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HolobiomicsLab

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1. ▌
   Unknown Sample Reference Comparison 2 · holobiomicslab

   Use when you have a preprocessed unknown sample spectrum (m/z peaks and intensities) from high-throughput mass spectrometry (DI-MS, ASAP-MS, or ambient ionization methods) and need to identify the species or authenticate a sample against a curated reference database of known spectra.
   0 installs
2. ▌
   Ion Mobility Machine Learning Training 2 · 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.
   2 installs
3. ▌
   Deletion Reason Logging And Traceability 2 · holobiomicslab

   Use when when processing OMSLs (Open Mass Spectra Libraries) with heterogeneous data quality, inconsistent annotations, or mixed ionmode/chromatographic modes (LC/GC), and you need to track which spectra were discarded, why, and potentially recover or reprocess them in future iterations.
   0 installs
4. ▌
   Mass Spectrometry Spectral Preprocessing 2 · holobiomicslab

   Use when you have raw mass spectrometry spectra from an unknown analyte or a synthetic compound library and need to feed them into PS2MS or similar deep learning classifiers for NPS detection.
   0 installs
5. ▌
   Metabolomics Library Generation Pipeline 2 · holobiomicslab

   Use when when you have cloned or accessed the Reverse_metabolomics_library_generation repository and need to verify that the Nextflow workflow is properly configured, executable, and produces expected spectral library outputs.
   0 installs
6. ▌
   Similarity Score Computation For Spectra 2 · holobiomicslab

   Use when you have a preprocessed unknown sample spectrum (m/z peaks and intensities) and need to identify the most likely species or reference entries by scoring it against a database of known spectra.
   0 installs
7. ▌
   Spectrum Filtering With Deletion Logging 2 · holobiomicslab

   Use when processing heterogeneous mass spectrometry libraries (e.g., from OMSLs) where chemical identifiers are unevenly populated across records.
   0 installs
8. ▌
   Tomcat Application Server Initialization 2 · holobiomicslab

   Use when when you need to deploy a Java web application packaged in a Tomcat Docker container to a specified HTTP endpoint, and must verify that the container starts successfully, the Tomcat server initializes, and the application becomes accessible at the mapped host port before proceeding with.
   0 installs
9. ▌
   High Resolution Spot To Spot Integration 2 · holobiomicslab

   Use when you have two spatial omics datasets (e.g., spatial transcriptome and metabolome spot matrices) collected from the same or adjacent tissue sections, with both feature matrices (X: np.ndarray) and spatial coordinates (D: np.ndarray containing location information in .
   0 installs
10. ▌
    Metabolomics Preprocessing Normalization 2 · holobiomicslab

    Use when you have acquired raw SIMS (secondary ion mass spectrometry) metabolite images aligned with tissue regions and segmented single-cell masks, and you need to extract normalized metabolite intensity values per cell before performing cell-type assignment, VAE embedding, or protein–metabolite.
    2 installs
11. ▌
    Spectral Peak Word Embedding Representation 2 · holobiomicslab

    Use when when you have MS/MS spectra (LC-MS or equivalent positive ionization mode data) that you intend to embed using Word2Vec or similar distributional semantic models, or when you need to prepare spectral data for training similarity models that learn peak co-occurrence patterns rather than.
    0 installs
12. ▌
    Adduct Form Prediction And Mass Calculation 2 · holobiomicslab

    Use when you have a characterized lipid species (with defined class and fatty acid composition) and need to predict which adduct forms will ionize under your experimental ionization mode (positive or negative ESI), and you require accurate precursor m/z values for DDA method configuration or.
    0 installs
13. ▌
    Baseline Method Comparison And Benchmarking 2 · holobiomicslab

    Use when you have developed or adapted an analytical method (e.g., NPFimg for GC–MS marker identification) and need to demonstrate its reliability or improved performance over a widely-used reference method (e.g., XCMS). Apply this skill when you have access to both the same raw input data (e.
    2 installs
14. ▌
    Binary Classification Output Interpretation 2 · holobiomicslab

    Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a structured CSV output file that maps molecule identifiers to their predicted class labels (bitter or not-bitter).
    0 installs
15. ▌
    Chemical Informatics Data Format Conversion 2 · holobiomicslab

    Use when when you have raw SMILES strings collected from multiple external databases that require standardization and deduplication before integration into a unified chemical structure database. Specifically, apply this skill when you need to convert interim/tables/0_original/structure/smiles.tsv.
    0 installs
16. ▌
    Coefficient Of Variation Threshold Analysis 2 · holobiomicslab

    Use when you have per-feature CV values from quality control analysis of NMR or MS metabolomic data and need to: (1) establish whether your dataset meets FDA reproducibility standards for downstream biomarker discovery or quantification; (2) benchmark data quality against regulatory thresholds;
    2 installs
17. ▌
    Collision Cross Section Bias Quantification 2 · holobiomicslab

    Use when you have ion mobility-mass spectrometry lipidomics data from samples spiked with U¹³C-labeled lipid internal standards (fully labeled yeast extract) and want to assess whether measured CCS values systematically deviate from a validated DT CCS N₂ reference library, indicating bias that may.
    0 installs
18. ▌
    Count Verification Against Published Values 2 · holobiomicslab

    Use when when you have access to a curated dataset (such as LOTUS) with published headline statistics in a peer-reviewed article or enriched index, and you need to validate data integrity, trace reporting accuracy, or establish a reproducible baseline before downstream analysis.
    0 installs
19. ▌
    Data Driven Similarity Layer Implementation 2 · holobiomicslab

    Use when you have untargeted metabolomics mass spectrometry data (MS2 spectra with m/z values and intensities) and an existing knowledge-driven metabolite network, and you need to enhance annotation accuracy and coverage by leveraging experimental similarity patterns rather than relying solely on.
    0 installs
20. ▌
    Deep Neural Network Training Regularization 2 · holobiomicslab

    Use when training a DNN on retention time prediction or similar continuous regression tasks where: (1) the feature space is very high-dimensional (thousands of molecular descriptors and fingerprints), (2) the training set is moderately sized (tens of thousands of molecules), (3) you observe or.
    2 installs
21. ▌
    Gaussian Process Uncertainty Quantification 2 · holobiomicslab

    Use when after collecting observed separation efficiency scores at sampled gradient conditions and you need to propose the next gradient to evaluate.
    0 installs
22. ▌
    Graph Neural Network Encoding For Molecules 2 · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a reference library of compounds.
    0 installs
23. ▌
    Mass Spectrometry File Inventory Management 2 · holobiomicslab

    Use when you have uploaded MS/MS data to MassIVE with validated sample-information metadata and need to subset public files by sample attributes (organism, tissue type, extraction method, ionization source, pre-MS separation) to create reproducible, manageable cohorts for molecular networking.
    0 installs
24. ▌
    Mass Spectrometry Scan Extraction By Target 2 · holobiomicslab

    Use when you have raw LC-MS/MS chromatogram files in mzML/mzXML format (converted from Thermo, Waters, or Bruker instruments) acquired in DDA or targeted MS/MS mode, and you need to isolate specific MS1 precursors and their corresponding MS2 fragments based on known m/z values and optional.
    0 installs
25. ▌
    Metabolite Feature Filtering By Missingness 2 · holobiomicslab

    Use when you have a raw metabolite abundance matrix (e.g., from MSPrep or another LC-MS/MS pipeline) with many features and samples, and you observe that a substantial fraction of metabolites are missing (NA or zero-valued) across replicates.
    1 install
26. ▌
    Metabolite Structure Annotation Integration 2 · holobiomicslab

    Use when you have a set of candidate transformed structures generated by biotransformation rules (e.
    0 installs
27. ▌
    Metabolomics Feature Integration Assessment 2 · holobiomicslab

    Use when after XCMS peak picking and fillPeaks() when you have xcmsEIC and filled xcmsSet objects and need to systematically flag low-quality or unreliable peak integrations prior to statistical modeling or machine learning classification.
    0 installs
28. ▌
    Missing Value Imputation Strategy Selection 2 · holobiomicslab

    Use when after mark_nas() has replaced non-NA missing-value codes (e.g., 0, 1) with R's NA in the exprs matrix of a MetaboSet object, and you need to decide whether to apply random forest imputation, simple imputation strategies, or defer imputation.
    0 installs
29. ▌
    Molecular Descriptor Fingerprint Generation 2 · holobiomicslab

    Use when you have a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or molecular property estimation.
    1 install
30. ▌
    Open Format Mass Spectrometry File Handling 2 · holobiomicslab

    Use when you have raw mass spectrometry data in vendor-proprietary formats (e.g., .raw, .d, .ms) that you need to upload to MassIVE for public sharing or submit to GNPS for spectral library matching and chemical annotation.
    0 installs
31. ▌
    Peak Annotation Refinement Structure Driven 2 · holobiomicslab

    Use when you have two related compounds (a known reference and its structural analog with unknown modification site), baseline peak annotations from cosine alignment, and newly available structural information (SMILES or molecular structure) for the modified compound.
    0 installs
32. ▌
    Python Workflow Execution And Orchestration 2 · holobiomicslab

    Use when you have raw LC/MS data in mzML format and need to execute a complete non-targeted screening workflow to extract and annotate chemical features.
    2 installs
33. ▌
    Reaction Pathway Assignment And Propagation 2 · holobiomicslab

    Use when you have detected and clustered unknown MS features from untargeted xenobiotic metabolomics data, computed fragmentation pattern similarity scores between features and reference spectra, and now need to systematically assign individual features to specific biotransformation reactions (e.
    2 installs
34. ▌
    Recursive Propagation Algorithm Development 2 · holobiomicslab

    Use when when you have constructed a two-layer metabolite annotation network (knowledge-driven and data-driven) and need to propagate initial seed annotations (e.
    0 installs
35. ▌
    Scan Number Mapping Dictionary Construction 2 · holobiomicslab

    Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable, memory-efficient lookup table that can be applied during feature alignment without recomputing the regression for every sample.
    2 installs
36. ▌
    Similarity Ranking And Retrieval Evaluation 2 · holobiomicslab

    Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
    0 installs
37. ▌
    Spectrum Alignment Performance Benchmarking 2 · holobiomicslab

    Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a spectral library search.
    0 installs
38. ▌
    Structured Molecule Relationship Evaluation 2 · holobiomicslab

    Use when when you have tandem mass spectra (MSMS) from related or candidate molecules and need to determine which similarity metric—cosine, modified cosine, or neutral loss— ranks structurally similar compounds in your dataset. Particularly useful when structural relationships are known a priori (e.
    0 installs
39. ▌
    Thread Utilization Profiling And Validation 2 · holobiomicslab

    Use when when deploying Mass2SMILES inference on CPU-only hardware (e.g., when GPU/CUDA support is unavailable), you need to verify that the InferenceModel cpu_threads parameter (e.g., cpu_threads=128) actually controls thread allocation during execution.
    2 installs
40. ▌
    Xenobiotic Metabolite Annotation From Ms Ms 2 · holobiomicslab

    Use when you have aligned MS/MS feature tables (e.g., from MSDial ver. 4.80) representing unknown metabolites suspected to be Phase I/II transformation products of xenobiotics, and you need to assign both chemical identity and biotransformation pathway context to each feature.
    0 installs
41. ▌
    Spectral Database Search And Scoring 2 · holobiomicslab

    Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected) from DI-MS, ASAP-MS, or LDI-MS instruments and need to identify unknown samples by comparing their spectral fingerprints against a validated reference database of known species or compounds.
    0 installs
42. ▌
    Collision Cross Section Bias Estimation 2 · holobiomicslab

    Use when when you have IM-MS lipidomics data spiked with U13C labeled lipid internal standards (e.g., fully labeled yeast extract) and want to assess whether measured CCS values deviate systematically from expected values in the DTCCS_N2 reference library.
    0 installs
43. ▌
    Conformer Filtering Threshold Selection 2 · holobiomicslab

    Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before quantum-chemical single-point energy evaluation.
    0 installs
44. ▌
    Machine Learning Model Training Sklearn 2 · holobiomicslab

    Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites with experimentally validated CCS values, and you plan to predict CCS values on target datasets containing 10,000+.
    0 installs
45. ▌
    Noise Threshold Filtering Spectral Data 2 · holobiomicslab

    Use when working with raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains low-abundance background noise, isolated high-intensity artifacts, or jagged peaks characteristic of low-abundance ions.
    0 installs
46. ▌
    Small Molecule 3d Structure Preparation 2 · holobiomicslab

    Use when when you have ionized adduct structures (SMILES or MOL format) from a prior ionization-state determination step and need to create multiple low-energy 3D conformations before filtering with machine-learning potentials (ASE-ANI) or quantum calculations.
    0 installs
47. ▌
    Cnn Architecture Design For Spectral Data 2 · holobiomicslab

    Use when when you have mass-spectrometry data (m/z and intensity pairs or spectral matrices) paired with ground-truth molecular fingerprints or InChIKeys, and you need to learn a non-linear mapping from spectral patterns to structural fingerprints for downstream metabolite ranking or annotation.
    0 installs
48. ▌
    Composite Map Data Structure Construction 2 · holobiomicslab

    Use when after mass track extraction and alignment across samples, when you have a MassGrid structure (m/z-aligned mass tracks) and corresponding retention time calibration dictionaries for each sample, and need to prepare input for composite peak detection rather than per-sample peak detection.
    2 installs
49. ▌
    Metabolomic Meta Analysis Workflow Design 2 · holobiomicslab

    Use when you have multiple metabolomic studies with aggregate summary statistics (p-values, fold-change estimates) and need to perform meta-analysis while harmonizing compound nomenclature across datasets. Use this skill when the underlying R package (e.
    0 installs
50. ▌
    Parameter Configuration Conditional Logic 2 · holobiomicslab

    Use when setting up a LipidMatch analysis run and you need to select among three mutually-exclusive analysis modes (PFAS, Lipid, or Tween-positive detection). The trigger is application-level metadata or user specification that indicates which detection mode should execute.
    0 installs
51. ▌
    Graph Database Indexing And Serialization 2 · holobiomicslab

    Use when you have retrieved and deduplicated chemical formulae and metadata from multiple heterogeneous sources (HMDB, ChEMBL, PubChem) and extracted both structural relationships (DBEdges) and biological reactant pairs (BioEdges from KEGG), and now need to merge them into a single queryable.
    0 installs
52. ▌
    Mass Spectrometry Peak Intensity Encoding 2 · holobiomicslab

    Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity dimensionality while preserving spatial relationships between measurement points, or (3) apply iterative peak picking.
    0 installs
53. ▌
    Word Embedding Aggregation For Spectral Data 2 · holobiomicslab

    Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular networking that correlate better with structural similarity than cosine-based methods.
    0 installs
54. ▌
    Word Embedding Based Spectrum Representation 2 · holobiomicslab

    Use when when comparing large numbers of MS/MS spectra against spectral libraries or in molecular networking, particularly when molecules differ by multiple structural modifications and cosine-based scores produce excessive false positives.
    0 installs
55. ▌
    Bayesian Model Update With Experimental Data 2 · holobiomicslab

    Use when you have completed one or more LC-MS gradient runs, extracted separation efficiency metrics from the resulting MS1 and MS2 spectra, and need to incorporate those real experimental observations into your Gaussian process model to improve the next gradient proposal.
    0 installs
56. ▌
    Bi Encoder Cross Encoder Architecture Design 2 · holobiomicslab

    Use when you have paired spectrum-compound reference data and need to simultaneously retrieve candidate compounds rapidly (bi-encoder) while also refining relevance scores through joint context modeling (cross-encoder).
    0 installs
57. ▌
    Blood Sample Processing Parameter Extraction 2 · holobiomicslab

    Use when when you have peripheral blood sample cohorts (plasma/serum) with multiple timestamps (e.
    0 installs
58. ▌
    Community Metabolic Reconstruction Synthesis 2 · holobiomicslab

    Use when you have draft metabolic reconstructions (in SBML or equivalent format) for multiple organisms sampled from a single ecological community (e.
    0 installs
59. ▌
    Exploitation Exploration Trade Off Balancing 2 · holobiomicslab

    Use when you are in the Bayesian optimization loop after fitting a Gaussian Process model to observed LC gradient runs, and you need to propose the next gradient to evaluate.
    0 installs
60. ▌
    Floating Point Numerical Accuracy Assessment 2 · holobiomicslab

    Use when when implementing or validating a lossy numeric codec for mass-spectrometry data (e.g., MSNumpressCoder in OpenMS). Specifically: after implementing both encoder and decoder, before shipping to production, or when comparing alternative compression schemes.
    0 installs
61. ▌
    Fragmentation Pattern Extraction And Ranking 2 · holobiomicslab

    Use when you have a collection of MS/MS spectra (≥2 spectra) and wish to identify fragmentation signatures common to subsets of those spectra.
    0 installs
62. ▌
    Gibbs Sampler Implementation And Convergence 2 · holobiomicslab

    Use when your metabolomics dataset contains missing values below a known detection limit (left-censored MNAR data), and you need to recover these values while respecting the truncation constraint.
    0 installs
63. ▌
    Graph Based Metabolite Similarity Assessment 2 · holobiomicslab

    Use when you have a collection of MS/MS spectra (stored as Spectrum2 objects in an ms2Lib class) and need to identify which spectra share identical fragmentation patterns—particularly when coupled to a GNPS molecular network to focus on explaining network components (connected components, cliques.
    2 installs
64. ▌
    Intensity Dependent Missing Value Simulation 2 · holobiomicslab

    Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real detector behavior where lower-intensity pixels are more likely to be missed or undetected.
    0 installs
65. ▌
    Internal Standardization With Isotope Labels 2 · holobiomicslab

    Use when your IM-MS lipidomics samples have been spiked with fully labeled isotopic internal standards (e.
    2 installs
66. ▌
    Ion Mobility Saturation Detection And Repair 2 · holobiomicslab

    Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which distorts peak shape and abundance estimates across the m/z and drift-time axes.
    0 installs
67. ▌
    Marker Feature Identification And Validation 2 · holobiomicslab

    Use when when processing GC–MS or LC–MS data as m/z vs retention time chromatograms and you need to identify biomarker or chemical marker features without conventional peak picking, particularly when false positive detection rates from peak detection algorithms are problematic.
    0 installs
68. ▌
    Metabolite Concentration To Spectrum Mapping 2 · holobiomicslab

    Use when when you have a list of known metabolite concentrations and their corresponding J-coupling constants (spin systems) and need to generate realistic 1D 1H NMR spectra or 2D correlation spectra (COSY, HSQC, HMQC) for simulation, validation, or educational purposes, without access to actual.
    0 installs
69. ▌
    Missing Value Imputation For Column Metadata 2 · holobiomicslab

    Use when when preparing raw HPLC column parameter arrays for featurization into feature vectors for retention time prediction models. Specifically apply this skill when column metadata contains empty strings (indicating missing diameter or pH values) or non-standard string encodings (e.g., '2.
    0 installs
70. ▌
    Molecular Fingerprint Bit Frequency Analysis 2 · holobiomicslab

    Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties before using them for classification, similarity search, or method validation.
    0 installs
71. ▌
    Multiple Linear Regression Model Application 2 · holobiomicslab

    Use when when you have an observed m/z value from mass spectrometry imaging and need to annotate it with a ranked list of candidate chemical formulae. Apply this skill when the KnownSet database (2.
    0 installs
72. ▌
    Non Targeted Feature Detection And Screening 2 · holobiomicslab

    Use when you have raw LC/MS data in mzML format and your analysis goal is to comprehensively detect and annotate all mass spectral features present, rather than measuring predefined target analytes.
    0 installs
73. ▌
    Peak Quality Metric Interpretation Alignment 2 · holobiomicslab

    Use when when you have loaded aligned peak-alignment data from a molecular networking task and need to distinguish high-confidence, reproducible peak alignments from noise or spurious matches.
    2 installs
74. ▌
    Pipeline End To End Execution And Validation 2 · holobiomicslab

    Use when you have a published computational pipeline with deposited code and validation data, and you need to verify that the pipeline can be executed end-to-end to reproduce reported validation metrics (annotation accuracy, coverage, or equivalent performance benchmarks).
    0 installs
75. ▌
    Pytorch Model Instantiation And Forward Pass 2 · holobiomicslab

    Use when after defining a multi-branch neural network architecture (e.
    0 installs
76. ▌
    Quality Control Metric Distribution Analysis 2 · holobiomicslab

    Use when after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
    0 installs
77. ▌
    Retention Time Alignment Mapping Application 2 · holobiomicslab

    Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for each sample, but before summing intensity vectors element-wise to construct the composite map.
    0 installs
78. ▌
    Retention Time Calibration Lowess Regression 2 · holobiomicslab

    Use when after mass track construction and before composite map building, when you need to align retention times across multiple LC-MS samples. Trigger conditions: (1) you have identified high-selectivity landmark peaks (mSelectivity > 0.99) in a reference sample;
    2 installs
79. ▌
    Retention Time Feature Distribution Analysis 2 · holobiomicslab

    Use when you have extracted retention times from top MS1 features in an LC-MS/MS experiment and need to assess whether the gradient configuration (start and end time in minutes) achieves adequate compound separation across the full chemical space.
    0 installs
80. ▌
    Sample Metadata Stratification And Filtering 2 · holobiomicslab

    Use when when you have retrieved a large, heterogeneous collection of tandem MS files from ReDU or MassIVE and need to isolate a subset sharing specific sample characteristics (e.
    2 installs
81. ▌
    Sample To Reference Retention Time Remapping 2 · holobiomicslab

    Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for each sample during prior alignment steps.
    0 installs
82. ▌
    Sterol Structure Representation And Curation 2 · holobiomicslab

    Use when when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or collision cross section (CCS) prediction workflows.
    0 installs
83. ▌
    Tandem Mass Spectrometry Data Interpretation 2 · holobiomicslab

    Use when you have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation and identification at systems scale.
    0 installs
84. ▌
    Spectral Peak Detection And Alignment 2 · holobiomicslab

    Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or vendor formats).
    0 installs
85. ▌
    U13c Labeled Standard Reference Matching 2 · holobiomicslab

    Use when you have IM-MS measurements of samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract) and need to assess whether measured CCS values systematically deviate from their true reference values.
    0 installs
86. ▌
    Raw Spectral Data Import And Preprocessing 2 · holobiomicslab

    Use when you have raw metabolomics data in mzML or mzXML format and need to convert it into a normalized feature table (CSV or mzTab) via automated batch processing.
    0 installs
87. ▌
    Computational Reproducibility Verification 2 · holobiomicslab

    Use when you have access to both raw data (deposited in a repository like Zenodo) and analysis scripts (in a GitHub repository), and you need to confirm that the published figures, tables, or quantitative findings are reproducible.
    0 installs
88. ▌
    Ion Image Augmentation Intensity Dependent 2 · holobiomicslab

    Use when training a contrastive encoder on mass spectrometry imaging (MSI) data in ISO mode (isotope ions from the same molecule).
    2 installs
89. ▌
    Iterative Peak Selection From Latent Space 2 · holobiomicslab

    Use when you have latent low-dimension peak features extracted by a Graph-attention autoencoder from imaging mass spectrometry (IMS) datasets, and you need to automatically identify a ranked subset of marker ions without manual inspection.
    0 installs
90. ▌
    Search Result Visualization Across Domains 2 · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to synthesize results across domains (e.
    0 installs
91. ▌
    Tissue Spatial Analysis Pipeline Execution 2 · holobiomicslab

    Use when you have raw IMC (protein imaging) and SIMS (metabolite imaging) data from tissue regions that require spatial co-registration, single-cell-level intensity quantification, and joint analysis of protein–metabolite relationships.
    0 installs
92. ▌
    Large Scale All Pairs Similarity Benchmarking 2 · holobiomicslab

    Use when you have multiple competing spectral similarity scoring methods (e.
    2 installs
93. ▌
    Word2vec Embedding Training Mass Spectrometry 2 · holobiomicslab

    Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture fragmentation patterns and neutral loss relationships.
    0 installs
94. ▌
    Col Mode Augmentation Pipeline Implementation 2 · holobiomicslab

    Use when when you have preprocessed mass spectrometry imaging (MSI) ion images and need to generate augmented image pairs for contrastive learning in co-localized ion discovery tasks.
    0 installs
95. ▌
    Comparative Classifier Performance Assessment 2 · holobiomicslab

    Use when you have a labeled peak quality dataset (development set with ground-truth pass/fail labels), a defined set of peak-quality metrics (e.
    0 installs
96. ▌
    Feature Network Construction And Partitioning 2 · holobiomicslab

    Use when you have a preprocessed LC-MS feature table (m/z, retention time, intensity columns) and need to identify which features belong together as isotopes or adducts of the same neutral compound.
    0 installs
97. ▌
    Lc Ms Gradient Encoding Vector Representation 2 · holobiomicslab

    Use when when you have a set of candidate LC gradients (parameter combinations) that you wish to evaluate with a Gaussian process model, or when you need to convert raw gradient specifications into a standardized numerical format for Bayesian optimization acquisition function computation.
    0 installs
98. ▌
    Mass Spectrum Normalization And Preprocessing 2 · holobiomicslab

    Use when you have raw tandem mass spectra data (mz/intensity pairs and precursor m/z values) and need to train interpretable machine learning models (regression or tree-based) where feature interpretability and direct chemical meaning are required.
    2 installs
99. ▌
    Metadata Extraction From Fixed Offset Records 2 · holobiomicslab

    Use when you have a binary file (e.g., NV format) with a known fixed-size header block (e.
    2 installs
100. ▌
     Oracle Mode Structural Constraint Integration 2 · holobiomicslab

     Use when when you have loaded both a known compound and its modified analog with MS/MS spectra, initially generated baseline modification probability scores, and then obtained or confirmed the structure of the modified compound.
     0 installs