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HolobiomicsLab

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1. ▌
   Annotation Confidence Scoring 2 · holobiomicslab

   Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final annotated metabolite identities.
   2 installs
2. ▌
   Binary Additive Flag Encoding 2 · holobiomicslab

   Use when constructing HPLC column feature vectors from raw metadata that includes additive composition flags (e.g., presence/absence or concentration of formic acid, acetic acid, TFA, or phosphoric acid in mobile phase eluents A and B).
   0 installs
3. ▌
   Cosine Similarity Computation 2 · holobiomicslab

   Use when when comparing two MS/MS spectra (query and reference) to quantify their spectral resemblance for compound identification or molecular networking, particularly when you need a simple, symmetric measure that is insensitive to precursor mass differences and does not require peak alignment.
   0 installs
4. ▌
   Cross View Similarity Scoring 2 · holobiomicslab

   Use when you have an experimental mass spectrum (query) and a set of molecular candidate structures, and you need to rank the candidates by how well their predicted spectral features match the query spectrum.
   0 installs
5. ▌
   Database Metadata Enumeration 2 · holobiomicslab

   Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) and need to verify the reported counts of unique entities (source databases, organisms, structures, and their pairs) to confirm dataset integrity, assess data coverage, or reproduce published statistics in a.
   0 installs
6. ▌
   Dda Acquisition Data Handling 2 · holobiomicslab

   Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators) to serve as input to the DNMS2Purifier customized model training workflow, or to prepare data for purification of.
   0 installs
7. ▌
   Decision Tree Path Extraction 2 · holobiomicslab

   Use when you have a trained shallow decision tree on ChemEcho feature vectors (sparse, high-dimensional representations of tandem mass spectra peaks and neutral losses) and need to convert it into an interpretable, deployable query for a domain-specific language like MassQL.
   0 installs
8. ▌
   Deep Learning Model Inference 2 · holobiomicslab

   Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to classify unknown compounds or generate prediction confidence scores for structural novelty analysis.
   0 installs
9. ▌
   Eic Data Extraction From Xcms 2 · holobiomicslab

   Use when after running XCMS getEIC() to generate xcmsEIC objects and fillPeaks() to produce a filled xcmsSet object, before computing the 12 peak-quality metrics (Apex Max-Boundary Ratio, Elution Shift, FWHM2Base, Jaggedness, Modality, Symmetry, Sharpness, Gaussian Similarity, Retention-Time.
   0 installs
10. ▌
    Feature Identifier Assignment 2 · holobiomicslab

    Use when after constructing MetaboSet objects from Excel-formatted LC-MS peak tables and before drift correction or quality flagging.
    0 installs
11. ▌
    Flat File Parsing And Loading 2 · holobiomicslab

    Use when when you have published LOTUS flat files (TSV or compressed TSV.GZ) containing structure-organism pairs and need to enumerate unique structures, group by organism prevalence, or validate record counts against gold-standard benchmarks.
    2 installs
12. ▌
    Fragment Ion Mass Calibration 2 · holobiomicslab

    Use when when comparing experimental spectra to reference library spectra and fragment ion m/z values show systematic drift or measurement noise that could distort neutral loss peaks or cosine similarity scores.
    0 installs
13. ▌
    Gradient Performance Encoding 2 · holobiomicslab

    Use when when you have extracted retention times from the top detected MS1 features in a LC-MS run and need to evaluate whether the gradient spreads those compounds efficiently across the available chromatographic time window—particularly during iterative gradient optimization where you need a.
    0 installs
14. ▌
    In Silico Fragment Prediction 2 · holobiomicslab

    Use when you have a collection of compound structures in SDF format (e.g., DNA adduct structures) and need to systematically generate predicted fragment spectra across a defined ionization level and mass range to populate a reference spectral database or validate experimental fragmentation patterns.
    0 installs
15. ▌
    Ion Image Augmentation Design 2 · holobiomicslab

    Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that reflect either co-localization relationships between different molecular ions (COL mode) or isotopic relationships.
    0 installs
16. ▌
    Lc Ms Feature Quality Scoring 2 · holobiomicslab

    Use when immediately after peak detection and feature table generation from LC-MS data, when you need to rank or filter features by confidence before annotation or statistical analysis.
    0 installs
17. ▌
    Metabolite Annotation Scoring 2 · holobiomicslab

    Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) from MS/MS spectra or external tools (SIRIUS, GNPS), sample metadata linking samples to organisms, and you need to prioritize candidates by both annotation quality AND biological.
    0 installs
18. ▌
    Metaboset Object Manipulation 2 · holobiomicslab

    Use when when you have read LC-MS peak table data from Excel (or equivalent) into R and need to organize it into a structured object that tracks feature abundances, sample information (injection order, QC status), and feature metadata (mass, retention time, Feature_ID) simultaneously.
    0 installs
19. ▌
    Molecular Formula Calculation 2 · holobiomicslab

    Use when you have user-specified lipid class constraints (e.
    0 installs
20. ▌
    Ms2 Annotation Interpretation 2 · holobiomicslab

    Use when after GNPS spectral library search has returned matched chemical annotations (with m/z values and cosine similarity scores) for MS/MS spectra.
    0 installs
21. ▌
    Multi Platform Ms Integration 2 · holobiomicslab

    Use when you have untargeted metabolomics data from multiple MS instruments (e.
    0 installs
22. ▌
    Mzml File Parsing And Loading 2 · holobiomicslab

    Use when when you have centroided mzML format LC–MS files from multiple runs (e.
    2 installs
23. ▌
    Neural Network Model Training 2 · holobiomicslab

    Use when you have downloaded LC-MS spectral peak data (DOI 10.25345/C5FD2F or equivalent) and need to build a supervised deep neural network classifier to distinguish peak classes in mass spectrometry data.
    0 installs
24. ▌
    Nps Classification Prediction 3 · holobiomicslab

    Use when you have an unknown mass spectrum from a suspicious analyte and need to determine whether it matches a known NPS or a derivative thereof. The analyte's mass spectrum is available in MSP or equivalent format, and you have a core drug structure to enumerate derivatives from.
    0 installs
25. ▌
    Pre Trained Model Fine Tuning 2 · holobiomicslab

    Use when you have a small training dataset for molecular property prediction (e.g., <500 samples from PredRet or MoNA databases) and a pre-trained GNN model is available that was trained on a related, larger molecular corpus.
    0 installs
26. ▌
    Precursor M Z Based Filtering 2 · holobiomicslab

    Use when you have an unknown MS/MS query spectrum with a known or measured precursor m/z value and need to search a spectral library (local or public: GNPS, MASSBANK, DrugBANK) to annotate the compound.
    0 installs
27. ▌
    Qc Sample Type Classification 2 · holobiomicslab

    Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization steps.
    0 installs
28. ▌
    Quality Metrics Summarization 2 · holobiomicslab

    Use when after running QC analysis on NMR or MS metabolomic data and obtaining per-feature CV values, use this skill to validate that the dataset meets FDA thresholds (CV < 0.30 for discovery, CV < 0.15 for quantification) and to report the proportion of features meeting each threshold.
    2 installs
29. ▌
    Raw Ms Data Format Conversion 2 · holobiomicslab

    Use when you have raw UPLC-HRMS data from ThermoFisher or Agilent instruments and need to feed it into MSThunder for nontargeted pollutant identification. Your input is a vendor binary format (.raw or .d) that MSThunder cannot directly ingest. Environment constraints (e.
    0 installs
30. ▌
    Smiles Canonicalization Rdkit 2 · holobiomicslab

    Use when when processing raw SMILES strings from external databases or user input that may contain non-canonical tautomeric forms, variable stereochemical notation, or redundant representations of the same chemical structure.
    1 install
31. ▌
    Smiles Parsing And Validation 2 · holobiomicslab

    Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing descriptors, generating mass spectra, or calculating chemical fingerprints.
    0 installs
32. ▌
    Spectral Embedding Generation 2 · holobiomicslab

    Use when you have a collection of pre-processed MS/MS spectra (binned, intensity-normalized) and a trained MS2DeepScore base network, and you need to compute structural similarity scores between spectrum pairs or visualize spectra in chemical space via dimensionality reduction (e.g., UMAP).
    0 installs
33. ▌
    Tensor Encoding Deep Learning 2 · holobiomicslab

    Use when when you have validated SMILES strings or RDKit molecule objects representing chemical structures and need to feed them into a pre-trained deep learning model (such as PS2MS, NEIMS, or DeepEI) that expects fixed-size numerical tensor inputs.
    0 installs
34. ▌
    C Python Interface Wrapping 2 · holobiomicslab

    Use when you have a mature C++ library (like OpenMS) with stable APIs that you want to make accessible from Python environments, and you need to preserve performance-critical C++ execution while supporting rapid prototyping or integration into Python-based data pipelines (e.
    0 installs
35. ▌
    Dna Adduct Characterization 2 · holobiomicslab

    Use when when you have a collection of DNA adduct compound structures in SDF format that requires validation for structural integrity and completeness, and you need to generate predicted fragment spectra at defined ionization levels and mass ranges for comparison against experimental mass.
    0 installs
36. ▌
    Local Maxima Identification 2 · holobiomicslab

    Use when you have raw LC-HRMS profile-mode data and need to identify candidate chromatographic peaks before classification or feature extraction.
    2 installs
37. ▌
    Openms API Surface Exposure 2 · holobiomicslab

    Use when when you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported and instantiated without errors in a Python environment.
    0 installs
38. ▌
    Runtime Comparison Analysis 2 · holobiomicslab

    Use when when a new version or variant of a tool claims performance improvements over a prior version (e.g., MASST+ vs. MASST), and you need empirical evidence that the claimed speedup (e.g., ~100-fold reduction in search time) is real, reproducible, and quantifiable.
    0 installs
39. ▌
    Schema Conformance Checking 2 · holobiomicslab

    Use when you have a collection of records in a standardized format (e.g., MassBank plain-text or structured records) that must be validated before commit or publication.
    0 installs
40. ▌
    Semantic Metabolite Ranking 2 · holobiomicslab

    Use when you have an unknown metabolite with unknown mass spectrum and need to prioritize structural candidates from databases (PubChem, HMDB) by their likelihood of being the true compound.
    0 installs
41. ▌
    Contrastive Pair Generation 2 · holobiomicslab

    Use when you have raw ion images from MSI data and need to train a contrastive encoder to learn stable, mode-specific representations.
    0 installs
42. ▌
    Ppm Mass Accuracy Filtering 2 · holobiomicslab

    Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes. Apply this skill after importing the .imzML metadata and .
    0 installs
43. ▌
    Mass Spectrometry Data Parsing 2 · holobiomicslab

    Use when you have raw mass spectrometry files in standard formats (mzML, mzXML, msp, MGF, JSON) and need to extract precursor m/z values, fragment peaks, neutral losses, retention times, and compound metadata into a structured, queryable spectrum object representation before performing MS/MS.
    0 installs
44. ▌
    4d Lcimmsms Feature Extraction 2 · holobiomicslab

    Use when you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values against a quantum chemistry calculation-assisted CCS prediction database.
    2 installs
45. ▌
    Artifact Checksum Verification 2 · holobiomicslab

    Use when when reproducing a prior software release (especially one generated by automated versioning tools like Semantic Release), you need to confirm that the artifacts produced in your environment match the original release byte-for-byte.
    0 installs
46. ▌
    Attention Mechanism Validation 2 · 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.
    0 installs
47. ▌
    Automated Lipid Identification 2 · holobiomicslab

    Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
    0 installs
48. ▌
    Compound Ground Truth Matching 2 · holobiomicslab

    Use when when you have pre-computed embeddings for query and reference MS/MS spectra, computed their cosine similarity matrix, and need to measure retrieval success by verifying whether the correct compound (identified by SMILES string) appears in the top-1, top-5, or top-10 ranked candidates from.
    0 installs
49. ▌
    Cross Split Metric Aggregation 2 · holobiomicslab

    Use when when you have a pre-trained model and need to report stable, generalizable performance on a fixed training set with multiple held-out test splits. Specifically: when you have 10 (or n) random query/reference splits on the same dataset (e.
    2 installs
50. ▌
    Docker Container Orchestration 2 · holobiomicslab

    Use when your analysis requires msconvert or another ProteoWizard tool on macOS, but native installation is infeasible or licensing-restricted. You need to convert vendor raw mass spectrometry files (.raw) to the open mzML format without installing ProteoWizard directly on your system.
    0 installs
51. ▌
    Feature Group Adduct Detection 2 · holobiomicslab

    Use when you have a feature table from LC-MS analysis (containing m/z, retention time, and intensity values) and need to identify which detected features represent the same molecular species ionized under different adduction states.
    0 installs
52. ▌
    File Format Robustness Testing 2 · holobiomicslab

    Use when when processing MS spectral data from multiple open mass spectra libraries (OMSLs) in mixed formats (MSP, MGF, JSON, CSV), especially when source data exhibits missing fields, malformed entries, inconsistent adduct representations, or non-standard format variants that may cause silent.
    2 installs
53. ▌
    Frequency Distribution Binning 2 · holobiomicslab

    Use when you have loaded a table of entity–attribute pairs (e.
    2 installs
54. ▌
    Gaussian Peak Shape Evaluation 2 · holobiomicslab

    Use when after peak detection on a composite mass track has identified candidate peaks in a mass chromatogram, and before compiling the final feature table.
    2 installs
55. ▌
    HTTP Connectivity Verification 2 · holobiomicslab

    Use when you need to confirm that a documented web service URL is live and reachable before attempting to submit analysis jobs, download results, or integrate the service into an automated pipeline. Use it as a prerequisite check when the service documentation claims academic or public availability.
    2 installs
56. ▌
    Imputation Algorithm Selection 2 · holobiomicslab

    Use when you have a metabolomics dataset with left-censored missing values (e.g., below limit of quantification in LC/MS or GC/MS) and need to evaluate multiple imputation approaches.
    0 installs
57. ▌
    Interpretable Machine Learning 2 · holobiomicslab

    Use when when you have tandem mass spectra data and need to predict a binary molecular property (e.g., presence of a functional group like a sulfo group) while maintaining full interpretability of the model's decision logic.
    0 installs
58. ▌
    Mass Spectral Feature Grouping 2 · holobiomicslab

    Use when you have untargeted metabolomics MS/MS spectra from multiple features and need to identify which features belong to the same molecular family or are related by biotransformation.
    0 installs
59. ▌
    Mass Spectrometry Data Parsing 3 · holobiomicslab

    Use when you have received raw or vendor-converted centroid mzML files from LC-MS, GC-MS, or DI-MS platforms and need to extract MS1 spectra before building mass tracks, performing peak detection, or constructing composite feature maps.
    0 installs
60. ▌
    Metabolights Dataset Retrieval 2 · holobiomicslab

    Use when you have a MetaboLights dataset identifier (e.g., MTBLS1124) and need to download a specific mzML file (e.g., QC07.mzML) from the public repository for visualization, quality control assessment, or integration into a metabolomics workflow. The USI format mzspec:MTBLS1124:QC07.
    0 installs
61. ▌
    Mnar Data Handling 2 · holobiomicslab

    Use when you have metabolomics data (targeted LC/MS or untargeted GC/MS) with left-censored missing values below the limit of quantification (LOQ) or limit of detection (LOD), and you need to impute these values while preserving the underlying distributional structure and avoiding bias from.
    1 install
62. ▌
    Mzml Mzxml Parsing 2 · holobiomicslab

    Use when you have raw LC-MS/MS data in mzML or mzXML format and need to isolate specific MS1/MS2 scan pairs for a targeted compound list or for building a local spectral library.
    0 installs
63. ▌
    Usi String Parsing 2 · holobiomicslab

    Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/Yao_Streptomyces/roseosporus/0518_s_BuOH.
    0 installs
64. ▌
    R Package API Usage 2 · holobiomicslab

    Use when you have tabular metabolomics data (tab-delimited or Sciex OS format) and need to apply a specialized R package's analysis pipeline—such as mzQuality—that requires sequential function calls (readData → buildExperiment → doAnalysis) to construct, validate, and transform experiment objects.
    0 installs
65. ▌
    Evidence Linking 2 · holobiomicslab

    Use when when evaluating a scientific manuscript that describes a computational analysis (e.g., a normalization or transformation pipeline), use this skill to trace each claimed finding to its source code, data, or prior publication.
    0 installs
66. ▌
    Peak List Formatting 2 · holobiomicslab

    Use when after successfully resolving a USI string to a specific mass spectrum scan, and before performing spectral matching, library search, or comparative analysis.
    0 installs
67. ▌
    Status Value Parsing 2 · holobiomicslab

    Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.
    0 installs
68. ▌
    JSON Response Parsing 2 · holobiomicslab

    Use when when querying a TensorFlow Serving metadata endpoint or similar REST API that returns JSON-formatted model metadata, and you need to programmatically extract and validate input/output layer names against known specifications (e.
    0 installs
69. ▌
    Ion Mobility Calibration Curve Fitting · holobiomicslab

    Use when you have TWIM-MS experimental data with arrival times and m/z values, and access to calibrant reference standards with known CCS values (typically loaded from a calibration template).
    0 installs
70. ▌
    Ion Mobility Machine Learning Training · holobiomicslab

    Use when you have a curated dataset of molecular structures (or molecular descriptors) paired with experimentally measured or reference collision cross section values, and you need to predict CCS values for a set of ≤10,000 novel molecules to filter or prioritize metabolomics identifications.
    0 installs
71. ▌
    Isotope Pattern Matching And Filtering · holobiomicslab

    Use when you have high-resolution centroided mzML files from Orbitrap or similar instruments, a target compound list with known formulas and monoisotopic m/z values, and need to quantify isotopologue abundances (M+0, M+1, M+2, etc.) for stable isotope labeling experiments.
    0 installs
72. ▌
    JSON Serialization Of Query Structures · holobiomicslab

    Use when you have parsed a MassQL query string into an AST representation and need to store, validate, transmit, or integrate the query structure with other tools or systems.
    0 installs
73. ▌
    Latent Group Discovery From Omics Data · holobiomicslab

    Use when you have a preprocessed metabolomics feature matrix and sample metadata but suspect hidden substructures or unknown groupings that are not explained by known experimental conditions.
    0 installs
74. ▌
    Lipid Abundance Statistical Comparison · holobiomicslab

    Use when after lipid matching is complete and you have a table of normalized lipid abundances aligned across samples, grouped into distinct experimental conditions or phenotypic categories (e.g., diseased vs. control, treated vs. untreated).
    0 installs
75. ▌
    Lipid Expression Pattern Visualization · holobiomicslab

    Use when after statistical analysis of lipid abundance data has produced a table of lipid identities, expression measurements, p-values, fold-changes, and condition labels.
    0 installs
76. ▌
    Local Sequence Availability Assessment · holobiomicslab

    Use when you need to determine which sequence files in a repository like MIBiG are unique to that resource and not mirrored in NCBI public databases.
    0 installs
77. ▌
    M Z Value Clustering Mass Spectrometry · holobiomicslab

    Use when processing extracted peak lists from MSI data and you need to annotate matrix-related signals but suspect that multiple ions with the same or very similar m/z values (isobaric ions) are present.
    0 installs
78. ▌
    Machine Learning Regulatory Prediction · holobiomicslab

    Use when you have matched multiomics data (CNV, mutations, DNA methylation, histone PTMs, transcriptomics, miRNA, lncRNA, proteomics, phosphoproteomics) and metabolomics measurements across a cell line panel or cohort, and you want to infer which molecular features (genes, regulatory marks, splice.
    0 installs
79. ▌
    Mass Spectrometry Image Reconstruction · holobiomicslab

    Use when you have paired .imzML (XML metadata) and .
    2 installs
80. ▌
    Mass Track Correspondence Verification · holobiomicslab

    Use when after constructing a LOWESS regression function (rt_cal_dict) to align retention times between a reference sample and a current sample, validate that high-selectivity landmark peaks in the reference sample (mSelectivity > 0.
    0 installs
81. ▌
    Matrix Algebra For Metabolite Networks · holobiomicslab

    Use when you have normalized and standardized metabolomics data (samples × metabolites matrix) and need to move beyond univariate or pairwise metabolite analysis to characterize the joint covariance structure or infer dynamic control relationships between metabolites under different growth.
    0 installs
82. ▌
    Metabolic Model Constraint Application · holobiomicslab

    Use when when you have a generic constraint-based metabolic model, RNA-seq expression data with GPR associations for reactions, experimentally measured nutrient uptake/secretion rates (from YSI bioanalyzer or similar), and intracellular/extracellular metabolomics data, and you need to generate.
    2 installs
83. ▌
    Metabolite Distance Metric Calculation · holobiomicslab

    Use when you have normalized peak intensity tables from FT-ICR MS data (or MetaboDirect pre-processed .csv output) with samples grouped by experimental treatments (e.
    0 installs
84. ▌
    Metabolite Feature Matrix Manipulation · holobiomicslab

    Use when you have raw metabolomics peak intensity or concentration data in matrix form (samples as rows, metabolites as columns) and need to prepare it for normalization or statistical analysis.
    2 installs
85. ▌
    Metabolite Intensity Matrix Extraction · holobiomicslab

    Use when when you have raw mass spectrometry peak intensity data (rows = peaks with IDs, columns = individual samples) and you need to align it with metabolite annotations (peak ID → KEGG or ChEBI compound ID mappings) before performing pathway-level analysis.
    0 installs
86. ▌
    Metabolite Network Covariance Analysis · holobiomicslab

    Use when you have normalized metabolite abundance data from MetaboAnalyst or similar preprocessing and need to transition from univariate/pairwise correlation analysis to network-level inference that captures conditional dependencies (partial correlations) between metabolites under specific.
    2 installs
87. ▌
    Metabolite Network Topology Extraction · holobiomicslab

    Use when after computing a Jacobian matrix from metabolomics covariance data, when you need to identify and visualize the structure of metabolite interactions (which metabolites regulate or influence which others) and their relative strengths.
    0 installs
88. ▌
    Metabolite Pathway Association Mapping · holobiomicslab

    Use when you have a list of metabolite names or identifiers detected in your samples and need to assign them to known metabolic pathways before computing pathway dysregulation scores, performing pathway-level machine learning, or conducting metabolite-pathway regression analysis.
    2 installs
89. ▌
    Metabolomics Feature Matrix Processing · holobiomicslab

    Use when you have a raw metabolomics intensity matrix with missing or zero values across samples in different experimental groups, and you need to input it into pathway activity scoring methods (PLAGE, ORA, GSEA) or metabolite set analysis pipelines that require normalized, zero-mean unit-variance.
    0 installs
90. ▌
    Metabolomics Workbench API Integration · holobiomicslab

    Use when when you need to analyze a publicly archived lipidomics study (identified by study_id like ST001111) and want to bypass manual data download and format conversion.
    0 installs
91. ▌
    Metadata Validation Rule Specification · holobiomicslab

    Use when mSMetaEnhancer retrieves metadata attributes (SMILES, InChI, CAS numbers, IUPAC names, formulas) from external services (CIR, CTS, PubChem, IDSM, BridgeDb) and you need to guarantee that only correctly formatted values are written back to .msp output files.
    2 installs
92. ▌
    Microbe Metabolite Attribution Scoring · holobiomicslab

    Use when after training multi-layer perceptron neural networks via cross-validation to predict metabolite abundances from microbiome composition, when you need to interpret which microbes drive predictions of specific metabolites and to identify groups of microbes with coherent metabolite.
    0 installs
93. ▌
    Microbial Biotransformation Prediction · holobiomicslab

    Use when when you have chemical structures (SMILES or molecular structure format) and need to forecast what metabolites environmental microbes would produce; particularly when assessing pollutant persistence, environmental fate, or xenobiotic degradation pathways in aquatic and terrestrial settings.
    0 installs
94. ▌
    Model Parameter Inspection And Logging · holobiomicslab

    Use when after instantiating a neural network model (such as TransG-Net) with multimodal inputs but before beginning training, to validate that the model architecture correctly accepts graph features and SMILES embeddings as separate modalities and produces expected output tensor shapes.
    0 installs
95. ▌
    Module Trait Association Visualization · holobiomicslab

    Use when after identifying and naming metabolic correlation modules from WGCNA on normalized, imputed metabolomic data, and you need to assess whether specific modules associate significantly with a binary or categorical sample trait (e.g., disease status, treatment group).
    2 installs
96. ▌
    Molecular Graph Feature Representation · holobiomicslab

    Use when when you have molecular structures (as SMILES, SDF, or graph adjacency) and need to predict continuous properties (e.
    0 installs
97. ▌
    Molecular Structure To Vector Encoding · holobiomicslab

    Use when when you have a collection of molecular structures (SMILES, InChI, or SDF format) and need to train or compare neural network-based spectrum predictors (such as NEIMS, MassFormer, or ICEBERG variants) on the same benchmark dataset.
    2 installs
98. ▌
    Multi Task Auxiliary Target Generation · holobiomicslab

    Use when training neural network models (MLP or GNN) for metabolite annotation on mass spectrometry data and you have access to a large unlabeled or weakly labeled spectral dataset.
    2 installs
99. ▌
    Multiassay Data Structure Construction · holobiomicslab

    Use when you have three separate data components from a metabolomics assay: (1) a matrix of metabolite measurements (assay) with samples as columns and metabolites as rows, (2) a table of metabolite annotations (rowData, e.
    0 installs
100. ▌
     Multimodal Spot Correspondence Mapping · holobiomicslab

     Use when when you have paired spatial transcriptome and metabolome datasets in h5ad format with spatial coordinate matrices (obsm['spatial']) and you need to establish spot-level correspondence across modalities for downstream integration or co-analysis.
     0 installs