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HolobiomicsLab

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1. ▌
   Spectrum Data Formatting 2 · holobiomicslab

   Use when you have acquired raw or semi-processed mass spectra and need to search them against curated domain-specific databases (microbeMASST, plantMASST, etc.) using standalone web applications or batch APIs.
   0 installs
2. ▌
   Spectrum Pair Prediction 2 · holobiomicslab

   Use when you have pairs of MS/MS spectra and need to estimate their structural similarity (Tanimoto score based on molecular fingerprints) as a proxy for compound relatedness.
   0 installs
3. ▌
   Tabular Data Tag Parsing 2 · 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
4. ▌
   C Module Integration 2 · holobiomicslab

   Use when you have raw mass spectrometry data in mzML or mzXML format and need to compress it using a format-agnostic compressor that expects a standardized spectral data contract.
   0 installs
5. ▌
   File Format Validation 3 · holobiomicslab

   Use when after writing parsed spectra to a new MSP file using mssearchr's MSP writer, or when integrating MSP files from external sources into an R analysis pipeline.
   0 installs
6. ▌
   Ion Feature Extraction 2 · holobiomicslab

   Use when you have raw mass-spectrometry data files (mzML, mzXML, or vendor formats) from untargeted metabolomics experiments and need to identify and quantify differential metabolic ion peaks.
   0 installs
7. ▌
   JSON Format Conversion 2 · holobiomicslab

   Use when when you have extracted file metadata or scan summaries as R list objects from .raw files using readFileHeader(), readIndex(), or readSpectrum(), and need to persist them to disk, share them across systems, or feed them into downstream tools that consume JSON (e.
   0 installs
8. ▌
   Lipidomics Data Mining 2 · holobiomicslab

   Use when when you have quantitative lipidomics data (either from Skyline CSV export or numerical matrix format) with sample annotations and a biological grouping variable (e.
   0 installs
9. ▌
   Mzml Output Validation 2 · holobiomicslab

   Use when after running AirdPro's CLI conversion pipeline (run-cli.sh with -i and -o arguments) to confirm the vendor raw file conversion to mzML has succeeded.
   0 installs
10. ▌
    Peak Table Compilation 2 · holobiomicslab

    Use when after peak detection has been applied to untargeted or targeted mass spectrometry data and peaks have been matched against metabolite databases and reference spectra.
    0 installs
11. ▌
    Candidate Match Retrieval 2 · holobiomicslab

    Use when when you have a query MS/MS spectrum (m/z and intensity pairs) and need to find potential structural analogues or exact matches in a large spectral library. Apply this skill after preprocessing your spectra (e.
    0 installs
12. ▌
    Feature Table Gap Filling 2 · holobiomicslab

    Use when you have an aligned feature table from untargeted LC-MS with missing intensity values (NA or zero entries) for features that are present in some samples but fell below detection threshold in others.
    0 installs
13. ▌
    Isotope Adduct Annotation 2 · holobiomicslab

    Use when after completing peak picking, sample alignment, and before final MS2 spectrum extraction, when you have identified individual ion peaks across samples and need to link isotopic variants (e.
    0 installs
14. ▌
    Library Import Validation 2 · holobiomicslab

    Use when you have raw .msp spectral library files (e.g., from MassBank or custom sources) and need to convert them into a structured CSV library format for use in metabolite annotation.
    0 installs
15. ▌
    Library Object Validation 2 · holobiomicslab

    Use when after applying mspcompiler pipeline transformation steps (e.g., reorganize_mona, assign_smiles, assign_ri, read_multilibs, separate_polarity, complete_mgf) to confirm the operation succeeded without data loss or structural corruption.
    0 installs
16. ▌
    Metabolic Network Mapping 3 · holobiomicslab

    Use when you have an untargeted metabolomics feature table (with m/z, retention time, and statistical significance values) and want to predict which metabolic pathways and functional modules are active in your sample, but you lack confident metabolite identifications or wish to bypass the.
    0 installs
17. ▌
    Model Metadata Extraction 2 · holobiomicslab

    Use when when you need to programmatically interface with a TensorFlow Serving model instance and must discover or validate the expected input names (e.
    0 installs
18. ▌
    Mpactr Filter Application 2 · holobiomicslab

    Use when you have a preprocessed peak table from tandem MS/MS data (e.
    0 installs
19. ▌
    Ms2lda Feature Annotation 2 · holobiomicslab

    Use when after creating a GNPS mass spectral molecular network and running an MS2LDA experiment, use this skill when you want to identify and visualize which substructural motifs (Mass2Motifs) are shared across clustered spectra, particularly to highlight fragmentation pattern similarities between.
    0 installs
20. ▌
    Multitask Model Inference 2 · holobiomicslab

    Use when you have a trained multitask model checkpoint and preprocessed spectral inputs (1D NMR spectra, 1H-only, 13C-only, or combined 1H+13C), and you need to generate simultaneous predictions of molecular formula and connectivity structure to quantify modality contributions, compare single vs..
    0 installs
21. ▌
    Python Workflow Scripting 2 · holobiomicslab

    Use when you have raw mass spectrometry spectral data in common formats (MGF, MSP, mzML, mzXML, JSON) that requires standardized metadata cleaning, validation, and peak filtering before comparative analysis. Use this skill when you need to encode data quality constraints (e.
    0 installs
22. ▌
    Smiles Parsing Validation 3 · holobiomicslab

    Use when when you have a dataset of molecular structures encoded as SMILES strings that will be processed downstream (e.
    0 installs
23. ▌
    Spectrum Metadata Parsing 2 · holobiomicslab

    Use when a user submits one or more MS/MS spectra (via .mgf file, USI list, or direct upload) and the downstream analysis requires dispatching to a specific domain-specific MASST tool (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST, or metadataMASST).
    0 installs
24. ▌
    Spectrum Query Formatting 2 · holobiomicslab

    Use when you have parsed LC-MS/MS spectral data (precursor m/z, ionization mode, collision energy, and a list of fragment m/z and intensity pairs) and need to submit it to the CSI:FingerID web service for molecular fingerprint prediction as part of a metabolite identification workflow.
    0 installs
25. ▌
    Arrow Table Serialization 2 · holobiomicslab

    Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist them to disk in Parquet format for downstream analysis, interoperability with other languages (R, .
    0 installs
26. ▌
    Chemical Ontology Mapping 2 · holobiomicslab

    Use when your analysis has produced both in silico structural predictions (e.
    0 installs
27. ▌
    CI CD Pipeline Monitoring 2 · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a passing build status.
    0 installs
28. ▌
    CI CD Workflow Monitoring 2 · holobiomicslab

    Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts, or fails in a reproducible manner.
    0 installs
29. ▌
    CI CD Workflow Triggering 2 · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that automated build infrastructure is functioning correctly.
    0 installs
30. ▌
    Conditional Routing Logic 2 · holobiomicslab

    Use when you have received a USI string (formatted as mzspec:<namespace>:<resource>:<identifier_type>:<identifier>) and need to retrieve the corresponding mass spectrum data.
    0 installs
31. ▌
    Custom Database Searching 2 · holobiomicslab

    Use when when you have LC-MS/MS data in Mascot Generic Format (mgf) files and need to identify compounds against a curated custom database (e.g., prepared using CFM-id for a specific metabolite class or organism) rather than relying on in-built commercial spectral libraries alone.
    0 installs
32. ▌
    Data Integrity Assessment 2 · holobiomicslab

    Use when immediately after importing raw mass spectrometry data from supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and before performing spectral similarity comparisons or statistical analysis.
    0 installs
33. ▌
    Descriptor Table Assembly 2 · holobiomicslab

    Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification. Use this skill after descriptor calculation is complete and before invoking BitterPredict.m for bitter/non-bitter predictions.
    0 installs
34. ▌
    Diffusion Model Inference 2 · holobiomicslab

    Use when when you have multi-modal spectroscopic data (IR, Raman, UV-Vis, mass spectra, or NMR) and need to recover the underlying molecular structure without relying on finite spectral libraries or autoregressive SMILES generation.
    0 installs
35. ▌
    Ei Spectrum Normalization 2 · holobiomicslab

    Use when you have raw electron ionization mass spectra (m/z and intensity pairs) that you intend to match against a library using the Identity (EI Normal) or Similarity (EI Simple) algorithms. Different ionization runs and instrument conditions produce spectra with varying absolute intensities;
    0 installs
36. ▌
    Feature Ablation Analysis 2 · holobiomicslab

    Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic properties, bond types, or higher-order graph descriptors—are driving the model's predictions.
    0 installs
37. ▌
    Field Type Identification 2 · holobiomicslab

    Use when when working with JSON project documents that must conform to a schema-defined structure, and you need to apply type-specific validation, sanitization, or transformation rules (e.g., URL whitespace detection, numeric range checking, mandatory field enforcement).
    0 installs
38. ▌
    Formula Database Querying 2 · holobiomicslab

    Use when you have calibrated m/z peak lists, configured adduct transformations (e.g., [M+H]+, [M+Na]+, [M-H]−), and need to annotate peaks with molecular formulae from KEGG, PubChem, or custom databases.
    0 installs
39. ▌
    Gensim Pipeline Execution 2 · holobiomicslab

    Use when you have an MS2 spectral file (MGF format) from LC-MS/MS metabolomics analysis and need to discover latent topics across fragmentation patterns for unsupervised characterization. Use it as the prerequisite step before topic visualization in the ms2lda web interface.
    0 installs
40. ▌
    Imzml File Format Parsing 3 · holobiomicslab

    Use when you have acquired imaging mass spectrometry (IMS) data stored in imzML format (accompanied by an .ibd ion binary data file) and need to load it into a Python-based spatial metabolomics workflow.
    0 installs
41. ▌
    Ion Mobility Peak Picking 3 · holobiomicslab

    Use when when you have extracted ion mobilograms from DIA-MS experiments and need to automatically identify peak boundaries and apex positions in the ion mobility dimension.
    0 installs
42. ▌
    Isotopic Pattern Matching 2 · holobiomicslab

    Use when after feature detection has produced candidate formula–adduct pairs and their corresponding m/z values, but before final compound identification.
    0 installs
43. ▌
    JSON Structured Reporting 2 · holobiomicslab

    Use when you need to persist and communicate the health status of multiple external web services queried during an annotation run.
    0 installs
44. ▌
    Lc Ms Peak Quantification 2 · holobiomicslab

    Use when after a CNN-Transformer peak detection model has been run on LC-MS ROI images and has output predicted peak locations with confidence scores.
    0 installs
45. ▌
    Lcms Data Format Handling 2 · holobiomicslab

    Use when you have raw LC-MS data from a vendor instrument or in netCDF format and need to ingest it into SLAW or similar untargeted LC-MS workflows. Use this skill when raw data must be converted to mzML, validated for centroiding and polarity uniformity, and prepared for peak-picking dispatch.
    0 installs
46. ▌
    Lipid Coverage Assessment 2 · holobiomicslab

    Use when after hierarchical fragmentation library matching has produced candidate lipid annotations for a multi-species LC-MS/MS dataset, and you have applied retention time–based filtering rules (e.
    0 installs
47. ▌
    Metabdata Object Handling 2 · holobiomicslab

    Use when you have a raw peak-picked untargeted LC-MS dataframe with columns containing mass-to-charge (m/z), retention time (rt), feature identifiers, adduct annotations, and sample measurements in non-standard column names or mixed column sets.
    0 installs
48. ▌
    Migration Time Extraction 3 · holobiomicslab

    Use when you have OnDiskMSnExp CE-MS objects with known marker compounds (e.g., Paracetamol EOF marker) and need to extract their migration time positions to establish a calibration reference.
    0 installs
49. ▌
    Model Metadata Validation 2 · holobiomicslab

    Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm that input layers are named 'input_2048' and 'input_4096' and output layer is named 'output'.
    0 installs
50. ▌
    Motif Metadata Annotation 2 · holobiomicslab

    Use when after LDA inference has produced a trained motifset (motifset.json or motifset_optimized.json) with Mass2Motif probability distributions over fragments and neutral losses.
    0 installs
51. ▌
    Ms Ms Spectrum Prediction 2 · holobiomicslab

    Use when you have MS/MS spectra (in MGF format) with required metadata fields (TITLE, PRECURSOR_MZ, PRECURSOR_TYPE, COLLISION_ENERGY) and need to predict candidate molecular formulas ranked by confidence.
    0 installs
52. ▌
    Ms2 Spectra Tic Filtering 2 · holobiomicslab

    Use when after concatenating replicate MS/MS spectra for each precursor feature (m/z and retention time), use this skill when you have multiple replicate scans per feature and need to reduce spectral count while preserving the highest-intensity, most-reliable spectra.
    0 installs
53. ▌
    Multi Tool Schema Mapping 2 · holobiomicslab

    Use when you have peak/feature table outputs from one or more peak-picking tools (MZmine, XCMS, MS-DIAL, Compound Discoverer) with different column names and metadata structures, and you need to ingest them into LipidMatch or another unified lipidomics pipeline that requires consistent column.
    0 installs
54. ▌
    Mzpeak File Io Operations 2 · holobiomicslab

    Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability across languages and tools; (2) load mzPeak spectrum or chromatogram data into memory as structured tables for analysis;
    0 installs
55. ▌
    Nmr Peak Table Generation 2 · holobiomicslab

    Use when you have raw 1D NMR spectra (in NMRPipe or similar format) from biological samples (urine, worm, or other metabolomics experiments) and need to extract a structured peak table with chemical shifts and intensities for downstream metabolite identification or quantification.
    0 installs
56. ▌
    Nmr Spectra Preprocessing 2 · holobiomicslab

    Use when when you have raw 1D NMR spectroscopic data (urine, worm, or other biological samples) in a format supported by NMRBox/NMRPipe and need to generate peak tables with automatic phasing, baseline correction, and spectral deconvolution without manual intervention.
    0 installs
57. ▌
    Openapi Schema Generation 2 · holobiomicslab

    Use when when you have a webservice codebase (Python, Java, etc.) with HTTP route definitions, parameter handling, and serialization logic, and you need to generate an OpenAPI 3.
    0 installs
58. ▌
    Optimal Transport Scoring 2 · holobiomicslab

    Use when when you have an observed NMR mixture spectrum and one or more candidate reconstructed spectra (each formed by combining single-compound reference spectra from a library), and you need a scalar similarity score to rank or select the approximation.
    0 installs
59. ▌
    Pathway Database Querying 2 · holobiomicslab

    Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full pathway database should serve as the statistical background, and which pathways contain how many metabolites overall.
    0 installs
60. ▌
    Pathway Score Aggregation 2 · holobiomicslab

    Use when you have a metabolite intensity matrix (samples × metabolites) or gene expression matrix (samples × genes) with corresponding pathway definitions (pathway IDs mapped to feature sets), and you need to rank pathways by activity level to identify which biological processes are most affected.
    0 installs
61. ▌
    Peptide Spectrum Matching 2 · holobiomicslab

    Use when when you have high-resolution tandem mass spectrometry data (in mzML or mzXML format) and a spectral library, and need to identify peptides including those with post-translational modifications.
    0 installs
62. ▌
    Proteome Dataset Handling 2 · holobiomicslab

    Use when you have a collection of MS/MS spectra in MGF format and need to prepare them for GPU-based clustering. Dataset size and available GPU memory are critical: use GTX 1080Ti for smaller proteome datasets; use GTX 3090 for datasets like PXD000561 that exceed GTX 1080Ti capacity.
    0 installs
63. ▌
    R Workflow Implementation 2 · holobiomicslab

    Use when you have raw mass spectrometry data in mzXML, mzML, or netCDF format from untargeted LC/HRMS analysis that has been pre-processed by IDSL.
    0 installs
64. ▌
    Release Branch Management 2 · holobiomicslab

    Use when you need to validate that a software project's release branch is stable and ready for distribution. Specifically, use it when: (1) a release tag has been created or code pushed to a release branch; (2) you need to confirm that CI/CD pipelines execute without failures;
    0 installs
65. ▌
    Repository Administration 2 · holobiomicslab

    Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing new versions, after merging changes to release branches, or when troubleshooting build failures that block distribution of.
    0 installs
66. ▌
    Resolver Url Construction 2 · holobiomicslab

    Use when when you have a USI string (comprising dataset identifier, spectrum index, and optional library reference) and need to generate a stable, machine-readable link that resolves to interactive spectrum visualization or programmatic access.
    0 installs
67. ▌
    Retention Time Prediction 3 · holobiomicslab

    Use when you have MS1-formatted mass spectrometry files from a liquid chromatography–mass spectrometry (LC-MS) experiment and need to predict the retention time of peptide ions without relying on spectral libraries, empirical models, or manual feature engineering.
    0 installs
68. ▌
    Schema Compliance Testing 2 · holobiomicslab

    Use when when uploading or ingesting a new paired omics project JSON document into the Pairing Omics Data Platform, or when programmatically submitting projects via the OpenAPI interface. Apply this skill before persisting the document to disk or indexing it for search.
    0 installs
69. ▌
    Signal Quality Assessment 3 · holobiomicslab

    Use when you have imported raw MSI spectral data in imzML format and need to improve signal-to-noise ratio before performing mean intensity calculations, ROI analysis, or database annotation.
    0 installs
70. ▌
    Sparse Matrix Computation 2 · holobiomicslab

    Use when clustering large collections of high-resolution MS/MS spectra (thousands to millions) and you have already converted spectra to low-dimensional vectors via feature hashing.
    0 installs
71. ▌
    Spectral Data Exploration 2 · holobiomicslab

    Use when you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
    0 installs
72. ▌
    Spectral Data Integration 2 · holobiomicslab

    Use when you have three distinct mass spectrometry data sources (quantification table, metadata table, and spectral data from an MS library or reference dataset like omsw_pleurotus_ms2deepscore) and need to combine them into a single JSON output that preserves all three modalities for interactive.
    0 installs
73. ▌
    Spectrum Array Validation 2 · holobiomicslab

    Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to confirm that the resulting arrays fall within specified m/z windows, intensity bounds, and peak count limits before.
    0 installs
74. ▌
    Survival Data Preparation 2 · holobiomicslab

    Use when when you have clinical survival outcomes (event status and follow-up time) and high-dimensional metabolomic or expression data, and you need to feed them into Cox-PH or Cox-nnet prognosis models.
    0 installs
75. ▌
    Suspect Database Matching 2 · holobiomicslab

    Use when you have LC-MS peak/feature data, a curated suspect compound database with known m/z, retention time, and fragment ion coordinates, and you observe that traditional peak extraction algorithms have failed to detect ions corresponding to suspected contaminants or chemicals of interest.
    0 installs
76. ▌
    Tandem Ms Peak Assignment 2 · holobiomicslab

    Use when when you have experimental tandem MS spectra (with peak m/z and intensity values) and need to annotate each peak with its chemical formula (SCARF) or molecular fragment origin (ICEBERG), particularly for structural elucidation campaigns where understanding the fragmentation pathway is.
    0 installs
77. ▌
    Thermo Raw Format Parsing 2 · holobiomicslab

    Use when when you have LC-MS data in Thermo .raw format (a proprietary binary output from Thermo mass spectrometers) and need to load it into a 3D LC-MS viewer or extract structured spectral metadata (retention time, m/z values, intensities, scan number, MS level) for visualization or quantitative.
    0 installs
78. ▌
    Vendor Format Abstraction 2 · holobiomicslab

    Use when you have mass-spectrometry raw data files from multiple vendors (e.g., Thermo, Waters, Bruker, Sciex) and/or mixed standard formats (mzML, mzXML) that must be processed by a single analysis pipeline.
    0 installs
79. ▌
    Word2vec Model Training 2 · holobiomicslab

    Use when when you have a collection of mass spectra (e.
    0 installs
80. ▌
    Peak Collision Flagging 2 · holobiomicslab

    Use when you have extracted a peak list from MSI data and need to annotate matrix-related signals, but overlapping peaks or isobaric ions (ions with identical or near-identical m/z values) risk being misclassified.
    0 installs
81. ▌
    Arrow Tabular Data Reading 2 · holobiomicslab

    Use when when you have Parquet-encoded tabular data (e.
    0 installs
82. ▌
    Custom Data Schema Mapping 2 · holobiomicslab

    Use when a practitioner has pre-computed features from an external feature-finding procedure (e.g., vendor software, alternative open-source tools) and wishes to incorporate them into PFΔScreen's PFAS prioritization pipeline without re-detecting features from raw mzML data.
    0 installs
83. ▌
    Distance Matrix Clustering 2 · holobiomicslab

    Use when you have a sparse pairwise distance matrix derived from nearest neighbor indexing of MS/MS spectra (or similar high-dimensional objects) and need to partition spectra into groups based on local density and neighborhood connectivity.
    0 installs
84. ▌
    External Registry Querying 2 · holobiomicslab

    Use when your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations. The platform needs to auto-populate these fields to enable browsing and cross-linking with public genomic databases. Trigger this skill when you have genome IDs (e.
    0 installs
85. ▌
    Fragment Ion Mass Matching 2 · holobiomicslab

    Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
    0 installs
86. ▌
    Hmdb Metabolite Extraction 2 · holobiomicslab

    Use when you have downloaded raw HMDB data (hmdb_metabolites.zip or pickle file) and need to generate a representative set of chemical objects for simulating LC-MS/MS acquisition strategies.
    1 install
87. ▌
    HTTP Post Request Assembly 2 · holobiomicslab

    Use when you have NMR peak data (1H and 13C chemical shift values) that must be submitted to a remote DeepSAT SMART 3 classification API for structural prediction, and you need to format the data correctly, validate the endpoint schema, and parse the response to extract predictions and confidence.
    0 installs
88. ▌
    Ionization Mode Annotation 2 · holobiomicslab

    Use when when converting MS/MS spectra from .msp format library files (e.g., MassBank) into a custom fragment library for metabolite annotation, and the source spectra are tagged with ionization mode information (positive or negative).
    0 installs
89. ▌
    Lc Ms Spectral Data Import 2 · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for interactive exploration using the specXplore dashboard.
    0 installs
90. ▌
    Memomatrix Object Handling 2 · holobiomicslab

    Use when you have generated one or more MemoMatrix objects (MS2 fingerprint matrices from separate sample sets) and need to combine them for cross-cohort alignment, validate structural consistency after merging, or prepare merged matrices for downstream filtering and visualization.
    0 installs
91. ▌
    Mzml Feature Table Parsing 2 · holobiomicslab

    Use when you have raw LCMS data in mzML format and a feature table (CSV) from a peak detection pipeline (e.g., MZmine) and need to prepare these inputs for NeatMS preprocessing, batch creation, or peak classification. This skill is the mandatory entry point for any NeatMS workflow.
    0 installs
92. ▌
    Qiime2 Artifact Inspection 2 · holobiomicslab

    Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly produced, before using it as input to downstream analyses.
    0 installs
93. ▌
    Schema Constraint Checking 2 · holobiomicslab

    Use when a user uploads a JSON project file to the platform and you need to verify it matches the required format defined in app/public/schema.json before accepting it into the database.
    0 installs
94. ▌
    API Endpoint Communication 2 · holobiomicslab

    Use when you have fingerprint or spectrum data that requires compound-class annotation but prefer not to run SIRIUS locally, or need to integrate predictions into an automated analysis pipeline.
    0 installs
95. ▌
    Build Status Documentation 2 · holobiomicslab

    Use when when you need to validate that a development build release workflow (such as dev_build_release.yml for a mass spectrometry data processing project) executes without failure and generates artifacts for downstream testing or distribution.
    0 installs
96. ▌
    CI Status Badge Deployment 2 · holobiomicslab

    Use when you have configured a GitHub Actions workflow that executes build, test, and quality checks, and you want to embed a machine-readable, auto-updating badge in your repository README to signal pipeline status at a glance.
    0 installs
97. ▌
    Cluster Assignment Mapping 2 · holobiomicslab

    Use when after density-based clustering (e.g., DBSCAN) has been performed on a sparse pairwise distance matrix derived from MS/MS spectra nearest neighbor indexes.
    0 installs
98. ▌
    Composite Spectra Analysis 2 · holobiomicslab

    Use when your untargeted LC/HRMS dataset contains Data-Independent Acquisition data (MS^E, AIF, or SWATH-MS) or MS1-only composite spectra where multiple precursor ions fragment simultaneously, and you need to deconvolve overlapping fragmentation spectra to enable accurate chemical structure.
    0 installs
99. ▌
    Compound Candidate Ranking 2 · holobiomicslab

    Use when after compound database dereplication has produced candidate annotations (from SIRIUS or MetFrag) and you need to select the most reliable candidates for final annotation.
    0 installs
100. ▌
     Compound Database Matching 2 · holobiomicslab

     Use when you have MS2 .mzML spectral data from untargeted metabolomics and need to assign chemical identities to detected precursor ions.
     0 installs