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HolobiomicsLab

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1. ▌
   JSON Document Enrichment 3 · holobiomicslab

   Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate those fields programmatically before storage or publication to enable full-text search, validation, or cross-linking.
   0 installs
2. ▌
   Chemical Formula Representation 2 · holobiomicslab

   Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and composition.
   1 install
3. ▌
   Lc Ms Feature M Z Rt Extraction 2 · holobiomicslab

   Use when you have preprocessed LC-MS intensity data (e.
   1 install
4. ▌
   Mass Spectrum Database Matching 4 · holobiomicslab

   Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your sample.
   2 installs
5. ▌
   Metabolomics Peak Table Loading 2 · holobiomicslab

   Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with sample metadata for reproducibility filtering, mispicked-ion removal, or group-based feature exclusion.
   1 install
6. ▌
   Ms Peak Table Format Validation 2 · holobiomicslab

   Use when immediately after loading a raw GC-MS CSV file and before executing the spreadOut() function. Use it when you have received peak table data from an instrument vendor (e.
   1 install
7. ▌
   Ms Spectrum Similarity Grouping 2 · holobiomicslab

   Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to a cluster group for downstream analysis such as peptide identification or spectral library construction.
   3 installs
8. ▌
   Ms2 Data Preprocessing Pipeline 2 · holobiomicslab

   Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that may contain multiple MS2 spectra per feature and require reduction or standardization before library matching.
   4 installs
9. ▌
   Neural Network Encoder Freezing 2 · holobiomicslab

   Use when when you have a pre-trained encoder (e.g., TCN spectrum encoder in FIDDLE) that has learned useful representations on a source task (e.g., MS/MS spectrum encoding), and you want to train lightweight task-specific modules (e.
   1 install
10. ▌
    Peak Table Row Count Validation 2 · holobiomicslab

    Use when when using mpactr filter functions (e.g., filter_mispicked_ions, filter_group, filter_cv) with R6 reference semantics and uncertain whether the copy_object parameter controls deep copying or in-place modification.
    2 installs
11. ▌
    Per Sample Spectral Aggregation 2 · holobiomicslab

    Use when you have raw MS2 spectra from a sample and need to collapse them into a single sample-level representation for comparison across multiple samples, particularly when samples have poor feature overlap, strong retention time shifts between LC methods, or were acquired on different mass.
    3 installs
12. ▌
    Roc Curve Auc Metric Evaluation 2 · holobiomicslab

    Use when after training a NeatMS CNN model on labeled MS1 peaks and generating predictions on a held-out test set, compute ROC-AUC to assess whether the model achieves the target discrimination threshold (AUC ≥ 0.9) without evidence of overfitting.
    3 installs
13. ▌
    Tcn Encoder Input Preprocessing 2 · holobiomicslab

    Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z (env[:, 0]) has been removed from the feature vector to avoid leakage of mass information into the model's learned.
    3 installs
14. ▌
    Algorithm Interface Abstraction 2 · holobiomicslab

    Use when you have multiple independent peak-picking algorithms available and need to allow end-users to select among them for the same analytical task (peak detection in untargeted LC-MS data) without coupling the rest of your pipeline to each algorithm's API.
    2 installs
15. ▌
    Batch Corrected Data Extraction 2 · holobiomicslab

    Use when after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for quality metrics calculation, internal standard recommendation, concentration estimation, or statistical modelling.
    3 installs
16. ▌
    Blank Intensity Ratio Filtering 3 · holobiomicslab

    Use when apply this filter after feature detection and before downstream statistical analysis when your experimental design includes blank samples (e.
    2 installs
17. ▌
    Mzpeak Format File Parsing 3 · holobiomicslab

    Use when you have an mzPeak file (uncompressed ZIP archive containing Parquet files) and need to extract and work with spectrum metadata (scan descriptions, precursors, selected ions), spectrum signal data (profile or centroid m/z and intensity arrays), or chromatogram data.
    1 install
18. ▌
    Richness Index Computation 3 · holobiomicslab

    Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular species across experimental conditions—for example, to test whether inoculation or environmental perturbation alters the.
    2 installs
19. ▌
    S4 Class Method Inspection 3 · holobiomicslab

    Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on NumericList or similar container objects, rather than inefficient loops or apply functions.
    2 installs
20. ▌
    Workflow Status Monitoring 3 · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
    1 install
21. ▌
    Numerical Equivalence Testing 2 · holobiomicslab

    Use when you need to confirm that omitting an optional input parameter (such as secondaryAssay in buildExperiment) produces the expected mathematical result—specifically, when a default value should neutralize a transformation (e.
    2 installs
22. ▌
    Spectral Metadata Integration 2 · holobiomicslab

    Use when after isotopologue and adduct grouping has been completed and you need to associate MS2 spectra with consolidated feature groups in DDA LC-MS experiments.
    0 installs
23. ▌
    Accurate Mass Database Search 3 · holobiomicslab

    Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z values to a reference database and want to recover HMDB identifiers, molecular formulas, and structural annotations for.
    1 install
24. ▌
    Blank Contamination Filtering 3 · holobiomicslab

    Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.
    3 installs
25. ▌
    Chemical Metadata Integration 3 · holobiomicslab

    Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared structural features or chemical families across spectral clusters.
    0 installs
26. ▌
    Coeluting Compound Resolution 4 · holobiomicslab

    Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw chromatogram.
    0 installs
27. ▌
    Feature Extraction Untargeted 2 · holobiomicslab

    Use when when you have raw untargeted LC/MS data in mzML or mzXML format and need to detect and quantify metabolite signals across mass-to-charge and retention time dimensions without prior knowledge of instrument parameters, batch effects, or optimal detection thresholds.
    3 installs
28. ▌
    Feature Hashing Vectorization 3 · holobiomicslab

    Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
    2 installs
29. ▌
    Feature Table Format Handling 2 · holobiomicslab

    Use when transitioning feature intensity data between pipeline stages (e.
    2 installs
30. ▌
    Form Encoded Request Handling 2 · holobiomicslab

    Use when when a web service must accept spectroscopic measurements (NMR peaks, IR/MS metadata) submitted as form-encoded POST parameters from a client, and those parameters need to be validated, reformatted into an external API query format, or passed to a downstream predictor service.
    2 installs
31. ▌
    Formula Sampler Configuration 3 · holobiomicslab

    Use when you need to generate a set of candidate chemical formulas for LC-MS/MS simulation—specifically when you want to populate a virtual mass spectrometer with realistic chemical structures drawn from a reference database (HMDB) or a uniform m/z distribution, and you need to apply m/z filtering.
    3 installs
32. ▌
    Lc Ms Data Preprocessing 3 · holobiomicslab

    Use when you have raw mzML files and corresponding feature tables (CSV format, mzmine-formatted) from untargeted LCMS experiments, and you need to convert them into uniformly-shaped peak matrices (2 × 120 per peak: margin + signal regions) as input for neural network classification of MS1 peak.
    4 installs
33. ▌
    Matlab Package Execution 3 · holobiomicslab

    Use when you have two separate LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to establish feature-to-feature correspondence between them.
    2 installs
34. ▌
    Peak Matrix Construction 3 · holobiomicslab

    Use when when you have raw mzML files and a corresponding feature table (CSV format, e.g., from mzmine) and need to generate peak matrices with fixed dimensions (e.g., 2 × 120) that encode margin vs. peak signal regions for training a neural network classifier to filter false positive LCMS peaks.
    3 installs
35. ▌
    Precursor Mass Filtering 3 · holobiomicslab

    Use when after retrieving top-scoring library candidates from a full MS2Deepscore comparison, but before or during final re-ranking.
    2 installs
36. ▌
    Candidate Match Retrieval 3 · 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.
    3 installs
37. ▌
    Feature Table Gap Filling 3 · 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.
    2 installs
38. ▌
    Isotope Adduct Annotation 3 · 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.
    2 installs
39. ▌
    Library Import Validation 3 · 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.
    3 installs
40. ▌
    Library Object Validation 3 · 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.
    2 installs
41. ▌
    Model Metadata Extraction 3 · 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.
    3 installs
42. ▌
    Mpactr Filter Application 3 · holobiomicslab

    Use when you have a preprocessed peak table from tandem MS/MS data (e.
    2 installs
43. ▌
    Ms2lda Feature Annotation 3 · 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.
    2 installs
44. ▌
    Multitask Model Inference 3 · 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..
    2 installs
45. ▌
    Python Workflow Scripting 3 · 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.
    3 installs
46. ▌
    Spectrum Metadata Parsing 3 · 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).
    1 install
47. ▌
    Mzml File Parsing 3 · holobiomicslab

    Use when you have raw LC- or GC-HRMS data from vendor instruments (ESI or APCI ionization) that needs to be converted to a vendor-neutral format for non-target screening, or you already have mzML files that require loading into a Python environment for downstream feature detection and MS2 spectral.
    3 installs
48. ▌
    Msp To CSV Parsing 3 · holobiomicslab

    Use when you have a .msp format MS/MS spectrum library (e.g., from MassBank or similar public databases) and need to convert it into individual CSV entries indexed by positive or negative ionisation mode for use as a custom fragment library in MetaboAnnotatoR annotation pipelines.
    4 installs
49. ▌
    Peak Count Capping 3 · holobiomicslab

    Use when apply peak-count capping when preprocessing tandem mass spectrometry (MS/MS) spectra for peptide identification or spectral library matching, particularly when working with high-resolution spectra that may retain numerous low-intensity noise peaks after intensity filtering.
    0 installs
50. ▌
    Gcf Mf Link Scoring 3 · holobiomicslab

    Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from the same microbial strains and need to rank which GCF–MF pairs are likely to represent true biosynthetic relationships.
    1 install
51. ▌
    Motif To Node Mapping 3 · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based mass spectral molecular network (graphml or JSON format) and a corresponding MS2LDA experiment with Mass2Motif assignments on the same spectra, and you want to visualize and quantify which structural motifs are shared within and across.
    1 install
52. ▌
    Newick Format Parsing 3 · holobiomicslab

    Use when you have a Chemical Feature Tree artifact (phylogeny) output from q2-qemistree's make-hierarchy method and need to verify its structural validity, count nodes (leaves and internal nodes), measure tree depth, and assess branching patterns before using it for alpha- or beta-diversity.
    2 installs
53. ▌
    Spectral JSON Parsing 3 · holobiomicslab

    Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
    1 install
54. ▌
    Library Integration Workflow 3 · holobiomicslab

    Use when you have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library, and you want to include them as matching candidates in your UHPLC-HRMS/MS fragment m/z matching workflow without modifying.
    3 installs
55. ▌
    Molecular Formula Validation 3 · holobiomicslab

    Use when when you have a feature list from HRMS with tentatively assigned molecular formulas (from in silico tools or databases) and need to assess formula plausibility before applying downstream PFAS-specific filters.
    3 installs
56. ▌
    Multi Omics Data Integration 3 · holobiomicslab

    Use when when you have matched transcriptomics (RNA-seq read counts), intracellular metabolomics (LC-MS abundance data), and extracellular flux measurements (YSI bioanalyzer or similar) from multiple biological samples or cell lines, and you need to determine whether differences in metabolic enzyme.
    1 install
57. ▌
    Multiblock Pls Model Fitting 3 · holobiomicslab

    Use when you have split multi-assay LC-MS intensity data into training (90%) and test (10%) subsets with assay-specific column prefixes, and you need to fit a discriminant or regression model that respects the block structure (separate assays) while jointly predicting a phenotypic outcome (e.
    1 install
58. ▌
    Pairwise Spectral Comparison 3 · holobiomicslab

    Use when you have a collection of preprocessed mass spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to quantify similarity relationships across all pairs—for instance, to identify redundant spectra in a library, cluster related compounds, or perform spectral library searches.
    2 installs
59. ▌
    Peak Filtering Noise Removal 3 · holobiomicslab

    Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library matching.
    2 installs
60. ▌
    Phylogenetic Tree Validation 3 · holobiomicslab

    Use when after generating a Chemical Feature Tree from q2-qemistree (or any tree artifact) and before using it for alpha-diversity or beta-diversity phylogenetic analyses.
    1 install
61. ▌
    Polarity Mode Filtering Lcms 3 · holobiomicslab

    Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run acquired in a specific polarity mode.
    2 installs
62. ▌
    Session Object Serialization 3 · holobiomicslab

    Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data object containing t-SNE embeddings (based on ms2deepscore similarity scores) and associated spectral metadata.
    3 installs
63. ▌
    Siamese Architecture Scoring 3 · holobiomicslab

    Use when after a TCN-based formula prediction model has generated initial formula candidates from MS/MS spectra, apply this skill to rescore and refine those candidates when you need to improve ranking accuracy.
    4 installs
64. ▌
    Spectral Data Format Parsing 3 · holobiomicslab

    Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for downstream spectral analysis, fragmentation tree computation, or metabolite identification.
    1 install
65. ▌
    Spectral Feature Engineering 3 · holobiomicslab

    Use when you have molecular structures (SMILES or graph representations) and need to predict or analyze infrared spectral properties using message passing neural networks.
    1 install
66. ▌
    Spectral Workflow Validation 3 · holobiomicslab

    Use when after implementing or modifying a cross-language integration layer that wraps Python mass spectrometry functions (e.g., spectral matching, peak detection, normalization from matchms or spectrum_utils) as R-callable functions within Spectra workflows.
    1 install
67. ▌
    Spectrum Metadata Extraction 3 · holobiomicslab

    Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including scan information, precursor m/z and charge, and ion selection parameters—into a queryable, vendor-agnostic tabular schema.
    3 installs
68. ▌
    API Endpoint Communication 3 · 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.
    3 installs
69. ▌
    Build Status Documentation 3 · 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.
    1 install
70. ▌
    Mandatory Field Verification 3 · holobiomicslab

    Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry data repository or sharing them with collaborators. Use it when specification compliance is a hard requirement (e.
    2 installs
71. ▌
    Msbackend API Implementation 2 · holobiomicslab

    Use when you need to create a new backend to integrate MS data from a novel file format, database, or in-memory storage system into the Spectra ecosystem. Use this skill when existing backends (MsBackendMemory, MsBackendMzR, MsBackendSql, etc.) do not support your data source or storage paradigm.
    2 installs
72. ▌
    Msp File Parsing And Writing 3 · holobiomicslab

    Use when you have one or more .msp spectral library files (NIST format) that need to be ingested for metadata curation, enrichment via web services, or export after transformation. Use this skill as the entry and exit point for any .msp-based annotation or analysis pipeline.
    2 installs
73. ▌
    Mzml Data Access Abstraction 3 · holobiomicslab

    Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
    0 installs
74. ▌
    Numeric List Slot Management 2 · holobiomicslab

    Use when when extending the MsBackend virtual class to create a custom backend for mass spectrometry data, and you need to store peak m/z and intensity values as variable-length numeric vectors indexed by spectrum.
    2 installs
75. ▌
    Peak Table Schema Validation 3 · holobiomicslab

    Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format. Use this skill when you need to verify that the converted file will be successfully read by LipidMatch before proceeding to lipid identification;
    0 installs
76. ▌
    Pull Request Change Tracking 3 · holobiomicslab

    Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query's two-branch workflow split) modified the codebase architecture, control flow, or data routing.
    2 installs
77. ▌
    Reference Database Screening 2 · holobiomicslab

    Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, use this skill to match those predictions against a curated reference database of known molecular embeddings.
    2 installs
78. ▌
    Repository Environment Setup 2 · holobiomicslab

    Use when when you have received a GitHub repository URL for a computational workflow (e.g., ENPKG full workflow) and need to prepare your local machine to execute the workflow.
    1 install
79. ▌
    Repository Source Code Setup 3 · holobiomicslab

    Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.
    3 installs
80. ▌
    Spectral Metadata Enrichment 3 · holobiomicslab

    Use when you have a .msp spectral library file with sparse or incomplete metadata (e.
    2 installs
81. ▌
    Spectrum Metadata Validation 2 · holobiomicslab

    Use when after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats using matchms, when you need to ensure that metadata fields (e.
    2 installs
82. ▌
    Tabular Data Standardization 2 · holobiomicslab

    Use when when you have received raw MRM lipidomics export files in vendor-specific formats (TSV, CSV) with inconsistent column naming, unparsed lipid identifiers (e.g., 'PC(36:1)' as a single string), and unknown data quality issues.
    2 installs
83. ▌
    Vendor Export Schema Mapping 2 · holobiomicslab

    Use when raw MRM lipidomics data arrives in vendor-specific export formats (e.g., Sciex, Waters, Thermo TSV/CSV) with inconsistent or proprietary column naming, numeric encoding, and lipid nomenclature.
    2 installs
84. ▌
    Module Loader Implementation 2 · holobiomicslab

    Use when you have mass spectrometry imaging data in multiple vendor or open-source formats and need to programmatically route each file to its correct processing handler based on file extension, avoiding hardcoded conditional chains and enabling extensible format support.
    2 installs
85. ▌
    Batch Generation And Validation 2 · holobiomicslab

    Use when you have raw mzML files and a feature table (CSV) from LCMS data processed by tools like mzMine, and you need to create train/test/validation batches with specific matrix dimensions (120 × 2) and verified margin/peak signal separation before training or evaluating a neural network.
    3 installs
86. ▌
    Peak Detection Targeted Metabolomics 2 · holobiomicslab

    Use when you have mass spectrometry data in .raw, .d, or mzXML format and a predefined list of target compounds (m/z and retention time ranges) you wish to quantify.
    2 installs
87. ▌
    Peak Mass Intensity Feature Encoding 2 · holobiomicslab

    Use when you have raw mass spectra (e.g., from NIST 2017 or MassBank) and need to prepare them for Word2vec embedding or other token-based neural models. Use it as a preprocessing step before training spectral embedding models, especially when scale and accuracy of spectrum matching are priorities.
    2 installs
88. ▌
    Raw Mass Spectrometry Data Ingestion 2 · holobiomicslab

    Use when you have raw mass spectrometry data in mzML, abf (Reifycs), or cdf (NetCDF) format and need to load it into MS-DIAL or a similar open-source metabolomics platform.
    2 installs
89. ▌
    Reactomics Annotation And Clustering 2 · holobiomicslab

    Use when you have a formula-assigned dataset from FT-ICR MS or other mass spectrometry with molecular formulas assigned to each mass feature, and you want to identify and quantify the molecular transformations (e.
    2 installs
90. ▌
    XML Spectrum Element Deserialization 2 · holobiomicslab

    Use when when you have retrieved a decompressed XML data block from an indexed gzip file (via GSGR bracket notation) and need to convert that raw XML string into a usable Python spectrum or chromatogram object for downstream analysis, filtering, or comparison.
    1 install
91. ▌
    Integrative Omics Pathway Enrichment 2 · holobiomicslab

    Use when you have a preprocessed peak table with statistically significant or differentially abundant metabolites (e.g., from ANCOVA or PLS/PLS-DA), and you want to move beyond individual peak-level interpretation to understand which biological pathways or metabolic networks are perturbed.
    1 install
92. ▌
    Candidate Metadata Record Serialization 2 · holobiomicslab

    Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage, sharing, and interpretation.
    1 install
93. ▌
    Dense Neural Network Layer Construction 2 · holobiomicslab

    Use when when you have a binned MS/MS spectrum vector (e.g., 9948-dimensional input from 10,000 equally-spaced m/z bins in the 10–1000 Da range) and need to compress it into a learned latent representation (e.
    2 installs
94. ▌
    Mass Spectrometry Structural Annotation 2 · holobiomicslab

    Use when after identifying statistically significant features (e.
    2 installs
95. ▌
    Mass Spectrometry Tolerance Calibration 2 · holobiomicslab

    Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
    2 installs
96. ▌
    Mass Spectrum Extraction And Formatting 3 · holobiomicslab

    Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical component prior to molecular networking, spectral matching, or metabolite identification workflows.
    0 installs
97. ▌
    Natural Products Workflow Orchestration 2 · holobiomicslab

    Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to generate a Wikidata-connected RDF knowledge graph for integrated natural products analysis, taxonomy-aware compound.
    2 installs
98. ▌
    Separation Technique Workflow Alignment 3 · holobiomicslab

    Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.
    2 installs
99. ▌
    Spectral Data Processing And Annotation 2 · holobiomicslab

    Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular features, build a molecular network from fragmentation spectra, and annotate those features using both spectral.
    1 install
100. ▌
     Aif Spectrum Fragment Database Matching 2 · holobiomicslab

     Use when you have a feature table from untargeted LC–MS all-ion fragmentation (AIF) chromatograms processed by xcms and RamClustR, and you want to assign metabolite annotations to individual features by comparing their experimental MS/MS spectra against curated fragment libraries (e.
     1 install