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HolobiomicsLab

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1. ▌
   Metabolomics Data Preprocessing 2 · holobiomicslab

   Use when you have raw LC/HRMS data files in mzXML, mzML, or netCDF format and need to identify individual and aggregated aligned peaks with their retention time and m/z values before applying spectral deconvolution or chemical annotation. This is the obligatory first step when using IDSL.
   2 installs
2. ▌
   Molecular Network Graph Parsing 3 · holobiomicslab

   Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for further metabolite assignment, comparative network analysis, or visualization.
   2 installs
3. ▌
   Molecular Structure Attribution 2 · holobiomicslab

   Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential for specific predictions or across a test set.
   5 installs
4. ▌
   Ms2 Peak Detection And Counting 3 · holobiomicslab

   Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when samples were acquired using different LC methods, mass spectrometer technologies, or exhibit poor feature overlap or large.
   2 installs
5. ▌
   Ms2 Spectra Parsing And Loading 3 · holobiomicslab

   Use when when beginning a MEMO analysis workflow with raw or unaligned MS2 spectra files and needing to extract fragmentation data and precursor information before counting MS2 peaks and neutral losses to generate sample fingerprints.
   1 install
6. ▌
   Ms2 Spectrum Feature Extraction 2 · holobiomicslab

   Use when you have DDA (data-dependent acquisition) LC-MS/MS data with MS2 spectra and want to discover metabolic features that may be missed by MS1-only peak picking, or when you need an alternative feature extraction workflow that leverages fragmentation patterns to identify true metabolite.
   2 installs
7. ▌
   Ms2lda Motif To Network Mapping 3 · holobiomicslab

   Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered substructural motifs to support structural elucidation and chemical family interpretation.
   1 install
8. ▌
   Spectrum Vector Serialization 3 · holobiomicslab

   Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
   2 installs
9. ▌
   Tandem Ms Data Reorganization 4 · holobiomicslab

   Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment fields rather than in dedicated SMILES/InChIKey fields, or when positive and negative ionization mode spectra are commingled.
   2 installs
10. ▌
    Total Ion Current Calculation 2 · holobiomicslab

    Use when after loading all MS1 scans from a raw or intermediate mass spectrum file (e.
    2 installs
11. ▌
    Train Test Split Verification 3 · holobiomicslab

    Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to confirm that the change produces the documented training/test split counts.
    4 installs
12. ▌
    Feature Ablation Analysis 3 · 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.
    2 installs
13. ▌
    Chemical Identifier Mapping 3 · 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).
    3 installs
14. ▌
    Error Handling Confirmation 3 · 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
15. ▌
    Package Integration Testing 3 · 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.
    2 installs
16. ▌
    Pandas Accessor Integration 2 · holobiomicslab

    Use when you have mass-spectrometry data in a Pandas DataFrame and need to expose plot kinds (spectrum, chromatogram, mobilogram, peakmap) as a `.plot(kind='...
    2 installs
17. ▌
    Repository History Analysis 3 · holobiomicslab

    Use when when you need to understand how a complex feature or architectural pattern was implemented in a codebase, particularly when the current README or documentation does not fully explain the control flow, decision criteria, or parameter passing between subsystems.
    4 installs
18. ▌
    Rust Build System Execution 3 · holobiomicslab

    Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library. Use this skill when the source includes a Cargo.
    2 installs
19. ▌
    Shifted Dot Product Scoring 2 · holobiomicslab

    Use when matching query mass spectra to a spectral library in the presence of unknown post-translational modifications (PTMs) or non-enzymatic modifications.
    3 installs
20. ▌
    Spectral Topic Modeling Lda 2 · holobiomicslab

    Use when when you have a collection of normalized mass spectrometry spectra (peak intensities or binned m/z representations) and seek to enrich neural network training signals for metabolite identification by discovering latent spectral patterns.
    2 installs
21. ▌
    Software Plugin Development 3 · holobiomicslab

    Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel reagent, derivatizing matrix, or analytical method (e.
    2 installs
22. ▌
    Attention Mechanism Validation 3 · holobiomicslab

    Use when after instantiating a transformer encoder module for mass spectrometry data processing (e.g., in IDSL_MINT), before training on large MS/MS datasets or running inference on test spectra.
    2 installs
23. ▌
    Peak Pairwise Comparison 3 · 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.
    2 installs
24. ▌
    Accuracy Metric Computation 3 · 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
25. ▌
    Chemical Class Node Mapping 3 · 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.
    1 install
26. ▌
    Command Line Tool Execution 3 · 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.
    1 install
27. ▌
    Graph Enrichment Operations 3 · 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.
    2 installs
28. ▌
    Java Source Code Inspection 4 · 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.
    2 installs
29. ▌
    Lcms Workflow Orchestration 3 · 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.
    2 installs
30. ▌
    Mass Chromatogram Alignment 4 · 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.
    2 installs
31. ▌
    Md Defect Ratio Calculation 3 · 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.
    2 installs
32. ▌
    Model Ablation Study Design 3 · 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.
    2 installs
33. ▌
    Network Topology Comparison 4 · 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.
    3 installs
34. ▌
    Network Topology Validation 3 · 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.
    2 installs
35. ▌
    Organism Metadata Retrieval 3 · 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.
    2 installs
36. ▌
    Pfas Feature Prioritization 3 · 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.
    3 installs
37. ▌
    Project Metadata Validation 3 · 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
38. ▌
    Centroided Ms Feature Detection 4 · holobiomicslab

    Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.
    2 installs
39. ▌
    Chemical Metadata Harmonization 2 · holobiomicslab

    Use when when aggregating MS/MS spectra from multiple public repositories (GNPS, MassBank, Mona) or in-house sources with inconsistent metadata naming conventions, missing or malformed adduct annotations, or incomplete chemical structure annotations (SMILES/InChI/InChIKey).
    2 installs
40. ▌
    Compound Identification Scoring 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectra (noise-filtered, normalized) and need to compute pairwise similarity or distance scores for compound library matching, when your goal is to rank candidate compounds by spectral match quality and maximize correct identification rate above dot-product.
    3 installs
41. ▌
    Configuration File Modification 2 · holobiomicslab

    Use when when you need to expand or contract a mass spectrometry dataset by adding or removing allowed instrument types (e.
    3 installs
42. ▌
    Correlation Matrix Construction 2 · holobiomicslab

    Use when after obtaining per-sample model predictions and metabolite signal intensities from a trained deep learning model (e.g., DeepMSProfiler) on LC-MS data from multiple disease groups, and you need to identify and visualize metabolite–disease associations as correlation strengths.
    4 installs
43. ▌
    Directive Engine Implementation 2 · holobiomicslab

    Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental metadata from tabular spreadsheets, you need to map certain fields to computed or filtered values, apply conditional.
    0 installs
44. ▌
    Distribution Channel Validation 2 · holobiomicslab

    Use when when preparing a software release, testing contribution workflows, or auditing package availability: verify that matchms can be installed and imported successfully from all advertised distribution channels (PyPI and Bioconda) to confirm the package metadata, dependencies, and entry points.
    1 install
45. ▌
    Document Structure Verification 2 · holobiomicslab

    Use when when uploading or ingesting paired omics project documents into the Pairing Omics Data Platform, or when you need to verify that a JSON project file conforms to the expected schema structure before processing MS/MS mass spectra linkages, genome associations, or submission to external.
    2 installs
46. ▌
    Drug Database Record Extraction 2 · holobiomicslab

    Use when when you have obtained a DrugBank release file (requiring access credentials) and need to integrate drug chemical structure, name, and identifier information into a metadata cleanup or chemical enrichment pipeline.
    4 installs
47. ▌
    Evaluation Data Object Handling 2 · holobiomicslab

    Use when after completing an Environment simulation run with save_eval flag enabled, when you need to preserve the EvaluationData object containing scan provenance, chemical source definitions, and fragmentation events for later inspection, validation, or reanalysis without re-running the full.
    1 install
48. ▌
    Fdr Correction Multiple Testing 2 · holobiomicslab

    Use when you have computed empirical p-values from randomized sampling (e.
    1 install
49. ▌
    Feature Grouping By Mass Defect 3 · holobiomicslab

    Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.
    2 installs
50. ▌
    Feature Quantification Analysis 2 · holobiomicslab

    Use when when you have loaded search result files from one or more DIA-MS analysis tools and need to assess the quantitative performance of identified features.
    2 installs
51. ▌
    Feature Specificity Calculation 2 · holobiomicslab

    Use when when you have a quantitative feature table from MZmine2/MZmine3 with peak area and m/z data aligned across multiple extract samples, and you need to identify which features are characteristic of individual samples (high specificity) versus ubiquitous across the extract set.
    0 installs
52. ▌
    Gap Filling Algorithm Selection 2 · holobiomicslab

    Use when when processing untargeted LC-MS data with SLAW and observing incomplete feature detection across the sample cohort—i.e., features present in some samples but with missing values (zeros or NAs) in others due to signal dropout, retention time drift, or mass calibration drift.
    4 installs
53. ▌
    Gc Ms Spectral Library Matching 2 · holobiomicslab

    Use when when you have GC-MS data with detected peaks that require structural annotation, retention index calibration has been applied (typically using FAMES standards), and you need to assign compound identities with confidence scores.
    2 installs
54. ▌
    Gc Ms Chromatogram Processing 4 · holobiomicslab

    Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against reference libraries such as PNNLMetV20191015.MSL.
    0 installs
55. ▌
    Large Scale Spectral Matching 3 · holobiomicslab

    Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all-pairs or many-to-many spectrum similarity to identify related compounds, build spectral libraries, or perform large-scale library searching.
    1 install
56. ▌
    Lcms Peak Intensity Filtering 2 · holobiomicslab

    Use when after XCMS peak picking, alignment, and grouping when you have identified putative incorporations (via PuInc_seeker) or base-peak isotopologue candidates and need to exclude low-intensity peaks that are likely noise or instrument artifacts.
    2 installs
57. ▌
    Lcms Retention Time Alignment 2 · holobiomicslab

    Use when when XCMS-aligned LC-MS data shows coefficient of variation (CV) above expected thresholds for known features, or when analyzing long-duration experiments (>1 week) or large cohorts (>100 samples) where global warping functions are known to fail due to compound-specific RT drift structures.
    2 installs
58. ▌
    Mass Spectral Data Validation 4 · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
    3 installs
59. ▌
    Mass Spectral Peak Annotation 3 · holobiomicslab

    Use when you have centroided MS2 spectra (in mzML format from data-dependent acquisition) and a list of known or suspect PFAS diagnostic fragment masses, and you need to systematically flag which detected features contain fragments characteristic of PFAS compounds (e.
    2 installs
60. ▌
    Molecular Fingerprint Parsing 3 · holobiomicslab

    Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract the predicted molecular fingerprint representation and associated scoring metrics for compound identification or CANOPUS.
    2 installs
61. ▌
    Mzml Metabolomics Data Import 3 · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in mzML or ABF format that needs to be processed through a reproducible pipeline. Use this skill when: (1) you have public or proprietary .mzML LC-MS datasets (e.g. from MetaboLights, MassIVE, or PRIDE);
    2 installs
62. ▌
    Polarity Aware Data Filtering 3 · holobiomicslab

    Use when when performing targeted peak detection on LC-MS data where compounds have been assigned expected ionization polarities (positive or negative mode) in the target list, and you want to prevent false peak assignments from the opposite polarity and avoid manual pre-filtering of raw data by.
    2 installs
63. ▌
    Precursor And Noise Filtering 2 · holobiomicslab

    Use when you have loaded raw tandem MS spectra (in MGF, mzML, or similar format) and need to prepare them for peptide identification, spectral library matching, or intensity-based analysis.
    2 installs
64. ▌
    Precursor Mz Window Filtering 2 · holobiomicslab

    Use when when preparing augmented training data for Siamese or contrastive learning architectures in mass spectrometry, specifically when you need to generate hard negative examples that are spectrally distinct but mass-similar to positive examples.
    2 installs
65. ▌
    Record Grouping And Collation 2 · holobiomicslab

    Use when you have multiple rows in a table that describe the same logical entity (e.g., multiple measurements from the same sample, or repeated attributes under a common identifier) and need to merge them into a single dictionary entry keyed by that shared field.
    1 install
66. ▌
    Replicate Spectrum Comparison 2 · holobiomicslab

    Use when you have multiple MS/MS spectra (replicates) for a single metabolic feature (same m/z and RT window) and need to identify which fragments are reproducibly detected across replicates versus noise.
    3 installs
67. ▌
    Retention Time Mass Alignment 3 · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to identify which features in one dataset correspond to features in the other.
    3 installs
68. ▌
    Spectral Noise Peak Filtering 2 · holobiomicslab

    Use when when working with raw or partially processed tandem mass spectrometry (MS/MS) spectra that contain low-intensity background noise peaks.
    1 install
69. ▌
    Spectrum Query Formatting 3 · 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.
    1 install
70. ▌
    Spectral Peak Filtering 3 · holobiomicslab

    Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata validation, or export.
    2 installs
71. ▌
    Arrow Tabular Data Reading 3 · holobiomicslab

    Use when when you have Parquet-encoded tabular data (e.
    2 installs
72. ▌
    Custom Data Schema Mapping 3 · 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.
    2 installs
73. ▌
    Distance Matrix Clustering 3 · 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.
    3 installs
74. ▌
    External Registry Querying 3 · 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.
    3 installs
75. ▌
    Fragment Ion Mass Matching 3 · holobiomicslab

    Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
    2 installs
76. ▌
    Hmdb Metabolite Extraction 3 · 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.
    4 installs
77. ▌
    HTTP Post Request Assembly 3 · 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
78. ▌
    Ionization Mode Annotation 3 · 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).
    3 installs
79. ▌
    Lc Ms Spectral Data Import 3 · 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.
    1 install
80. ▌
    Memomatrix Object Handling 3 · 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.
    3 installs
81. ▌
    Mzml Feature Table Parsing 3 · 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.
    4 installs
82. ▌
    Qiime2 Artifact Inspection 3 · 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.
    1 install
83. ▌
    Schema Constraint Checking 3 · 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.
    2 installs
84. ▌
    Code Repository Analysis 3 · 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).
    1 install
85. ▌
    Interoperability Testing 3 · holobiomicslab

    Use when when a new file format specification exists as a living document (e.
    3 installs
86. ▌
    Genome Sequence Mining 3 · holobiomicslab

    Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format) from the same organism, and you want to identify novel RiPPs by linking gene cluster predictions to observed mass spectra.
    0 installs
87. ▌
    Ms Ms Spectrum Parsing 3 · holobiomicslab

    Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak lists (m/z and intensity pairs) along with metadata (precursor m/z, charge, ionization mode) to feed into MS2Query or.
    3 installs
88. ▌
    Cosine Distance Scoring 3 · holobiomicslab

    Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of spectra to identify similar compounds, search spectral libraries, or build a similarity network for spectral clustering or.
    1 install
89. ▌
    Error Report Generation 3 · holobiomicslab

    Use when when a user uploads a JSON project document to the Pairing Omics Data Platform and you need to determine whether it satisfies the platform's data structure requirements, including all mandatory fields, proper data types, and constraint satisfaction for paired omics metadata (e.
    3 installs
90. ▌
    Gnps Network Processing 3 · holobiomicslab

    Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or chemical class information.
    1 install
91. ▌
    Hdf5 File Io Operations 4 · holobiomicslab

    Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS calibration), or when you need to export annotated feature tables with isotopologue metadata back to HDF5 for archival.
    0 installs
92. ▌
    Lc Ms Output Validation 3 · holobiomicslab

    Use when after executing a Nextflow-based LC-HRMS metabolomics workflow with Docker or Singularity containerization on .mzML LC-MS data, before proceeding to downstream statistical or visualization analyses.
    3 installs
93. ▌
    Mass Defect Calculation 3 · holobiomicslab

    Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS candidates.
    2 installs
94. ▌
    Module Coverage Mapping 4 · holobiomicslab

    Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation techniques.
    2 installs
95. ▌
    Msp File Format Parsing 4 · holobiomicslab

    Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign SMILES, retention indices, or combine multiple libraries into a single consolidated MSP file for MS-DIAL.
    2 installs
96. ▌
    Smiles Notation Parsing 3 · holobiomicslab

    Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields rather than a dedicated SMILES field, or when assigning SMILES from external structure databases (SDF files) to library.
    2 installs
97. ▌
    Xcms Workflow Execution 4 · holobiomicslab

    Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the cohort.
    4 installs
98. ▌
    Module Import Testing 3 · holobiomicslab

    Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional after upstream updates. Use it as a gate before finalizing a release to catch installation or import breakage early.
    0 installs
99. ▌
    Genome Identifier Lookup 3 · holobiomicslab

    Use when a paired omics project JSON document contains genome identifiers (e.g. IMG IDs, NCBI accessions) but lacks corresponding organism names.
    1 install
100. ▌
     Hrms Data Format Parsing 3 · holobiomicslab

     Use when you have raw or processed HRMS/MS data from Q-Exactive, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF instruments in formats such as mzML, CSV peaklists, or vendor-specific formats, and you need to extract experimental fragment m/z values and their intensities for comparison against.
     2 installs