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HolobiomicsLab

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1. ▌
   Mass Spectrum Database Matching 2 · holobiomicslab

   Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your sample.
   0 installs
2. ▌
   Mass Spectrum Semantic Encoding 2 · holobiomicslab

   Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format) and need to identify structurally related metabolites from a reference database by computing similarity in learned semantic space rather than direct spectral matching.
   0 installs
3. ▌
   Metabolite Structure Prediction 2 · holobiomicslab

   Use when you have a parent compound (or set of compounds) in SMILES, MOL, or SDF format and need to predict plausible metabolite structures and pathways in a specific biological context (mammalian Phase I/II metabolism, human gut microbiota, or soil/aquatic microbial degradation).
   0 installs
4. ▌
   Metadata Annotation Integration 2 · holobiomicslab

   Use when you have chemical annotations (GNPS spectral library matches) assigned to MS/MS samples and a validated ReDU sample-information template (TSV) with categorical metadata (e.g., sample type, extraction method, ionization source).
   0 installs
5. ▌
   Molecular Descriptor Extraction 3 · holobiomicslab

   Use when you have a collection of chemical structures in SMILES format and need to create paired structure–spectrum training data for a generative model, but do not have experimental MS/MS spectra available.
   0 installs
6. ▌
   Ms Modification Site Evaluation 2 · holobiomicslab

   Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the true structure of the unknown compound (oracle mode) or a reference modification site annotation.
   2 installs
7. ▌
   Ms Ms Spectral Library Matching 2 · holobiomicslab

   Use when you have experimental MS/MS spectra from nontargeted metabolomics data and need to assign molecular identities or identify structurally related analogs.
   0 installs
8. ▌
   Ms2 Spectrum Format Preparation 2 · holobiomicslab

   Use when you have raw or unstructured MS2 spectral data (from untargeted tandem mass spectrometry experiments) and plan to run MS2MP inference for KEGG pathway prediction.
   2 installs
9. ▌
   Nmr Spectral Feature Extraction 2 · holobiomicslab

   Use when when you have raw or preprocessed 1H NMR spectral tensors from flavor or chemical mixtures and need to generate high-level feature representations that capture both fine-grained local patterns (e.g., peak multiplet structure, coupling constants) and global spectral context (e.
   0 installs
10. ▌
    Peak Quality Metric Computation 2 · holobiomicslab

    Use when you have completed XCMS preprocessing (getEIC() and fillPeaks()) on untargeted LC-MS metabolomics data and need to assign per-peak quality scores prior to manual curation, classifier training, or downstream statistical analysis.
    0 installs
11. ▌
    Peak Removal Robustness Testing 2 · holobiomicslab

    Use when when validating a metabolomics pathway analysis method (particularly decomposition-based approaches like PLAGE) against data quality degradation, or when comparing robustness across methods (PLAGE vs. ORA vs. GSEA).
    2 installs
12. ▌
    Qc Type Color Marker Assignment 2 · holobiomicslab

    Use when configuring a new injection-plate design template in InjectionDesign if you have multiple QC types to position on a plate and need to visually distinguish them in the final worksheet.
    0 installs
13. ▌
    Random Forest Regression Tuning 2 · holobiomicslab

    Use when your MetaboSet object contains missing values (marked as NA) in the expression matrix after quality flagging, but you need complete data for multivariate analysis.
    0 installs
14. ▌
    Rank Order Correlation Analysis 2 · holobiomicslab

    Use when when you have run a pathway ranking method (such as PALS/PLAGE) on clean metabolomics data and wish to assess how sensitive the resulting pathway activity rankings are to realistic data quality issues—specifically Gaussian noise and random peak dropout—which are prevalent in untargeted.
    0 installs
15. ▌
    Retention Time Window Filtering 2 · holobiomicslab

    Use when you have mzML/mzXML chromatogram files from Thermo, Waters, or Bruker instruments and need to extract MS1 and MS2 scans matching both a target m/z value AND a known or suspected retention time range.
    0 installs
16. ▌
    Separation Metric Normalization 2 · holobiomicslab

    Use when you have extracted retention times from top MS1 features across an LC-MS run and need a single, comparable metric to evaluate how effectively a gradient spreads compounds across the chromatographic window.
    0 installs
17. ▌
    Spectral Data Normalization Tic 2 · holobiomicslab

    Use when apply TIC normalization when you have raw, unprocessed mass spectrometry data (Cardinal objects or imaging matrices with 10,000+ m/z features and 1,000+ spectra) where signal intensity varies across spatial locations or samples due to instrumental drift, uneven sample preparation, or.
    0 installs
18. ▌
    Spectral Retrieval Ranking Task 2 · holobiomicslab

    Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by similarity to each query for compound identification or structural similarity retrieval.
    2 installs
19. ▌
    Spectral Scan Metadata Matching 2 · holobiomicslab

    Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name, molecular weight, and annotation fields), and you need to pair each scan set with its corresponding chemical record to build.
    2 installs
20. ▌
    Structure Organism Pair Binning 2 · holobiomicslab

    Use when when you have loaded a structure-organism pairs table from a natural products database (e.g., LOTUS) and need to answer questions about the distribution of chemical diversity—specifically, how many unique 2D structures appear in exactly 1 organism versus many organisms.
    2 installs
21. ▌
    Theoretical Spectrum Generation 2 · holobiomicslab

    Use when you have a defined set of lipid species (identified by class and fatty acid composition) and need to create a high-throughput spectral library for mass spectrometry-based lipid identification.
    2 installs
22. ▌
    Tracer Metabolite Pair Matching 2 · holobiomicslab

    Use when you have acquired LC-MS peak tables from both unlabeled (12C) and isotope-labeled (13C) samples from a stable isotope tracing experiment, paired with sample metadata distinguishing case and control groups, and you need to systematically identify which unlabeled features correspond to.
    2 installs
23. ▌
    Usi Spectrum Identifier Parsing 2 · holobiomicslab

    Use when when you have a USI string (e.g., mzspec:MTBLS1124:QC07.
    0 installs
24. ▌
    Vendor Instrument Data Handling 2 · holobiomicslab

    Use when you have acquired raw mass spectrometry data in vendor-proprietary formats (ThermoFisher, Agilent, or equivalent) and need to analyze it using MSThunder for unknown organic pollutant identification.
    2 installs
25. ▌
    Distance Geometry Embedding 2 · holobiomicslab

    Use when when you have ionized adduct structures (in SMILES or MOL format) from an upstream ionization-state determination step and need to produce multiple low-energy 3D conformations for collision cross section prediction, metabolite annotation, or structure-property modeling.
    0 installs
26. ▌
    Imms Data Format Conversion 2 · holobiomicslab

    Use when when you have raw Agilent MassHunter (.d) or UIMF IM-MS data files from drift tube (DT) or structure for lossless ion manipulations (SLIM) instruments and need to ingest them into a preprocessing pipeline that requires standardized in-memory or intermediate representations for.
    0 installs
27. ▌
    Ionization State Prediction 2 · holobiomicslab

    Use when when you have SMILES strings representing neutral organic molecules and need to enumerate the likely protonated (e.g., [M+H]+) and deprotonated (e.
    0 installs
28. ▌
    Chromatographic Peak Labeling 2 · holobiomicslab

    Use when you have a user-defined reference list of isolated, high-confidence chromatographic peaks (ground-truth) matched across multiple LC-HRMS samples, and you need to produce a labelled training dataset large enough to train a CNN model that discriminates true peaks from background noise and.
    2 installs
29. ▌
    Cross Dataset Entry Filtering 2 · holobiomicslab

    Use when you have received MSBERT-preprocessed spectral data from GNPS, MoNA, or MTBLS1572 and need to ensure data integrity before training a spectral embedding model.
    0 installs
30. ▌
    JSON Spectral Data Processing 2 · holobiomicslab

    Use when you have raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize field names, validate chemical identifiers (SMILES, InChI, InChIKey), remove duplicates, filter by quality criteria.
    0 installs
31. ▌
    Mass Spectrometry Calibration 2 · holobiomicslab

    Use when after peak detection when you have a detected peaks table with m/z values and need to correct systematic mass drift or inaccuracy before peak alignment across multiple batches.
    0 installs
32. ▌
    Metabolite Similarity Scoring 2 · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in .
    0 installs
33. ▌
    Peak Border Center Estimation 2 · holobiomicslab

    Use when you have LC-HRMS chromatograms in retention time × m/z matrix format and need to automatically localize chromatographic peak positions and extents prior to matching against a reference peak library or generating CNN training instances.
    0 installs
34. ▌
    R Function Workflow Execution 2 · holobiomicslab

    Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE barocycler-based concurrent multiomics method and need to perform integrative preprocessing (spectral normalization and alignment across samples) followed by multivariate analysis to identify differential lipids.
    0 installs
35. ▌
    Spectral Database Compilation 2 · holobiomicslab

    Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a persistent, queryable database that mirrors the schema of an existing online spectral reference (such as the predicted-fragments.
    0 installs
36. ▌
    Imzml File Loading And Import 2 · holobiomicslab

    Use when when you have one or more imzML files containing mass spectrometry imaging data and need to import them into LipidQMap for ion image extraction, isotopic correction, and quantitative analysis.
    0 installs
37. ▌
    Latent Feature Interpretation 2 · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) data preprocessed into an h5py-backed feature matrix, and a trained graph-attention autoencoder has already extracted latent low-dimensional peak features.
    0 installs
38. ▌
    Lipid Category Classification 2 · holobiomicslab

    Use when a spatial metabolomics dataset contains semicolon-delimited isomer name annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to collapse multiple lipid nomenclature variants into their parent lipid categories and classes.
    0 installs
39. ▌
    Per Root Metabolite Profiling 2 · holobiomicslab

    Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root linear-axis metabolite profiling outputs to validate reported genotype-level results (e.
    0 installs
40. ▌
    Fragmentation Pattern Annotation 2 · holobiomicslab

    Use when you have custom lipid species (not covered by the 500,000+ built-in LipidMatch entries) that you need to match against experimental MS/MS data, or you are extending LipidMatch's coverage for specialized lipid classes.
    2 installs
41. ▌
    Mass Spectral Network Annotation 2 · holobiomicslab

    Use when you have a GNPS-generated molecular network (graphml or JSON format) and corresponding MS2LDA experiment results or chemical class assignments, and you want to annotate network nodes with substructural motifs or chemical classes to facilitate structural interpretation and identify.
    0 installs
42. ▌
    Annotation Complexity Comparison 2 · holobiomicslab

    Use when you have MS imaging or LC-MS data with pre-annotated m/z values that include multiple isomer or metabolite names per m/z (stored as semicolon-delimited or multi-record strings), and you want to measure whether a refinement step (e.
    0 installs
43. ▌
    Ccs Prediction Model Application 2 · holobiomicslab

    Use when you have structural input data (SMILES or molecular geometry files) for N-Me derived unsaturated sterol lipids and need to generate a predicted CCS dataset indexed by lipid identifier and structural isomer class.
    2 installs
44. ▌
    Chemical Space Structure Ranking 2 · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities in .
    0 installs
45. ▌
    Chemical Structure Deduplication 2 · holobiomicslab

    Use when after applying biotransformation rules to generate candidate product structures from input molecules, when the same transformed structure can be produced via multiple transformation pathways or rule applications, and you need a single canonical representation while tracking which rules and.
    2 installs
46. ▌
    Chemical Structure Featurization 2 · holobiomicslab

    Use when when you have molecular structures (SMILES, SDF, or molecular graphs) and need to train a spectrum prediction or molecular property model, and you want to learn task-specific representations rather than use fixed descriptors.
    0 installs
47. ▌
    Feature Detection Rate Filtering 2 · holobiomicslab

    Use when after constructing a MetaboSet object with LC-MS peak abundances, sample metadata (pData with QC labels), and feature metadata (fData), and after marking missing values as NA.
    2 installs
48. ▌
    Feature Group Isotope Annotation 2 · holobiomicslab

    Use when you have a feature table from nontargeted LC-MS peak detection (containing m/z, retention time, and intensity values) and need to disambiguate whether detected features represent the same molecular entity under different ionization/modification states or are true independent signals.
    0 installs
49. ▌
    Fragmentation Pattern Annotation 3 · holobiomicslab

    Use when when you have an experimental MS/MS spectrum (query spectrum as m/z–intensity pairs) and need to identify the compound by comparing its fragmentation pattern to a spectral library.
    0 installs
50. ▌
    Ion Image Embedding Optimization 2 · holobiomicslab

    Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions (representation collapse) during contrastive learning—specifically when optimizing for maximized similarity between augmentations.
    0 installs
51. ▌
    Mass Spectral Feature Annotation 2 · holobiomicslab

    Use when you have m/z values from spatially-resolved mass spectrometry imaging (e.g., MALDI-MSI, DESI-MSI) and need to assign molecular formulae to thousands of features with higher precision than traditional LC-MS approaches.
    2 installs
52. ▌
    Mass Spectrum Peak Normalization 2 · holobiomicslab

    Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra have been acquired under different instrumental conditions, ionization efficiencies, or detector gains that produce.
    0 installs
53. ▌
    Mass Track Consensus Computation 2 · holobiomicslab

    Use when after mass tracks have been aligned across all samples (either via pairwise alignment for ≤10 samples or nearest-neighbor clustering for larger cohorts), and you need to generate a single representative m/z per aligned bin for downstream feature extraction and annotation.
    1 install
54. ▌
    Metabolite Dataset Preprocessing 2 · holobiomicslab

    Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs. serum], cohort identifiers) and need to investigate how delays affect measured metabolic parameters.
    0 installs
55. ▌
    Metabolite Identifier Annotation 2 · holobiomicslab

    Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by comparing them to computationally predicted metabolism pathways.
    0 installs
56. ▌
    Metabolomics Matrix Manipulation 2 · holobiomicslab

    Use when you have a raw metabolomics abundance table (e.g., LC/MS or GC/MS peak intensities or concentrations) with non-normal distributions and missing values, and you need to prepare it for Gibbs sampler or other model-based imputation.
    0 installs
57. ▌
    Missing Data Simulation In Omics 2 · holobiomicslab

    Use when when comparing the robustness of multiple pathway ranking methods (e.g., PLAGE, ORA, GSEA) on metabolomics or other omics data, and you need to establish which method is least sensitive to peak dropout, instrumental noise, or annotation uncertainty.
    0 installs
58. ▌
    Model Inference And Tokenization 2 · holobiomicslab

    Use when you have MS/MS spectra in .msp format and need to retrieve similar compounds or compute spectral similarities for compound identification. The input spectra should already be cleaned (malformed or invalid SMILES removed), and you have access to a pre-trained SpecEmbedding model checkpoint.
    0 installs
59. ▌
    Msms Spectral Database Retrieval 2 · holobiomicslab

    Use when when you have a target compound (modified or unmodified) and need to obtain its experimental MS/MS spectrum and metadata to serve as a known reference for ModiFinder analysis, or when benchmarking evaluation methods like average_distance scoring.
    0 installs
60. ▌
    Neutral Loss Formula Computation 2 · holobiomicslab

    Use when you have tandem mass spectra with precursor m/z and observed fragment peak m/z values (as mz/intensity pairs), and you need to construct interpretable feature vectors where each axis corresponds to a real chemical entity (peak or neutral loss) rather than a latent dimension.
    0 installs
61. ▌
    Nmr Spectrum Object Construction 2 · holobiomicslab

    Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
    0 installs
62. ▌
    Peak Deconvolution Preprocessing 2 · holobiomicslab

    Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you intend to perform HRdm demultiplexing or peak deconvolution to resolve co-eluting or structurally similar ions.
    2 installs
63. ▌
    Peak Quality Threshold Filtering 2 · holobiomicslab

    Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
    0 installs
64. ▌
    Qc Sample Reliability Evaluation 2 · holobiomicslab

    Use when after drift correction has been applied to your LC-MS peak table and you need to identify low-quality metabolic features that exhibit high internal spread (RSD, RSD*) or excessive QC-versus-biological variation (D-ratio) before imputation and batch correction.
    0 installs
65. ▌
    Qc Workflow Component Inspection 2 · holobiomicslab

    Use when you have acquired a versioned QC workflow definition file (YAML or JSON) from a metabolomics QC system release (e.g., v1.0.
    1 install
66. ▌
    Replicate Consistency Assessment 2 · holobiomicslab

    Use when after NMR or MS data acquisition and preprocessing (phasing, baseline correction) when you have a SummarizedExperiment object containing assay intensity matrix with QC sample columns designated.
    0 installs
67. ▌
    Spearman Correlation Computation 2 · holobiomicslab

    Use when : (1) you have metabolomic data (NMR or MS-derived) and a continuous phenotype variable; (2) you need to quantify associations while controlling for known confounders (age, gender, disease status);
    0 installs
68. ▌
    Spectral Data Quality Assessment 2 · holobiomicslab

    Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type, precursor m/z, retention time), low-intensity noise peaks, or spectra with invalid or inconsistent metadata fields.
    0 installs
69. ▌
    Spectral Peak Embedding Encoding 2 · holobiomicslab

    Use when when you have variable-length MS/MS peak lists (m/z and intensity arrays) that must be fed into a transformer-based model for spectra analysis, and you need deterministic, normalized embeddings that preserve peak frequency information across multiple scales.
    2 installs
70. ▌
    Summarized Experiment Subsetting 2 · holobiomicslab

    Use when when you have a SummarizedExperiment containing metabolomic abundances and a corresponding vector of quality metrics (e.g., coefficient of variation computed across QC samples), and you need to filter to retain only features meeting a reproducibility threshold (e.g., CV ≤ 0.
    0 installs
71. ▌
    Reproducibility Gap Detection 2 · holobiomicslab

    Use when when evaluating a computational method described in a peer-reviewed article, particularly when the work references a public repository or provides supplementary code.
    0 installs
72. ▌
    M Z Intensity Calibration 2 · holobiomicslab

    Use when you have raw or processed MS spectrum data (m/z and intensity pairs) from DI-MS, ASAP-MS, or other high-throughput mass spectrometry instruments that requires automated peak detection.
    0 installs
73. ▌
    Artifact Removal In Ims Data 2 · holobiomicslab

    Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated detector signals that distort elution and mobility profiles.
    0 installs
74. ▌
    Protonation State Assignment 2 · holobiomicslab

    Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
    2 installs
75. ▌
    Smiles Structure Preparation 2 · holobiomicslab

    Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
    0 installs
76. ▌
    Batch Spectrum Quality Control 2 · holobiomicslab

    Use when when ingesting spectra from multiple open mass spectrometry libraries (OMSLs) in .mgf, .msp, .json, or .csv format and you observe mixed experimental protocols, inconsistent adduct annotations, or partial metadata.
    0 installs
77. ▌
    Vocabulary Coverage Validation 2 · holobiomicslab

    Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before deploying the unified vocabulary in a language model.
    0 installs
78. ▌
    Mass Error Tolerance Filtering 2 · holobiomicslab

    Use when when annotating full-scan MS or MS imaging data against a metabolite database (e.g., LipidMaps, HMDB) and you need to control the stringency of m/z matching. Use this filter to balance annotation sensitivity against specificity: tighter ppm tolerances (e.
    0 installs
79. ▌
    Mass Spectrometry Data Extraction 2 · holobiomicslab

    Use when after peak picking, sample alignment, and isotopologue/adduct grouping steps have been completed in an untargeted LC-MS workflow.
    2 installs
80. ▌
    Mass Spectrometry Data Processing 2 · holobiomicslab

    Use when you have raw mass spectrometry outputs (peak areas/heights across samples and fragmentation spectra) that need to be formatted and validated before running the tima taxonomically informed annotation workflow.
    0 installs
81. ▌
    Mass To Charge Tolerance Matching 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table (with m/z and retention time columns) and a metabolic network database with compound chemical formulas, and you want to connect observed features to known metabolic reactions and pathways using mass matching rather than metabolite.
    0 installs
82. ▌
    Spectral Metadata Standardization 2 · holobiomicslab

    Use when when importing mass spectrometry spectral data from public repositories or multi-source MGF/MSP files where metadata fields are inconsistent, missing, or non-standard;
    0 installs
83. ▌
    Bayesian Meta Learning Projection 2 · holobiomicslab

    Use when you need to transfer retention time predictions from one chromatographic method to another, but have access to only a small number (≥10) of molecules with known retention times in both methods.
    2 installs
84. ▌
    Composite Mass Track Construction 2 · holobiomicslab

    Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you need to detect peaks across the entire cohort.
    0 installs
85. ▌
    Compound Structure Representation 2 · holobiomicslab

    Use when when you have experimental MS/MS data (peak lists, precursor m/z, charge state, adduct type) paired with a chemical structure (SMILES or structural identifier), and need to create a unified Compound object for spectral alignment, modification-site prediction, or comparative fragmentation.
    0 installs
86. ▌
    Cosine Similarity Ranking Metrics 2 · holobiomicslab

    Use when when you have pre-computed spectral embeddings (vectors) for both query spectra and a reference library, and you need to measure retrieval performance by ranking reference compounds by similarity to each query.
    0 installs
87. ▌
    Count Verification And Validation 2 · holobiomicslab

    Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity, medium-diversity, high-diversity) match published or curated reference values.
    0 installs
88. ▌
    Custom Metabolite Set Integration 2 · holobiomicslab

    Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
    0 installs
89. ▌
    Dependency Requirement Validation 2 · holobiomicslab

    Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints. Use this skill when you have access to an R environment and need to confirm that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.
    0 installs
90. ▌
    Differential Metabolite Detection 2 · holobiomicslab

    Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
    0 installs
91. ▌
    Endianness Detection And Handling 2 · holobiomicslab

    Use when when reading a binary file format with a magic integer or fixed checksum field at a known offset, and endianness is not explicitly declared in file metadata or header comments.
    2 installs
92. ▌
    Fuzzy Analog Search Fragmentation 2 · holobiomicslab

    Use when when you have experimental MS/MS spectra and want to discover structurally similar compounds beyond exact spectral library matches—particularly useful for identifying chemical analogs, homologs, or isomers that share fragmentation logic but differ in molecular structure.
    2 installs
93. ▌
    Github Actions Workflow Execution 2 · holobiomicslab

    Use when you have a GitHub repository containing scientific records (e.
    0 installs
94. ▌
    Image Processing For Metabolomics 2 · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map (m/z vs retention time) and need to identify analyte signals and marker features while minimizing false peak detections.
    0 installs
95. ▌
    Ion Image Quantification Workflow 2 · holobiomicslab

    Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.
    0 installs
96. ▌
    Isotope Labeling Data Integration 2 · holobiomicslab

    Use when you have LC-MS peak tables from parallel unlabeled and labeled (isotope-traced) sample cohorts, sample metadata defining groups and conditions, and you seek to identify metabolic intermediates that accumulate differentially in a perturbed system (e.
    0 installs
97. ▌
    Lcms Spectral Peak Classification 2 · holobiomicslab

    Use when you have raw LC-MS spectral peak data (in the format provided by DOI 10.25345/C5FD2F) and need to build a classifier that can distinguish valid peaks from false positives or background noise without manual feature engineering.
    0 installs
98. ▌
    M Z Metabolite Annotation Mapping 2 · holobiomicslab

    Use when when you have a spatial metabolomics or LC-MS dataset with detected m/z features (as a feature matrix or SpaMTP Seurat object) and need to assign metabolite identities. Specifically: you have observed m/z values, you know the ionization polarity and expected adduct form (e.
    0 installs
99. ▌
    Mass Spectrometry Database Search 2 · holobiomicslab

    Use when you have an unknown mass spectrum (or a representative metabolite spectrum from public data) and need to identify it by comparing it against a large reference library—particularly when the database contains billions of spectra and earlier tools like MASST are too slow or resource-intensive.
    0 installs
100. ▌
     Mass Spectrometry File Validation 2 · holobiomicslab

     Use when after MSConvert has converted vendor-specific raw mass spectrometry data (ThermoFisher, Agilent, or equivalent formats) on a Linux system and before initiating analysis in MSThunder.
     0 installs