mapping · holobiomicslab

    Use when you have a GNPS mass spectral molecular network (in graphml or cytoscape format) and want to enrich its nodes with chemical class information derived from GNPS public library spectral matches.
    0 installs
81. ▌
    Command Line Tool Execution · holobiomicslab

    Use when you have tandem MS/MS spectrum data in standard peak file formats (mzML, mzXML, or MGF) and need to cluster spectra based on precursor mass and fragment ion similarity.
    0 installs
82. ▌
    Compound Count Verification · holobiomicslab

    Use when after modifying a FIDDLE configuration file to add or remove instrument types from the allowlist (e.g., adding 'ftms' to gnps_orbitrap), run the full preprocessing pipeline and validate that the resulting training and test set sizes match documented targets.
    0 installs
83. ▌
    Confusion Matrix Generation · holobiomicslab

    Use when after training or evaluating a classification model (e.g., MS2DeepScore or other neural networks) when you have paired arrays of predicted class labels and ground-truth labels and need to assess per-class prediction accuracy, false positive/negative rates, or class imbalance effects.
    0 installs
84. ▌
    Cross Assay Feature Linkage · holobiomicslab

    Use when when you have structural clusters from multiple LC-MS assays (e.g., positive and negative ion modes, or reversed-phase and HILIC methods) and need to identify which features across assays represent the same underlying metabolite.
    0 installs
85. ▌
    Cross Method Rt Calibration · holobiomicslab

    Use when when you have predicted retention times from a DNN model trained on one chromatographic method (CM) and need to rank or filter metabolite candidates on a different chromatographic method, but have only a small set of calibration molecules (≥10) with known RTs on both source and target.
    0 installs
86. ▌
    D Ratio Threshold Filtering · holobiomicslab

    Use when after signal drift correction (step 4) has computed per-feature D-Ratio values, and before normalization (step 7).
    0 installs
87. ▌
    Database Similarity Scoring · holobiomicslab

    Use when you have one or more MS/MS spectra (query spectra in mzML, mzXML, or MGF format) and need to identify unknown compounds by comparing them against curated spectral databases organized by biological domain (microbe, plant, tissue, microbiome, food).
    0 installs
88. ▌
    Dia Data Format Recognition · holobiomicslab

    Use when you have raw mass spectrometry data from a DIA acquisition method and need to determine whether it is MS^E, All-Ion Fragmentation (AIF), or SWATH-MS before loading into IDSL.CSA for fragmentation spectra deconvolution.
    0 installs
89. ▌
    Dia File Quality Prediction · holobiomicslab

    Use when you have a batch of DIA mass spectrometry raw files (.raw, .d, or .wiff formats) from known instrument types (timsTOF, TripleTOF, or Orbitrap) and need to classify each file as pass/fail or assign a quality label.
    0 installs
90. ▌
    Feature Fidelity Prediction · holobiomicslab

    Use when you have a feature table (CSV with m/z and retention time columns) and corresponding .mzXML or .mzML mass spectrometry files from an LC-MS metabolomics experiment, and you need to filter out false or low-quality chromatographic peaks before downstream analysis.
    0 installs
91. ▌
    Feature Metadata Annotation · holobiomicslab

    Use when you have processed mass spectrometry data consisting of three separate tables (quantification features, sample metadata, and spectral annotations) and need to combine them into a single, queryable artifact that preserves relationships between features, samples, and their chemical.
    0 installs
92. ▌
    Feature Table Normalization · holobiomicslab

    Use when you have peak/feature tables from one or more peak picking tools (MZmine, XCMS, MS-DIAL, Compound Discoverer) and need to ingest them into LipidMatch or combine results from multiple tools in a single lipidomics workflow.
    0 installs
93. ▌
    Formula Stratified Sampling · holobiomicslab

    Use when when preparing MS/MS spectral training data where: (1) the initial TCN train/test split contains imbalanced positive and negative examples, (2) certain molecular formulas are over-represented in the positive class, (3) you are training a Siamese architecture rescore model that requires.
    0 installs
94. ▌
    Gnps Data Schema Validation · holobiomicslab

    Use when after extracting a GNPS molecular networking job archive using GNPSExtractor, before calling npl.load_data().
    0 installs
95. ▌
    Gpu Accelerated Computation · holobiomicslab

    Use when when processing large-scale mass spectrometry datasets (>1 million spectra) where CPU-based clustering runtime would exceed minutes to hours, and when the analysis pipeline includes: (1) encoding raw spectra into high-dimensional binary vectors, (2) computing pairwise distance matrices.
    0 installs
96. ▌
    Graph Enrichment Operations · holobiomicslab

    Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived substructural motifs (from classical or feature-based LDA experiments) in a single integrated operation, typically for.
    0 installs
97. ▌
    Lcms Feature Classification · holobiomicslab

    Use when you have an LCMS feature table annotated with MS2 spectral data and need to distinguish in-source fragments (mass loss patterns, same retention time, MS2 spectral relationships) from true metabolite features.
    0 installs
98. ▌
    Lcms Result Table Structure · holobiomicslab

    Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have an analysis results object containing identified ISF features and need to generate a shareable, tabular export that documents feature annotations, hierarchical parent–fragment relationships, and.
    0 installs
99. ▌
    Lcms Workflow Orchestration · holobiomicslab

    Use when starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z, retention time, and intensity values across all samples.
    0 installs
100. ▌
     Lipid Library Format Schema · holobiomicslab

     Use when you have identified lipid species unique to your experimental system (e.
     0 installs