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HolobiomicsLab

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1. ▌
   Taxonomy Database Querying 2 · holobiomicslab

   Use when a paired omics project record contains a genome identifier (e.g., from GenBank or NCBI) but lacks the corresponding organism scientific name.
   0 installs
2. ▌
   Transformer Model Training 3 · holobiomicslab

   Use when you have a dataset of augmented simulated overlapped GC-MS peaks and need to train a Transformer model to automatically deconvolve them into pure component mass spectra.
   0 installs
3. ▌
   User Interface Integration 2 · holobiomicslab

   Use when when you have a multi-step computational workflow (e.g., peak detection, filtering, manual review) implemented in R and need to expose it to end-users who lack R expertise.
   0 installs
4. ▌
   Workflow Status Monitoring 2 · holobiomicslab

   Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
   0 installs
5. ▌
   Hdf5 Schema Validation 2 · holobiomicslab

   Use when after converting proprietary vendor mass spectrometry files (Thermo .raw, Agilent .d, Bruker .d, or mzML) to MZA HDF5 format using the MZA executable.
   0 installs
6. ▌
   Feature Table Subsetting 2 · 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
7. ▌
   Gc CI Ms Data Processing 2 · 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
8. ▌
   Mass Spectrum Simulation 2 · 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
9. ▌
   Open Modification Search 2 · 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
10. ▌
    Peak List Column Mapping 2 · 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
11. ▌
    Retention Time Windowing 2 · 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
12. ▌
    Msi Spectral Data Import 2 · 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
13. ▌
    Smiles Molecular Parsing 2 · 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
14. ▌
    Accuracy Metric Computation 2 · holobiomicslab

    Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular formulas and connectivity graphs that need to be compared against known ground truth structures.
    0 installs
15. ▌
    Chemical Class Node Mapping 2 · 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
16. ▌
    Command Line Tool Execution 2 · 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
17. ▌
    Graph Enrichment Operations 2 · 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
18. ▌
    Java Source Code Inspection 3 · 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
19. ▌
    Lcms Workflow Orchestration 2 · 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
20. ▌
    Mass Chromatogram Alignment 3 · 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
21. ▌
    Md Defect Ratio Calculation 2 · holobiomicslab

    Use when you have a feature table from LC- or GC-HRMS data (either detected via pyOpenMS or imported as a custom feature list) containing m/z, retention time, and intensity values, and you want to rapidly filter to candidate PFAS features that exhibit the elevated mass defects typical of.
    0 installs
22. ▌
    Model Ablation Study Design 2 · holobiomicslab

    Use when you need to measure how much a specific model capability or architectural feature contributes to prediction performance, especially when that capability is non-obvious or orthogonal to baseline methods.
    0 installs
23. ▌
    Network Topology Comparison 3 · 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
24. ▌
    Network Topology Validation 2 · 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
25. ▌
    Nextflow Workflow Execution 3 · holobiomicslab

    Use when you have .mzML or .abf LC-HRMS metabolomics raw data files and need to perform peak detection, feature identification, and chromatogram alignment reproducibly across different compute environments (local workstations, HPC clusters).
    0 installs
26. ▌
    Organism Metadata Retrieval 2 · holobiomicslab

    Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context for downstream biosynthetic gene cluster or chemical ecology analysis.
    0 installs
27. ▌
    Pfas Feature Prioritization 2 · holobiomicslab

    Use when you have detected features in LC- or GC-HRMS data (via pyOpenMS or custom feature tables) and need to systematically rank them for likelihood of being PFAS compounds.
    0 installs
28. ▌
    Project Metadata Validation 2 · holobiomicslab

    Use when when a user uploads a JSON project document to the Pairing Omics Data Platform, before accepting it into the repository or indexing it for search. Use this skill to catch missing required fields, incorrect field types, and constraint violations early in the submission workflow.
    0 installs
29. ▌
    Qc Summary Table Extraction 2 · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain a structured report of which ions passed or failed each filter.
    0 installs
30. ▌
    R6 Object Method Invocation 2 · holobiomicslab

    Use when when working with large metabolomics peak tables (e.
    0 installs
31. ▌
    Repository Code Integration 2 · holobiomicslab

    Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public repository, and you need to apply that method to new experimental data (e.
    0 installs
32. ▌
    Scoring Module Unit Testing 2 · holobiomicslab

    Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring logic into an existing MS2Query pipeline.
    0 installs
33. ▌
    Snr Based Signal Validation 3 · holobiomicslab

    Use when after composite map peak detection has generated a full unfiltered peak list with SNR values computed for each candidate peak.
    0 installs
34. ▌
    Spec2vec Similarity Scoring 2 · holobiomicslab

    Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation pattern against a pre-indexed spectral library using learned spectral embeddings.
    0 installs
35. ▌
    Spectral Mz Range Filtering 2 · holobiomicslab

    Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment (e.g., 100–1400 m/z for typical tryptic peptides).
    0 installs
36. ▌
    Spectral Similarity Ranking 2 · holobiomicslab

    Use when you have a query MS/MS spectrum and need to identify the -matching library spectrum from a large spectral database, particularly when the research goal requires distinguishing between exact matches and structural analogues without separate workflows.
    2 installs
37. ▌
    Spectral Similarity Scoring 4 · 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
38. ▌
    Spectrum Cluster Assignment 2 · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters. Use this skill when: (1) you have a sparse similarity or distance matrix as input;
    0 installs
39. ▌
    Unique Compound Enumeration 2 · 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
40. ▌
    Web Service API Integration 2 · holobiomicslab

    Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular fingerprint predictions, de-novo candidate structures, or chemical class annotations without maintaining local neural network.
    0 installs
41. ▌
    Batch Document Verification 2 · holobiomicslab

    Use when when you have deposited a collection of JSON project documents in a platform and need to verify that all conform to the published schema before public release or after schema updates.
    0 installs
42. ▌
    Batch Prediction Comparison 2 · holobiomicslab

    Use when when you have a trained molecular classifier (like BitterPredict) that accepts structured descriptor input, and you need to understand which chemical descriptor subgroups drive prediction outcomes.
    0 installs
43. ▌
    Benchmark Harness Execution 2 · 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
44. ▌
    Binary Data Base64 Encoding 2 · 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
45. ▌
    Chemical Identifier Mapping 2 · holobiomicslab

    Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular formulas).
    0 installs
46. ▌
    Compound Count Verification 2 · 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
47. ▌
    Compound Identifier Mapping 3 · holobiomicslab

    Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and MS/MS spectra ready for annotation.
    0 installs
48. ▌
    Confusion Matrix Generation 2 · 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
49. ▌
    Cross Assay Feature Linkage 2 · 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
50. ▌
    D Ratio Threshold Filtering 2 · holobiomicslab

    Use when after signal drift correction (step 4) has computed per-feature D-Ratio values, and before normalization (step 7).
    0 installs
51. ▌
    Database Similarity Scoring 2 · 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
52. ▌
    Dia Data Format Recognition 2 · 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
53. ▌
    Dia File Quality Prediction 3 · 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
54. ▌
    Ei Mass Spectrum Simulation 2 · 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
55. ▌
    Embedding Vector Validation 2 · holobiomicslab

    Use when after instantiating and invoking a sinusoidal formula embedding layer (such as SCARF embeddings in MIST-CF) on chemical formula inputs, validate that the output embeddings meet dimensionality and value constraints before using them for downstream transformer or ranking tasks.
    0 installs
56. ▌
    Error Handling Confirmation 2 · holobiomicslab

    Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak data.
    0 installs
57. ▌
    Feature Fidelity Prediction 2 · 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
58. ▌
    Feature Metadata Annotation 2 · 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
59. ▌
    Feature Table Normalization 2 · 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
60. ▌
    Formula Stratified Sampling 2 · 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
61. ▌
    Gcms Spectrum Deconvolution 2 · 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
62. ▌
    Gnps Data Schema Validation 2 · holobiomicslab

    Use when after extracting a GNPS molecular networking job archive using GNPSExtractor, before calling npl.load_data().
    0 installs
63. ▌
    Gpu Accelerated Computation 2 · 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
64. ▌
    Graph Serialization Graphml 2 · holobiomicslab

    Use when after constructing a network graph where nodes represent Mass2Motifs (or spectra) and edges encode pairwise spectral similarity scores, and you need to export the network for visualization, post-processing, or sharing with collaborators using standard graph software (e.
    0 installs
65. ▌
    Instrument Metadata Parsing 3 · 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
66. ▌
    JSON Response Serialization 2 · holobiomicslab

    Use when when a backend service receives structured prediction results from an external API (e.g., nmrshiftdb peak predictions) and must return them to a client application via HTTP POST response.
    0 installs
67. ▌
    Lcms Feature Classification 2 · 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
68. ▌
    Lcms Result Table Structure 2 · 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
69. ▌
    Lipid Library Format Schema 2 · holobiomicslab

    Use when you have identified lipid species unique to your experimental system (e.
    0 installs
70. ▌
    Mass Spectral M Z Alignment 2 · holobiomicslab

    Use when after you have (1) identified putative labelled features with intensity and m/z measurements from LC/MS data (e.g., via basepeak_finder output in geoRge), (2) defined a list of expected ionization adducts (e.
    0 installs
71. ▌
    Mass Spectrum M Z Alignment 3 · holobiomicslab

    Use when when working with multidimensional MS data (LC–IM–MS/MS) converted to MZA format where spectra are stored in jagged arrays with m/z values distributed across individual HDF5 datasets per scan, and you need to ensure m/z consistency for downstream peak detection, isotope analysis, or.
    0 installs
72. ▌
    Mass Spectrum Peak Matching 2 · 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
73. ▌
    Mass Spectrum Preprocessing 2 · holobiomicslab

    Use when you have raw MS/MS spectra in MGF format with variable peak quality, mixed charge states, or instrument artifacts that could confound clustering or similarity measures.
    0 installs
74. ▌
    Mass Spectrum Visualization 3 · holobiomicslab

    Use when when you have extracted m/z and intensity arrays from an MZA file (or similar HDF5-backed MS data structure) and need to visually inspect a single MS1 or MS2 spectrum, verify peak characteristics, or diagnose data quality issues before downstream analysis (peak fitting, isotope pattern.
    0 installs
75. ▌
    Matlab Scientific Computing 3 · 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
76. ▌
    Metabolite Ms Ms Annotation 2 · holobiomicslab

    Use when when you have SWATH-MS raw data (mzML or vendor format) containing multiplexed MS/MS spectra from multiple co-eluting precursor ions and need to separate these spectra into individual, annotatable component spectra for metabolite identification.
    0 installs
77. ▌
    Metabolite Score Projection 3 · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics assay output (metabolite concentrations in a samples × features matrix) and you want to compute a published metabolic risk score or surrogate biomarker (mortality risk, metabolic age, cardiovascular event risk, type-2 diabetes risk, COVID-19.
    0 installs
78. ▌
    Metadata Integrity Checking 2 · holobiomicslab

    Use when after processing LCMS feature data through Blueshift or Gravity but before finalizing results.
    0 installs
79. ▌
    Mixture Spectrum Comparison 2 · holobiomicslab

    Use when you have an observed NMR mixture spectrum and one or more candidate reconstructed spectra (each formed by summing weighted single-compound spectra), and need a continuous, transportable distance metric to score how well the reconstruction approximates the observed mixture.
    0 installs
80. ▌
    Molecular Candidate Ranking 2 · holobiomicslab

    Use when after a trained CNN model has generated molecular embeddings for query spectra, and you need to retrieve the most likely candidate molecules from a reference database.
    0 installs
81. ▌
    Ms2 Spectral Interpretation 2 · holobiomicslab

    Use when you have extracted an MS1 feature table (from XCMS or custom CSV with m/z, retention time, and intensity columns) and one or more DDA mzXML files from the same or related LC-MS runs, and you need to annotate features with MS2 spectral data and match them against a standard spectral library.
    0 installs
82. ▌
    Msflo Metabolite Annotation 3 · 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
83. ▌
    Multi Module Joint Training 2 · holobiomicslab

    Use when when you have a pretrained encoder that captures domain knowledge (e.g., spectral feature extraction) and need to train task-specific decoder or scoring modules on top of it without degrading the encoder's learned representations.
    0 installs
84. ▌
    Mzml File Format Generation 3 · 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
85. ▌
    Nmr Peak JSON Serialization 2 · holobiomicslab

    Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API. The peaks must be reformatted from their native instrument output into JSON before submission to the /api/smart3/search endpoint.
    0 installs
86. ▌
    Nmr Spectrum Peak Detection 2 · holobiomicslab

    Use when you have a loaded INADEQUATE NMR spectrum file (after referencing via basic shifting) and need to identify individual peak positions and intensities as input to downstream peak network clustering or metabolite matching.
    0 installs
87. ▌
    Package Integration Testing 2 · holobiomicslab

    Use when you need to verify that a Python package (or similar installable software) passes its declared integration test suite as a prerequisite to trusting its reliability in production or downstream analysis. Specifically, apply it when you observe a periodic testing CI workflow badge (e.
    0 installs
88. ▌
    Pairwise Matrix Computation 2 · holobiomicslab

    Use when when you have a cleaned MS/MS dataset with chemical structure annotations (SMILES, InChI, or InChIKey) and need to generate ground-truth structural similarity labels for training a deep learning model.
    0 installs
89. ▌
    Parent Tp Mapping Structure 2 · holobiomicslab

    Use when you have generated a TP object (from generateTPs) with structural information (SMILES) for predicted or library-derived transformation products, and you need to either (1) construct a MetFrag-compatible database that preserves parent compound records alongside TPs, or (2) componentize.
    0 installs
90. ▌
    Pathway Coverage Assessment 2 · holobiomicslab

    Use when when preparing to run Over-representation Analysis (ORA) on a metabolomics study, after constructing the background set but before running the enrichment test.
    0 installs
91. ▌
    Peak Detection In Lcms Data 2 · holobiomicslab

    Use when after retention-time correction has been completed on centroided LC-MS data (mzML or mzXML format) and you need to identify all detected peaks as a unified feature table across a cohort of samples.
    0 installs
92. ▌
    Peak Table Format Detection 2 · holobiomicslab

    Use when when receiving a peak or feature table output from an unknown or variable upstream peak-picking tool, and you need to route it to the correct ingestion adapter (e.g., in LipidMatch) to normalize and validate it before lipid identification.
    0 installs
93. ▌
    Pubchem Structure Retrieval 2 · holobiomicslab

    Use when you have an experimental tandem mass spectrum and chemical formula for an unknown compound, and need to identify the true structure among all PubChem entries with that formula.
    0 installs
94. ▌
    Molecular Representation Encoding 2 · holobiomicslab

    Use when when you have a molecular target compound defined by SMILES, InChI, or chemical formula and need to feed it into a pretrained spectrum prediction model (ICEBERG or SCARF) to generate tandem mass spectra or conduct structural elucidation.
    0 installs
95. ▌
    Ms Dial Peak Character Estimation 2 · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering, containing m/z, retention time, and peak intensity metrics for each feature) and need to group features into clusters that represent true metabolite signals rather than instrumental or chemical artifacts.
    0 installs
96. ▌
    Ms1 Scan Extraction And Filtering 2 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file from an Orbitrap instrument and need to programmatically retrieve MS1 spectral attributes (base-peak m/z, intensity, retention time) for downstream statistical analysis or quality control in R, rather than relying on external preprocessing.
    0 installs
97. ▌
    Multi Database Structure Querying 3 · holobiomicslab

    Use when after cleaning and clustering LC-MS features in MS-CleanR, when you need to assign putative compound identities to a feature set with MS/MS spectra, and when candidate compounds may exist across multiple specialized databases (e.g., natural products, pharmaceuticals, contaminants).
    0 installs
98. ▌
    Multi Inheritance Class Hierarchy 2 · holobiomicslab

    Use when when you need to support multiple plotting library backends (static or interactive) for the same data visualization domain (e.
    0 installs
99. ▌
    Multi Instrument Data Integration 3 · holobiomicslab

    Use when you have DIA mass spectrometry raw files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) in their native formats (.raw, .d, .
    0 installs
100. ▌
     Multi Service Integration Testing 2 · holobiomicslab

     Use when when building or modifying an asynchronous annotation pipeline that dispatches metadata enrichment requests to multiple heterogeneous web services and must verify that each service's HTTP calls succeed, response parsing is correct, and enriched fields are correctly merged into the output.
     0 installs