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HolobiomicsLab

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1. ▌
   Gc Ms Spectral Similarity Clustering 3 · holobiomicslab

   Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct a molecular network.
   0 installs
2. ▌
   Jupyter Notebook Workflow Automation 2 · holobiomicslab

   Use when when you have raw LC-MS/MS spectral data in .
   0 installs
3. ▌
   Lc Hrms Metabolomics Data Processing 2 · holobiomicslab

   Use when you have LC-HRMS raw data files (.mzML or .abf format) from metabolomics experiments and need to extract, align, and annotate features in a reproducible manner across multiple computational environments.
   0 installs
4. ▌
   Lc Ms Scan Acquisition Orchestration 2 · holobiomicslab

   Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that strategy will acquire MS1 and MS2 scans over a defined retention-time window.
   0 installs
5. ▌
   Mass Spectral Fingerprint Generation 2 · holobiomicslab

   Use when you have unaligned MS2 spectra from one or more samples (in formats like .mgf, .mzML, or .mzXML) and need to compare them in a retention-time-agnostic manner.
   0 installs
6. ▌
   Mass Spectral Metadata Harmonization 2 · holobiomicslab

   Use when you have multiple mass spectral libraries in different formats (NIST MSP + MOL folder, MoNA MSP, RIKEN MSP, SWGDRUG MSP) and need to merge them into a single, MS-DIAL-compatible MSP file with consistent SMILES assignments, Kovats retention indices (RI), and polarity annotations across all.
   0 installs
7. ▌
   Mass Spectrometry Benchmark Analysis 2 · holobiomicslab

   Use when you have implemented or modified a tandem mass spectrometry formula inference model and need to measure whether a specific architectural change (e.
   0 installs
8. ▌
   Mass Spectrometry Data Visualization 2 · holobiomicslab

   Use when after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or EicSimilarityParam). Use when you need to visually confirm that grouped features belong to the same compound—i.
   0 installs
9. ▌
   Metabolomic Feature Table Imputation 2 · holobiomicslab

   Use when after feature detection and peak alignment have produced a feature table with zero or missing values across samples.
   0 installs
10. ▌
    Metabolomics Feature Table Filtering 2 · holobiomicslab

    Use when when you have a raw LC-MS peak table imported from vendor software (e.
    0 installs
11. ▌
    Molecular Network Graph Manipulation 2 · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you need to embed substructural motif identifiers, confidence scores, or chemical class labels as node/edge attributes for.
    0 installs
12. ▌
    Prm Acquisition Event Identification 3 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is happening at regular intervals consistent with your instrument method design.
    0 installs
13. ▌
    Prominence Controlled Peak Selection 3 · holobiomicslab

    Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing prominence values and need to reduce the number of detected features while maintaining signal quality.
    0 installs
14. ▌
    Sample Centric Metabolite Annotation 2 · holobiomicslab

    Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra) and sample-level taxonomical metadata, and you want to assign both spectral identity and predicted chemical structure to.
    0 installs
15. ▌
    Simulation Control Loop Architecture 3 · holobiomicslab

    Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic window selection) would perform without access to real instrument time.
    0 installs
16. ▌
    Sirius Spectral Request Construction 2 · holobiomicslab

    Use when when you have processed LC-MS/MS data with precursor m/z, ionization mode, collision energy (if available), and fragment peak lists (m/z and intensity pairs), and need to query CSI:FingerID for molecular fingerprint predictions as part of an automated metabolite identification workflow.
    0 installs
17. ▌
    Spectral Similarity Network Building 2 · holobiomicslab

    Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical hierarchy for comparative metabolomic analysis.
    0 installs
18. ▌
    Spectrum Filtering And Normalization 2 · holobiomicslab

    Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or quantitative analysis.
    0 installs
19. ▌
    Web Application Documentation Mining 3 · holobiomicslab

    Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you need to produce a machine-readable inventory of those applications with verified live URLs and associated publications for.
    2 installs
20. ▌
    Amino Acid Level Accuracy Evaluation 2 · holobiomicslab

    Use when you have predicted peptide sequences from a de novo sequencing tool (e.g., Casanovo) and want to understand the fine-grained accuracy of the predictions beyond exact-match peptide-level scoring.
    0 installs
21. ▌
    Anova Feature Significance Filtering 2 · holobiomicslab

    Use when you have a normalized LC-MS/MS metabolite abundance matrix (e.g., from MS-DIAL preprocessing) with multiple samples across experimental groups (e.
    0 installs
22. ▌
    Asynchronous Converter Instantiation 2 · holobiomicslab

    Use when building a metadata enrichment system that must support multiple pluggable converter backends and you need to automatically discover all available converters at runtime, extract their conversion specifications, and generate Job tuples that can be dispatched to an async annotation engine.
    0 installs
23. ▌
    Centroided Peak Extraction From Hrms 2 · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA/ddMS2) mzML files from LC- or GC-HRMS measurements and need to systematically detect and characterize MS1 features across the mass-to-charge and retention-time dimensions prior to compound prioritization or suspect screening.
    0 installs
24. ▌
    Chemical Noise Tagging And Filtering 2 · holobiomicslab

    Use when you have MS/MS spectra contaminated with chemical noise (spurious fragment ions that do not correspond to real chemical bonds or rearrangements), a known or predicted molecular formula or SMILES structure for the precursor, the adduct type (e.
    0 installs
25. ▌
    Compound Isotope And Adduct Grouping 3 · holobiomicslab

    Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per compound. Use it when your data contains isotopic peaks (e.g., ¹³C variants) and multiple ionization products (e.
    0 installs
26. ▌
    Container Image Build And Deployment 2 · holobiomicslab

    Use when you have a Dockerfile and source repository for a bioinformatics tool (e.g., CloMet) and need to verify that the tool can be containerized, deployed, and made executable in an isolated environment.
    0 installs
27. ▌
    Coverage Accuracy Metric Computation 2 · holobiomicslab

    Use when you have two sets of lipid annotations—one from baseline spectral library matching and one from an enhanced method (e.
    0 installs
28. ▌
    Docker Container Health Verification 2 · holobiomicslab

    Use when when you have deployed NP Classifier using Docker Compose and need to confirm that both the server and TensorFlow Serving containers are running and healthy before sending SMILES strings to the /classify endpoint.
    0 installs
29. ▌
    Fragment Peak Subformula Enumeration 2 · holobiomicslab

    Use when you have a list of fragment peak m/z values and intensities from tandem MS/MS data and need to assign chemical subformulae to each peak for downstream formula ranking or structure inference.
    0 installs
30. ▌
    Graph Neural Network Model Inference 2 · holobiomicslab

    Use when you have a trained GNN model (stored as .h5 weights) and molecular graph representations (SMILES strings and/or 3D coordinates), and you need to compute predicted CCS values or perform feature importance analysis via ablation or gradient-based saliency mapping.
    0 installs
31. ▌
    Interactive Plot Customization Bokeh 2 · holobiomicslab

    Use when when you have loaded extracted ion chromatogram traces (via SqMassLoader from sqMass files) and need to render them as interactive web-based visualizations where users can pan, zoom, hover for metadata, mute individual traces, and optionally visualize peak boundaries from OpenSwath results.
    0 installs
32. ▌
    Isotope Labeling Data Interpretation 2 · holobiomicslab

    Use when you have LC-MS FAM measurements from an isotope-labeling experiment and need to correct them to obtain true MDV values.
    0 installs
33. ▌
    Mass Difference Network Construction 4 · holobiomicslab

    Use when you have a preprocessed peak list (m/z values and assigned molecular formulas) from direct injection FT-ICR MS of a complex organic mixture (e.
    0 installs
34. ▌
    Mass Distribution Vector Calculation 2 · holobiomicslab

    Use when you have raw LC-MS fractional abundances (FAM) data from isotope labeling experiments and need to obtain true mass distribution vectors (MDV) that represent only the isotopic labeling contribution.
    0 installs
35. ▌
    Mass Spectrometry Feature Annotation 2 · holobiomicslab

    Use when when you have peak-detected LC-MS/MS data (MGF files with MS1 and MS2 spectra, plus a feature abundance table from MZmine2) and need to assign chemical structures and molecular properties to individual MS1 features rather than relying on mass-to-charge alone.
    0 installs
36. ▌
    Mass Spectrometry Feature Clustering 2 · holobiomicslab

    Use when after XCMS feature detection and alignment when you have a CSV-formatted feature table with m/z and retention time annotations and want to deduplicate isotopic peaks, adducts, and in-source fragments into compound-level clusters before molecular weight inference or spectral matching.
    0 installs
37. ▌
    Mass Spectrometry Peak Pair Analysis 2 · holobiomicslab

    Use when you have preprocessed MSI data (as a CSV intensity matrix or Cardinal MSProcessedImagingExperiment object) and suspect that observed peaks include both parent ions and their adducts formed with matrix or salt species.
    0 installs
38. ▌
    Metabolite Stoichiometry Computation 2 · holobiomicslab

    Use when when you have quantified intracellular metabolite abundances (LC-MS normalized values) for multiple cell lines or samples, a metabolic network model with reaction stoichiometry, and you need to predict how substrate availability translates into metabolic flux differences.
    0 installs
39. ▌
    Metadata Transformation Verification 2 · holobiomicslab

    Use when you have extracted raw tabular metadata into JSON form using the MESSES extract command and need to confirm the extraction is accurate before conversion to a repository-specific format. Specifically, use it when the conversion target format has strict schema requirements (e.
    0 installs
40. ▌
    Molecular Network Feature Annotation 2 · holobiomicslab

    Use when when you have both (1) a molecular network graph from GNPS with MS/MS feature nodes and edges, and (2) a quantitative bioassay matrix (fractions × bioactivity measurements) from parallel LC-MS/MS fractionation of the same sample extract.
    0 installs
41. ▌
    Molecular Network Graph Construction 2 · holobiomicslab

    Use when after completing dereplication and cosine similarity clustering in the MolNotator pipeline, when you have merged deduplicated molecular predictions and ion annotations and need to construct the final network representation for visualization and compound identification.
    0 installs
42. ▌
    Ms1 Feature Detection And Annotation 3 · holobiomicslab

    Use when you have FIA-MS, LC-MS, or GC-MS full-scan data in mzML format and need to identify unknown molecular features by accurate mass.
    0 installs
43. ▌
    Nmr Chemical Shift Interval Matching 3 · holobiomicslab

    Use when you have isolated one or more regions-of-interest (ROIs) from a proton NMR spectrum (defined as lower and upper chemical-shift bounds in ppm) and need to systematically generate a list of plausible metabolite assignments from a reference database.
    0 installs
44. ▌
    Score Distribution Visualization 2 · holobiomicslab

    Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient separation between validated links and the background population.
    0 installs
45. ▌
    Spectral Intensity Normalisation 2 · holobiomicslab

    Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
    0 installs
46. ▌
    Web Application Endpoint Mapping 2 · holobiomicslab

    Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that spectrum to the appropriate domain-specific MASST application for searching.
    0 installs
47. ▌
    Annotation Confidence Assessment 3 · holobiomicslab

    Use when after MS-FINDER in silico annotation has been executed on exported LC-MS features and multiple database matches (with HRR scores) have been returned.
    0 installs
48. ▌
    Batch Effect Correction Workflow 2 · holobiomicslab

    Use when you have a feature table generated from LC-MS/MS non-targeted metabolomics data that spans multiple sample preparation batches, instrumental runs, or experimental conditions.
    0 installs
49. ▌
    Batch Effect Matrix Construction 2 · holobiomicslab

    Use when when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods. Use this skill when: (1) you want reproducible, ground-truth batch effects overlaid on condition-only variation;
    0 installs
50. ▌
    Bit Vector Substructure Encoding 2 · holobiomicslab

    Use when you need to represent natural product molecules as fixed-length bit vectors for downstream machine learning (e.
    0 installs
51. ▌
    Ce Ms Migration Time Measurement 2 · holobiomicslab

    Use when when processing raw CE-MS data and need to establish a baseline migration time scale before transforming to effective mobility.
    0 installs
52. ▌
    Centered Log Ratio Normalization 2 · holobiomicslab

    Use when apply CLR normalization when you have count-based microbiome or metabolome compositional data (e.g., 16S rRNA gene abundances, LC-MS/MS metabolite abundances) that will be used as input to multivariate predictive models (neural networks, regression, correlation analysis).
    0 installs
53. ▌
    Chemical Mass Tolerance Matching 3 · holobiomicslab

    Use when when you have a metabolomics peak list (m/z values with optional retention times) from LC-MS or GC-MS and want to filter a computationally expanded chemical library to only compounds whose calculated masses (accounting for ionization adducts) fall within a defined tolerance of observed.
    2 installs
54. ▌
    Cheminformatics Library Querying 2 · holobiomicslab

    Use when you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to assess which library compounds are structurally similar to your queries, retrieve their categorical annotations (e.
    0 installs
55. ▌
    Chromatographic Alignment Tuning 2 · holobiomicslab

    Use when when processing a cohort of centroided mzML LC-MS files with high sample-to-sample retention time and m/z drift, and you need reproducible alignment of detected peaks across all samples before gap-filling and feature consolidation.
    0 installs
56. ▌
    Cross Sample Metabolite Matching 2 · holobiomicslab

    Use when after feature extraction (MS1 peak picking, MS2 recognition, or targeted list extraction) from multiple individual samples and before annotation.
    0 installs
57. ▌
    Data Format Conformance Checking 2 · holobiomicslab

    Use when you have retrieved a complete set of project JSON documents from a data platform and need to verify that each document's structure, field types, and required properties match a canonical JSON Schema definition (e.g., app/public/schema.json).
    0 installs
58. ▌
    Database Accessor Initialization 2 · holobiomicslab

    Use when a Python module declares optional/conditional dependencies (e.g., sqlalchemy for database access) and you need to confirm that the module can be imported and instantiated without exceptions when those dependencies are present in the environment.
    0 installs
59. ▌
    Deep Learning Feature Extraction 2 · holobiomicslab

    Use when you have preprocessed and normalized LC-MS metabolomics data from multiple disease groups (e.g., healthy, disease-A, disease-B) and need to identify which m/z features or their patterns discriminate between phenotypes.
    0 installs
60. ▌
    Descriptor Subgroup Partitioning 2 · holobiomicslab

    Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which descriptor categories (e.g., molecular weight, lipophilicity, topological, pharmacophoric) drive prediction decisions.
    0 installs
61. ▌
    False Positive Mitigation Tuning 2 · holobiomicslab

    Use when after running Paramounter's peak-height optimization on XCMS CentWave-extracted metabolomic features, if the downstream analysis or feature validation reveals an unacceptable rate of false positives, or if the extraction workflow is experiencing software crashes or timeout failures due to.
    0 installs
62. ▌
    Feature Node Identifier Matching 2 · holobiomicslab

    Use when you have created a feature-based GNPS molecular network and a corresponding MS2LDA experiment, and you need to propagate substructural motif annotations from the MS2LDA output back to the network nodes by matching feature IDs.
    0 installs
63. ▌
    Fragment Ion Scoring And Ranking 2 · holobiomicslab

    Use when when you have an experimental MS/MS spectrum (centroid mode) and need to convert it into a scored fragment library entry, or when you must rank candidate fragments by confidence before performing spectrum-to-spectrum matching in metabolite annotation workflows.
    0 installs
64. ▌
    Genomic Metabolomic Link Ranking 2 · holobiomicslab

    Use when you have paired genomic (BGCs clustered into GCFs via BiG-SCAPE) and metabolomic data (MS2 spectra grouped into MFs), with strain/sample co-occurrence patterns and predicted BGC–spectrum IOKR scores, and you need to prioritise which GCF–MF pairs are most likely to represent true natural.
    0 installs
65. ▌
    Ion Filter Status Categorization 2 · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a peak table, when you need to quantify how many ions passed or failed each filter and summarize the overall filtering impact by status distribution.
    2 installs
66. ▌
    Ion Mobility Dimension Detection 3 · holobiomicslab

    Use when when processing raw mass spectrometry data files of unknown or mixed provenance, and you need to automatically route IMS inputs to their corresponding analysis pipeline.
    0 installs
67. ▌
    Lcms Feature Probability Scoring 2 · holobiomicslab

    Use when you have an untargeted LC/MS feature table (m/z, retention time, intensity columns) and need to move beyond single-hit matching to probabilistic annotation.
    0 installs
68. ▌
    Lipid Species Abundance Counting 2 · holobiomicslab

    Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type categories present.
    0 installs
69. ▌
    Mahalanobis Distance Calculation 2 · holobiomicslab

    Use when after data normalization (Box-Cox transformation) and before hypothesis testing in Step 9 of untargeted metabolomic workflows.
    0 installs
70. ▌
    Mass Action Kinetics Formulation 2 · holobiomicslab

    Use when you have intracellular metabolomics concentration measurements across multiple cell lines or conditions, a stoichiometric metabolic network model with reaction-metabolite associations, and you need to predict how differences in substrate availability (independent of enzyme expression).
    0 installs
71. ▌
    Mass Spectral Network Annotation 3 · holobiomicslab

    Use when you have a GNPS molecular network (classical or feature-based) and MS2LDA LDA experiment output (Mass2Motif assignments with probability and overlap scores) from the same experiment, and you want to annotate network nodes with structural motifs and chemical classes to infer molecular.
    0 installs
72. ▌
    Mass Spectrometry Data Alignment 3 · holobiomicslab

    Use when you have two LC-MS feature tables (each containing m/z, retention time, and intensity columns) from the same or related biological samples and need to identify which features in dataset A correspond to which features in dataset B.
    0 installs
73. ▌
    Mass Spectrum Similarity Scoring 2 · holobiomicslab

    Use when when you have a query MS/MS spectrum (m/z and intensity pairs) that you need to match against a library of reference spectra, and you want to identify the -matching library entry while accounting for unmatched peaks that may indicate spectral contamination or chimerism.
    4 installs
74. ▌
    Mass Tolerance Optimization Hrms 2 · holobiomicslab

    Use when you have experimental peak lists (m/z, retention time, intensity) from peak-picking software (MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to match them against a simulated lipid fragment library (500,000+ lipid species).
    0 installs
75. ▌
    Match Factor Threshold Filtering 2 · holobiomicslab

    Use when you have a GC-MS dataset with Match.Factor scores for each detected compound (output from Agilent Unknowns Analysis or equivalent), and you want to reduce the number of query chemicals passed to computationally intensive cheminformatics functions (categorate, mzExacto, or exactoThese).
    0 installs
76. ▌
    Metabolite Database Construction 2 · holobiomicslab

    Use when when performing untargeted metabolomics annotation at scale and you need to estimate false discovery rates for candidate metabolite identifications.
    0 installs
77. ▌
    Metabolite Feature Normalization 2 · holobiomicslab

    Use when you have loaded two or more nontargeted LCMS feature tables from the same analytical method that contain m/z, retention time, and intensity values, and these datasets exhibit differences in metadata scale, distribution, or format that could confound cross-dataset feature matching or.
    0 installs
78. ▌
    Metabolite Identifier Conversion 2 · holobiomicslab

    Use when your metabolomics dataset contains metabolite identifiers in multiple formats (e.
    0 installs
79. ▌
    Metabolomics Data Representation 3 · holobiomicslab

    Use when you have a raw MGF file containing fragmented LC-MS-MS metabolomics spectra and want to apply Latent Dirichlet Allocation (LDA) to discover hidden topics (molecular families, biochemical patterns) across your sample set.
    0 installs
80. ▌
    Missing Value Imputation With Na 2 · holobiomicslab

    Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which ones are explicitly stored in your backend.
    0 installs
81. ▌
    Model Metadata Schema Inspection 2 · holobiomicslab

    Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names and schema, especially before implementing or updating code that constructs JSON payloads for the /api/smart3/search.
    0 installs
82. ▌
    Molecular Connectivity Inference 2 · holobiomicslab

    Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its molecular formula and connectivity graph.
    0 installs
83. ▌
    Molecular Descriptor Calculation 2 · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
    0 installs
84. ▌
    Molecular Fingerprint Prediction 2 · holobiomicslab

    Use when you have tandem MS/MS spectra paired with known molecular structures (for training) or unknown spectra requiring structure identification, and you want to predict dense molecular fingerprint vectors that encode structural similarity.
    0 installs
85. ▌
    Molecular Similarity Calculation 2 · holobiomicslab

    Use when you have two or more molecular structures (represented as SMILES or spectral data) and need to rank transformation product candidates by structural plausibility, filter isomeric or duplicate TP predictions, or group features into components based on chemical relatedness.
    0 installs
86. ▌
    Ms Peak Blank Signal Subtraction 2 · holobiomicslab

    Use when you have an MS-DIAL feature table from DDA or DIA LC-MS analysis that includes blank injection samples (at least 3 recommended), and you need to eliminate features that are artifactual contamination rather than genuine metabolites.
    0 installs
87. ▌
    Ms Spectra Dataset Preprocessing 2 · holobiomicslab

    Use when when you have a raw or partially processed MS/MS spectra collection (e.g., GNPS-sourced Orbitrap or Q-TOF spectra in MGF format) and need to (1) restrict to a specific instrument type (e.
    0 installs
88. ▌
    Ms2 Fragment Pattern Recognition 2 · holobiomicslab

    Use when you have data-dependent acquisition (DDA) MS2 spectra from HRMS measurements (ESI or APCI ionization) and need to prioritize potential PFAS features from a large pool of detected ions.
    0 installs
89. ▌
    Network Diffusion Prioritization 2 · holobiomicslab

    Use when after clustering and filtering KEGG candidates for LC-MS features, when you have a ranked set of candidate metabolites per feature and access to a metabolite interaction network (e.g., from FELLA).
    0 installs
90. ▌
    Neural Network Weight Extraction 2 · holobiomicslab

    Use when you have trained MLPNN models on paired microbiome-metabolome data (via 10-fold cross-validation repeated across multiple iterations) and need to derive interpretable microbe-metabolite interaction scores rather than treating the network as a black box.
    0 installs
91. ▌
    Numerical Method Scheme Analysis 2 · holobiomicslab

    Use when when correcting LC-MS isotope labeling data and existing numerical schemes (e.
    0 installs
92. ▌
    Peak Detection Mass Spectrometry 2 · holobiomicslab

    Use when you have raw mass-spectrometry data files (mzML, mzXML, or vendor formats) from untargeted metabolomics experiments and need to extract differential metabolic ion peaks for downstream statistical or annotation analysis.
    0 installs
93. ▌
    Peak Detection Signal Processing 2 · holobiomicslab

    Use when after feature extraction from mzML/mzXML breath analysis data when you have a numerical array or dataframe of feature intensities across retention time or m/z dimensions and need to identify which features represent genuine volatile organic compound (VOC) signals rather than noise or.
    0 installs
94. ▌
    Peak List Parsing And Validation 2 · holobiomicslab

    Use when when importing raw mass spectrometry data from vendor or open formats (mzML, mzXML, msp, MGF, JSON, metabolomics-USI) and you need to extract peak m/z and intensity pairs into a standardized representation.
    0 installs
95. ▌
    Peak Matching And Mass Alignment 2 · holobiomicslab

    Use when when you have raw MS2 spectra (m/z and intensity pairs) and a curated reference peak list from a large training dataset (e.
    0 installs
96. ▌
    Peak Picking Algorithm Selection 2 · holobiomicslab

    Use when at the entry point of SLAW processing when you have centroided mzML or netCDF LC-MS files and need to decide which peak-picking algorithm to use. Trigger this skill when: (1) raw LC-MS data must be converted into a feature matrix;
    0 installs
97. ▌
    Python Environment Configuration 2 · holobiomicslab

    Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
    0 installs
98. ▌
    Ranked Annotation Prioritization 2 · holobiomicslab

    Use when you have completed cluster-based filtering of KEGG candidate assignments in untargeted LC-MS metabolomics and need to rank those candidates by biological plausibility using a metabolite interaction network. Specifically, use it after `clusterBased.
    0 installs
99. ▌
    Reference Semantics Verification 2 · holobiomicslab

    Use when when applying sequential filters to a large metabolomics peak table (e.g., mispicked ions, group, CV, or in-source filters) and you need to confirm that setting copy_object=FALSE actually modifies the input object in-place rather than creating a hidden copy.
    0 installs
100. ▌
     Relative Abundance Preprocessing 2 · holobiomicslab

     Use when when you have raw count tables from 16S rRNA sequencing (microbiome) or LC-MS/MS metabolomics (metabolome) and need to train neural network or regression models for microbe-metabolite relationship prediction.
     0 installs