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HolobiomicsLab

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1. ▌
   Build Artifact Retrieval And Validation 2 · holobiomicslab

   Use when when you need to verify that a GitHub Actions workflow (such as dev_build_release.
   3 installs
2. ▌
   Candidate Formula Ranking By Mass Error 3 · holobiomicslab

   Use when after querying a formula database (KEGG, PubChem, or user-supplied) with neutral mass values derived from observed m/z peaks and adduct transformations, when multiple candidate formulae fall within the configured mass tolerance window (ppm or Da) and you need to rank them by likelihood.
   5 installs
3. ▌
   Changelog Maintenance And Documentation 2 · holobiomicslab

   Use when you have added or modified user-facing parameters to a model class (such as L1/L2 regularization in SiameseModel), written unit tests to verify the new functionality, and need to communicate these changes to users and maintain a historical record.
   3 installs
4. ▌
   Chromatogram Peak Matching Registration 2 · holobiomicslab

   Use when you have multiple LC-MS samples in mzML or mzXML format with variable retention times, at least one designated as a quality control (QC) reference file, and you need to correct for RT drift before peak/feature detection.
   1 install
5. ▌
   Ei Spectral Library Parsing And Merging 2 · holobiomicslab

   Use when you need to build a comprehensive EI spectral reference library for GC-MS compound identification in MS-DIAL, starting from raw downloads of NIST, RIKEN, MoNA, or SWGDRUG libraries that have inconsistent metadata organization (SMILES in different fields or absent, RI values missing or.
   5 installs
6. ▌
   Electron Ionization Spectral Comparison 3 · holobiomicslab

   Use when you have a query electron ionization (EI) mass spectrum in msp format and wish to identify it by matching against a reference spectral library. Apply this skill when you need ranked similarity scores between the query and each library entry to prioritize candidate identifications.
   4 installs
7. ▌
   Feature Missingness Threshold Filtering 2 · holobiomicslab

   Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage before feature alignment.
   5 installs
8. ▌
   Feature Table Blank Intensity Detection 2 · holobiomicslab

   Use when after loading an MZmine3-exported feature quantification table from non-targeted LC-MS/MS data when your experiment includes blank (negative control) samples and you need to remove features attributable to contamination or instrument background before downstream statistical analysis.
   5 installs
9. ▌
   Feature Wise Spectrum Count Aggregation 2 · holobiomicslab

   Use when when you have extracted concatenated MS/MS spectra for multiple features from replicate mzML files and need to verify that a TIC-based filtering step (e.g., top x% TIC extraction) reduces per-feature spectrum counts to expected target levels.
   4 installs
10. ▌
    Ion Current Calculation And Aggregation 2 · holobiomicslab

    Use when when raw LC-MS feature tables exhibit inter-sample intensity variation due to instrument sensitivity drift, sample ionization efficiency differences, or loading differences, and you need to normalize intensities to a common reference scale before downstream statistical analysis.
    4 installs
11. ▌
    Mass Action Kinetics Propensity Scoring 2 · holobiomicslab

    Use when you have intracellular metabolomics measurements (absolute metabolite abundances) for multiple biological samples and want to identify which metabolic reactions are controlled by substrate availability rather than gene expression.
    4 installs
12. ▌
    Metabolomics Npp Reliability Assessment 2 · holobiomicslab

    Use when you have completed NPP runs from one or more metabolomics tools on a set of LC-HRMS mzML files AND you have reference information (target molecule list with molecular formula, main adduct, and RT boundaries) available for a subset of expected compounds in those files.
    3 installs
13. ▌
    Ms1 Feature Peak Detection In Full Scan 3 · holobiomicslab

    Use when you have merged MS1 spectra (output from spectral binning/merging steps) from a full-scan FIA-MS or LC-MS acquisition and need to identify distinct molecular features before accurate mass annotation or background filtering.
    4 installs
14. ▌
    Nmr Peak Prediction Via Database Lookup 2 · holobiomicslab

    Use when you have extracted peak data (chemical shift values in ppm, multiplicities, integration) from a processed NMR spectrum (JCAMP, RAW, or mzML format) and need to match these peaks against known NMR signals to propose or confirm structural assignments.
    3 installs
15. ▌
    Parameter Driven Preprocessing Pipeline 3 · holobiomicslab

    Use when you have converted mass spectrometry data in mzXML or mzML format and need to extract metabolic features via region-of-interest (ROI) search followed by preprocessing and augmentation.
    3 installs
16. ▌
    Peptide B Y Ion Theoretical Calculation 2 · holobiomicslab

    Use when when you have a peptide sequence and need to predict which fragment ions (B and Y series) should appear in an MS2 spectrum at a known isotopic abundance (e.g., natural 13C at 1.07%, or stable isotope labeling at 50% enrichment).
    3 installs
17. ▌
    Per Sample Feature Composition Analysis 2 · holobiomicslab

    Use when when you have aligned and quantified mass spectrometry features from multiple natural extracts (via MZmine2/3), paired with in silico annotation results (ISDB or SIRIUS), and you need to prioritize samples for chemical discovery based on the proportion of unannotated, extract-specific.
    3 installs
18. ▌
    Podp Metadata Retrieval And Integration 2 · holobiomicslab

    Use when when running NPLinker in PODP mode (as opposed to local mode), you need to fetch and validate project metadata from PODP, orchestrate downloads of GNPS molecular networking data, AntiSMASH BGC predictions, BigScape clustering results, and MIBiG reference metadata, then organize them into.
    5 installs
19. ▌
    Pooled Statistical Significance Testing 2 · holobiomicslab

    Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test whether a combined scoring strategy (e.
    4 installs
20. ▌
    Python Package Installation From Source 2 · holobiomicslab

    Use when when you need to verify a Python package installs successfully from a cloned or local repository, validate that all tests pass after installation, or prepare a development environment for contributing to the package.
    5 installs
21. ▌
    Quantum Mechanical Property Calculation 2 · holobiomicslab

    Use when when you have interpolated or optimized molecular geometries (from geodesic_interpolate or CREST conformer ensembles) and need to compute ab initio electronic energies, orbital properties, or transition state characteristics to populate a fragmentation reaction network or validate.
    3 installs
22. ▌
    Rt Transformation Parameter Calculation 2 · holobiomicslab

    Use when you have centroided mzML or mzXML LC-MS files from a single batch run that exhibit systematic retention-time drift between samples, one or more designated QC reference file(s), and you need to harmonize RT coordinates across all samples before feature detection to reduce false positive and.
    5 installs
23. ▌
    Spectral Feature Scrambling Permutation 2 · holobiomicslab

    Use when when performing large-scale untargeted metabolomics annotations where you need to assess the false discovery rate of metabolite identifications but lack sufficient negative control samples or decoy compound databases.
    5 installs
24. ▌
    Spectral Library Matching With Taxonomy 2 · holobiomicslab

    Use when you have MS/MS spectra (.mgf) and candidate metabolite annotations (with m/z, retention time, chemical identifiers) linked to a known organism or taxon, and you want to rank annotations by both spectral similarity AND biochemical likelihood in that organism's lineage.
    4 installs
25. ▌
    Spectral Motif Inference And Extraction 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (converted to bag-of-fragments format with neutral losses extracted and noise filtered) and seek to identify recurring fragmentation patterns indicative of molecular substructures across a spectral cohort.
    5 installs
26. ▌
    Spectral Similarity Scoring And Ranking 2 · holobiomicslab

    Use when after discovering Mass2Motifs via LDA topic modeling on MS/MS data, when you need to assign putative structural annotations to those motifs by comparing their fragmentation signatures (weighted fragment and neutral loss distributions) to a curated reference database of known motifs and.
    3 installs
27. ▌
    Spectral Similarity Scoring Computation 4 · holobiomicslab

    Use when you have a query spectrum (or set of query spectra) and need to rank candidate library spectra by their likelihood of sharing the same chemical structure.
    5 installs
28. ▌
    Structured Data Compilation From Readme 2 · holobiomicslab

    Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic coverage) in its README, and you need to create a machine-readable inventory for downstream indexing, validation, or reuse.
    4 installs
29. ▌
    Tensorflow Serving Endpoint Integration 2 · holobiomicslab

    Use when you have nuclear magnetic resonance (NMR) peak data (1H and 13C measurements) that you need to classify using a deployed SMART 3 model, and you want to submit peaks programmatically rather than through a web UI.
    4 installs
30. ▌
    Mass Spectrometry Tune Data Loading 2 · holobiomicslab

    Use when you have positive- or negative-mode tune reference compound data stored in HDF5 format (e.g., example_tune_pos.h5) and need to extract the tune mass spectrum for CCS calibration. This skill is the entry point before applying deimos.calibration.
    5 installs
31. ▌
    Dashboard Data Loading And Validation 2 · holobiomicslab

    Use when after generating a dashboard_data.json file from the msFeaST Jupyter pipeline, use this skill to verify that the JSON file is correctly formatted and completely loaded into the interactive dashboard before conducting visual exploration or sharing the dashboard with collaborators.
    5 installs
32. ▌
    Differential Peak Abundance Detection 2 · holobiomicslab

    Use when after raw mass spectrometry data has been converted to a peak feature table (CSV or tabular format) containing mass-to-charge ratios, retention times, and intensity values across samples, and you need to reduce noise and identify which peaks show meaningful differential patterns between.
    5 installs
33. ▌
    Feature Filtering And Quality Control 2 · holobiomicslab

    Use when after batch correction and concentration normalization have been applied to a merged m/z peak table and metadata file, but before statistical testing or machine learning.
    5 installs
34. ▌
    Molecular Formula Property Derivation 2 · holobiomicslab

    Use when you have filtered FT-ICR MS peak data with valid molecular formula assignments (C, H, O, N, S, P elemental counts) and need to quantify molecular properties that predict metabolite reactivity, bioavailability, and biochemical role.
    5 installs
35. ▌
    Msimagingexperiment Subset Operations 2 · holobiomicslab

    Use when after peak alignment with peakAlign(), when you have an MSImagingExperiment with many detected peaks but want to retain only those present in a sufficient fraction of pixels.
    5 installs
36. ▌
    Spectral Library Matching And Scoring 3 · holobiomicslab

    Use when when you have extracted a mean or ROI spectrum from MSI data (via centroid or profile mode conversion) and need to identify the biochemical composition by comparing against curated reference libraries such as LIPID MAPS, HMDB, or a custom metabolite database.
    4 installs
37. ▌
    Ablation Study Design And Interpretation 2 · holobiomicslab

    Use when when you have a neural network or machine learning model with multiple tunable hyperparameters (layer size, regularization strength, dropout) or design choices (e.
    3 installs
38. ▌
    Compound Structural Similarity Retrieval 2 · holobiomicslab

    Use when you have a collection of preprocessed MS/MS spectra with structural annotations (InChIKey, SMILES, or InChI) and need to identify pairs of compounds that are structurally related above a specified similarity threshold.
    5 installs
39. ▌
    Correlation Matrix Heatmap Visualization 2 · holobiomicslab

    Use when after computing a correlation matrix (e.g., Pearson correlation across samples) on statistically significant LC-MS features, particularly when you need to inspect hierarchical dendrogram structure, validate cluster assignments from different flattening methods (constant-threshold vs..
    5 installs
40. ▌
    Metabolic Model Constraint Specification 2 · holobiomicslab

    Use when you have a generic constraint-based metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, YSI or bioanalyzer extracellular flux measurements) for multiple biological samples and need to create sample-specific models that discriminate whether.
    4 installs
41. ▌
    Missing Value Imputation In Metabolomics 2 · holobiomicslab

    Use when after feature extraction and quality control filtering (blank masking, sample dropping, normalization) have been applied, but before statistical analysis or machine learning.
    4 installs
42. ▌
    Neural Network Regularization Techniques 2 · holobiomicslab

    Use when when training a deep neural network on paired MS/MS spectra to predict structural similarity scores, especially when the training dataset is moderate-sized (109,734 spectra across 15,062 molecules) and overfitting risk is high.
    3 installs
43. ▌
    Pathway Activity Decomposition Via Plage 3 · holobiomicslab

    Use when you have a log2-transformed, standardized peak intensity matrix (rows = metabolite features, columns = samples) with compound annotations mapped to curated pathway databases (KEGG, Reactome, or custom metabolite sets), and you need to rank pathways by their activity level while tolerating.
    5 installs
44. ▌
    Siamese Network Inference Spectrum Pairs 2 · holobiomicslab

    Use when you have a collection of preprocessed tandem mass spectra (binned into 10,000 equally-sized m/z bins, intensities square-root transformed, top 1,000 peaks retained), a trained MS2DeepScore Siamese model, and you need to predict structural similarity scores (Tanimoto or Dice) for all or a.
    5 installs
45. ▌
    Spectral Library Compilation And Merging 2 · holobiomicslab

    Use when you have multiple mass spectral library files in different formats (MSP, MGF, MOL folders) from sources like NIST, MoNA, RIKEN, or GNPS, and need to produce a single consolidated MSP file with complete SMILES, InChIKey, and experimental retention index (RI) annotations for metabolomics or.
    5 installs
46. ▌
    Bioconductor Backend Architecture Design 2 · holobiomicslab

    Use when you are building a new mass spectrometry data backend or storage layer and need to integrate it with the Spectra ecosystem. Triggers include: (1) you have a novel data source (raw files, databases, web APIs) that should be accessible through Spectra objects;
    3 installs
47. ▌
    Combined Table Extraction And Inspection 2 · holobiomicslab

    Use when after constructing a metabCombiner object by grouping features from two metabData objects by m/z, and before proceeding to anchor selection, RT mapping, or alignment scoring.
    5 installs
48. ▌
    Database Schema Design For Spectral Data 2 · holobiomicslab

    Use when you have MS/MS spectral library data currently stored in file-based formats (JSON, CSV, binary, MGF, MSP) and need to migrate to database-backed storage to support fast queries by metadata filters (precursor m/z, ion mode, retention time) and computed similarity scores against query.
    5 installs
49. ▌
    Experimental Design Metadata Integration 3 · holobiomicslab

    Use when when you have LC-MS raw data and need to process it through a feature detection and quantification pipeline in KNIME, but lack a structured mapping between sample identifiers, experimental conditions, and the raw LC-MS runs.
    4 installs
50. ▌
    Installation Verification And Validation 2 · holobiomicslab

    Use when after cloning the ENPKG repository and installing dependencies using uv sync or conda, before executing the workflow on metabolomics datasets.
    3 installs
51. ▌
    Lc Ms Feature Grouping By Retention Time 2 · holobiomicslab

    Use when immediately after chromatographic peak detection (findChromPeaks) when you have detected peaks across multiple samples and need to identify which peaks represent the same feature across the sample cohort.
    1 install
52. ▌
    Mass Difference Calculation And Matching 2 · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA) MS2 spectra from LC- or GC-HRMS and need to annotate detected features with PFAS-specific diagnostic fragments. Use it after feature detection (e.
    5 installs
53. ▌
    Mass Spectrometry Qc Criteria Definition 2 · holobiomicslab

    Use when when setting up a new LC-MS QC workflow or modifying existing QC rules: you have access to internal standards and target analytes, know their expected retention times and m/z values, and need to establish pass/fail boundaries for sample acceptance before or concurrent with instrument runs.
    5 installs
54. ▌
    Mass Spectrometry Raw Data Preprocessing 3 · holobiomicslab

    Use when when you have raw DIA mass spectrometry data files (.raw, .d, .
    4 installs
55. ▌
    Mass Spectrum Prediction Neural Networks 2 · holobiomicslab

    Use when when you have molecular structures (SMILES, InChI, or chemical formula) and need to predict their tandem mass spectra for structural elucidation or compound ranking against databases. Use SCARF when operating at the chemical formula level;
    6 installs
56. ▌
    Metabolite Abundance Threshold Filtering 2 · holobiomicslab

    Use when you have intracellular metabolomics data paired with constraint-based metabolic model predictions and need to identify metabolically controlled reactions.
    5 installs
57. ▌
    Molecular Formula Inference From Adducts 2 · holobiomicslab

    Use when when you have grouped features consolidated into empirical compounds (EmpCpds) with inferred adduct assignments from khipu, and need to perform MS1-level annotation by matching neutral formulas against JMS-compliant reference libraries (HMDB, LMSD).
    4 installs
58. ▌
    Smiles Structure Representation Handling 2 · holobiomicslab

    Use when you have generated a TPs object (via generateTPs) containing transformation products with structural information and need to export these structures for MetFrag database creation, suspect screening list construction, or chemical similarity filtering.
    3 installs
59. ▌
    Spectral Library Metadata Reorganization 3 · holobiomicslab

    Use when when ingesting mass spectral libraries (EI or MS2) where SMILES information is embedded in the Comment field rather than in a dedicated SMILES metadata field—particularly common in MoNA GC-MS and LC-MS/MS exports.
    3 installs
60. ▌
    Structured Logging And Metric Extraction 2 · holobiomicslab

    Use when when executing a multi-converter annotation workflow on mass spectra metadata (.
    4 installs
61. ▌
    Theoretical Isotope Envelope Calculation 2 · holobiomicslab

    Use when when processing mass spectrometry data from stable isotope probing (SIP) experiments where peptides contain known levels of heavy isotope incorporation (13C, 15N, 2H, 18O), and you need to annotate observed MS2 peaks by matching them to theoretical B and Y ion fragments.
    1 install
62. ▌
    Feature Abundance Correlation Grouping 2 · holobiomicslab

    Use when after performing retention-time-based feature grouping (e.g., 10–20 second windows), when you observe large feature groups that may conflate multiple independent compounds with coincidentally similar retention times.
    0 installs
63. ▌
    Hit Score Consolidation Across Domains 2 · holobiomicslab

    Use when you have executed batch spectral searches against two or more domain-specific MASSTs (via the Fast Search API or individual MASST tools) and need to combine the resulting hit lists, match scores, and taxonomic/metadata annotations into a single ranked table for downstream analysis.
    5 installs
64. ▌
    Isotope Pattern Matching And Filtering 2 · 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.
    5 installs
65. ▌
    Windows Desktop Application Deployment 2 · holobiomicslab

    Use when when you have cloned a .NET Framework or .NET Core WPF project from a GitHub repository and need to compile it into an executable binary for Windows deployment. Specifically, when the project uses ReactiveExtensions/ReactiveProperty packages, declares a .NET Framework 4.7.2 or .
    4 installs
66. ▌
    Conda Environment Setup And Activation 2 · holobiomicslab

    Use when preparing a fresh system or user account to run MSIGen for mass spectrometry imaging data processing, or when you need to isolate MSIGen installation from other Python projects to avoid dependency conflicts.
    3 installs
67. ▌
    M Z Value Clustering Mass Spectrometry 2 · 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.
    5 installs
68. ▌
    Bgc Spectrum Ranking By Kernel Similarity 2 · holobiomicslab

    Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or predicted structures (e.
    5 installs
69. ▌
    Chemical Structure Fingerprint Comparison 3 · holobiomicslab

    Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method actually reflects true chemical structural similarity.
    4 installs
70. ▌
    Comparative Machine Learning Benchmarking 2 · holobiomicslab

    Use when you have developed a new machine learning model for predicting metabolomic profiles from microbiome data and need to quantify its performance improvement over existing methods.
    5 installs
71. ▌
    Ionisation Method Hardware Correspondence 3 · holobiomicslab

    Use when when evaluating whether a mass spectrometry analysis platform (such as mzmine) has comprehensive module support across multiple ionisation and separation techniques (LC, GC, IMS, MALDI MS imaging), or when planning a multi-technique MS study and needing to confirm that all intended.
    3 installs
72. ▌
    JSON Payload Construction For Nmr Spectra 2 · holobiomicslab

    Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.
    5 installs
73. ▌
    Knowledge Graph Generation And Validation 2 · holobiomicslab

    Use when after completing all per-sample annotation steps (molecular networking, ISDB/spectral matching, SIRIUS/CSI:FingerID, and compounds metadata enhancement with Wikidata IDs and NPClassifier ontology).
    4 installs
74. ▌
    Lcms Feature Detection And Quantification 2 · holobiomicslab

    Use when you have raw LC-MS data (mzML or equivalent format) from a metabolomics experiment and need to extract a reproducible, quantified feature table with intensity measurements before conducting metabolite identification or statistical analysis.
    4 installs
75. ▌
    Metabolite Feature Annotation Aggregation 2 · holobiomicslab

    Use when after selecting statistically significant features from multi-assay LC-MS metabolomics datasets (e.g., via MB-VIP and permutation testing with p < 0.01).
    1 install
76. ▌
    Metabolomics Peak Detection Configuration 3 · holobiomicslab

    Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram alignment.
    4 installs
77. ▌
    Microbiome Metabolome Prediction Modeling 3 · holobiomicslab

    Use when you have paired microbiome (16S rRNA, metagenomic) and metabolomic (LC-MS, GC-MS) abundance tables from the same biosamples, and you want to predict which metabolites are recoverable from microbial composition alone and identify groups of microbes and metabolites with correlated.
    4 installs
78. ▌
    Molecular Structure Prediction Evaluation 2 · holobiomicslab

    Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
    1 install
79. ▌
    Singular Value Decomposition Metabolomics 3 · holobiomicslab

    Use when when you have a log2-normalized, zero-mean, unit-variance intensity matrix (rows=metabolites, columns=samples) and a curated metabolite set database (e.
    5 installs
80. ▌
    Software Feature Inventory And Comparison 3 · holobiomicslab

    Use when you need to assess whether a newly developed FT-ICR MS pipeline (e.
    3 installs
81. ▌
    Analytical Pipeline Feature Documentation 2 · holobiomicslab

    Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses it supports—particularly when the pipeline is positioned as an alternative to or improvement over established tools.
    4 installs
82. ▌
    Call Graph Construction And Visualization 2 · holobiomicslab

    Use when when you need to understand the computational structure of a modular scientific application (especially one with multiple subprojects or plug-in architectures) and static code inspection alone does not reveal algorithm entry points, parameter propagation, or intermediate data.
    4 installs
83. ▌
    Charge State Determination And Assignment 2 · holobiomicslab

    Use when when analyzing high-resolution mass spectrometry data from natural-abundance or labeled peptides where multiple charge states (+2, +3, +4, etc.) may be present within the same m/z isolation window (e.g., 880–890 m/z).
    4 installs
84. ▌
    Chromatogram Extraction And Visualization 2 · holobiomicslab

    Use when you have sqMass files containing pre-extracted transition group chromatograms from DIA-MS experiments and need to interactively visualize individual peptide precursor chromatograms, inspect peak quality via Q-values (typically 1% FDR cutoff), and overlay peak boundaries or apply on-the-fly.
    5 installs
85. ▌
    Constraint Based Model Output Integration 2 · holobiomicslab

    Use when when you have (1) transcriptomics data and a metabolic network model with GPR rules to compute RAS scores; (2) constraint-based model predictions (RPS from optGpSampler or similar) quantifying how gene expression differences translate to flux differences;
    4 installs
86. ▌
    Statistical Hypothesis Testing Mean Comparison 2 · holobiomicslab

    Use when you have computed raw or standardised correlation scores (or other link-ranking metrics) for all possible GCF-MF pairs in a dataset and want to verify that validated links (those with known strain co-occurrence or experimental confirmation) are significantly enriched at higher score values.
    4 installs
87. ▌
    Chromatogram Baseline Correction Preprocessing 2 · holobiomicslab

    Use when you have raw or folded 2D-TIC chromatogram data (typically imported from NetCDF files into RGCxGC chromatogram objects) that exhibits baseline drift, chemical noise, or instrumental artifacts that would obscure true metabolite peaks.
    5 installs
88. ▌
    Feature Based Molecular Network Interpretation 2 · holobiomicslab

    Use when you have a feature-based molecular network generated from non-targeted LC-MS/MS metabolomics data (e.
    5 installs
89. ▌
    Feedforward Neural Network Architecture Design 2 · holobiomicslab

    Use when you have preprocessed molecular structures as fixed-length feature vectors and need to establish a fair-comparison baseline model for tandem mass spectrum prediction.
    1 install
90. ▌
    Machine Learning Performance Metric Evaluation 2 · holobiomicslab

    Use when after training a binary MS/MS spectral classifier on labeled data, apply this skill to quantify classifier performance before deployment.
    4 installs
91. ▌
    Mass Spectra Clustering Hyperdimensional Space 2 · holobiomicslab

    Use when you have large-scale MS/MS spectra datasets (hundreds of thousands to millions of spectra) in MGF format that need to be grouped by similarity, and you have access to NVIDIA GPU hardware (GTX 1080Ti or GTX 3090).
    3 installs
92. ▌
    Ms Ms Spectral Preprocessing And Normalization 2 · holobiomicslab

    Use when you have a labelled dataset of raw MS/MS spectra annotated as 'relevant' (compounds of interest) or 'other' (reference standards or non-target compounds) and need to prepare them for supervised classifier training.
    5 installs
93. ▌
    Neural Network Layer Design And Implementation 2 · holobiomicslab

    Use when when replacing deprecated model components (e.
    5 installs
94. ▌
    Univariate Statistical Analysis Interpretation 2 · holobiomicslab

    Use when you have a preprocessed feature table from non-targeted LC-MS/MS metabolomics data (after data merging, cleanup, blank removal, and batch correction) and need to test whether individual metabolomic features show statistically significant differences between experimental groups or.
    4 installs
95. ▌
    Word2vec Model Inference Unknown Word Handling 4 · holobiomicslab

    Use when when applying a pre-trained Word2Vec model to mass spectra at inference time (e.g., library matching or molecular networking), especially when the query spectra may contain fragment peaks or neutral losses not represented in the model's training vocabulary.
    5 installs
96. ▌
    Ft Icr Ms Data Processing Pipeline Execution 2 · holobiomicslab

    Use when you have FT-ICR MS peak abundance data in Formularity .
    4 installs
97. ▌
    Spectral Similarity Scoring With Mass Shifts 2 · holobiomicslab

    Use when you have an unknown query spectrum suspected to carry a post-translational modification and need to match it against a library of unmodified reference spectra.
    5 installs
98. ▌
    In Source Fragment Adduct Candidate Flagging 2 · holobiomicslab

    Use when you have aligned, imputed time-resolved mass spectrometric data from direct-injection plasma ionization (e.g., DBDI, DESI) without chromatographic separation, and you suspect multiple m/z features belong to the same neutral analyte as in-source fragments or oxygen-bound adducts.
    5 installs
99. ▌
    Bag Of Words Document Representation Generation 2 · holobiomicslab

    Use when you have raw MS/MS spectral data in standard mass spectrometry formats and need to prepare it for unsupervised substructure discovery via topic modeling.
    7 installs
100. ▌
     Ionization Mode Specific Preprocessing Handling 2 · holobiomicslab

     Use when you have raw MS/MS spectra in supported formats (.mgf, .mzML, or .msp) from mixed ionization modes and need to prepare them for downstream topic modeling (LDA) or motif discovery.
     5 installs