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HolobiomicsLab

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1. ▌
   Spectral Peak Alignment With Mass Offset 2 · holobiomicslab

   Use when when comparing two MS/MS spectra where the precursor m/z values differ (indicating potential mass modifications, adducts, or related compounds), and you want to detect structurally conserved fragmentation patterns that would be missed by direct m/z matching.
   0 installs
2. ▌
   Spectral Peak Smoothing Artifact Removal 2 · holobiomicslab

   Use when raw Agilent MassHunter (.d) or UIMF mass spectrometry files exhibit jagged or noisy peaks, particularly for low-abundance ions where signal-to-noise ratio is poor.
   2 installs
3. ▌
   Spectral Similarity Network Construction 2 · holobiomicslab

   Use when after acquiring MS/MS spectral data from untargeted metabolomics experiments and having candidate transformed structures from biotransformation rule application.
   0 installs
4. ▌
   Spectrum Preprocessing And Normalization 2 · holobiomicslab

   Use when you have raw MS/MS spectra in MGF or other standard formats that need to be ingested into a machine learning pipeline for cross-modal matching against molecular structures, or when spectra from different collision energy levels or instruments require standardization before comparative.
   0 installs
5. ▌
   Time And Memory Complexity Visualization 2 · holobiomicslab

   Use when when deploying a metabolomics processing tool (such as asari) and needing to predict resource requirements or validate claimed scalability on laptop-class hardware (≤16 GB RAM, single CPU core).
   2 installs
6. ▌
   Uncertainty Quantification Rt Prediction 2 · holobiomicslab

   Use when you have trained a DNN retention time predictor and need to rank candidate metabolites for an unknown compound: the DNN outputs both point estimates and uncertainty bounds for each candidate's RT, and you need to convert these into probabilistic scores that reflect confidence in each.
   0 installs
7. ▌
   Untargeted Metabolomics Feature Analysis 2 · holobiomicslab

   Use when you have a feature table from untargeted metabolomics (with m/z, retention time, and p-values from differential abundance testing) but lack or wish to bypass metabolite annotation.
   0 installs
8. ▌
   Cloud Hosted Computational Chemistry 2 · holobiomicslab

   Use when you have a curated dataset of ≤10,000 molecular structures with known collision cross section values for training, a target set of ≤10,000 molecules requiring CCS predictions, a compatible browser, and either lack local Python installation or prefer cloud-based execution to avoid.
   0 installs
9. ▌
   Conformer Generation And Enumeration 2 · holobiomicslab

   Use when you have SMILES strings of molecules at specific ionization states (e.g., protonated or deprotonated adducts) and need to predict collision cross section values for mass spectrometry-based metabolite annotation.
   0 installs
10. ▌
    Frame Metadata Extraction And Export 2 · holobiomicslab

    Use when after completing multidimensional smoothing and saturation repair on Agilent MassHunter (.
    2 installs
11. ▌
    Molecular Structure Dataset Curation 2 · holobiomicslab

    Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values, and you need to format and validate them as input to a machine learning CCS prediction model.
    2 installs
12. ▌
    Spike Artifact Detection And Removal 2 · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that exhibits isolated high-intensity noise artifacts or instrumental artifacts that appear as discrete, non-continuous signals in the retention time, ion mobility, or m/z dimensions.
    2 installs
13. ▌
    Batch Effect Correction Chromatography 2 · holobiomicslab

    Use when when analyzing untargeted LC/HRMS data from population-scale projects (n > 500) spanning multiple sample batches or instrument runs, peaks with identical or near-identical m/z values appear at systematically shifted retention times across batches due to instrument drift, column aging, or.
    0 installs
14. ▌
    Chemical Similarity Metric Aggregation 2 · holobiomicslab

    Use when when you have an unknown metabolite compound with mass spectral data, have retrieved candidate structures from a molecular structure database (PubChem, HMDB), and have obtained predictions of structurally related metabolites from a deep-learning semantic similarity model (e.g., DeepMASS2).
    2 installs
15. ▌
    Chemical Structure Format Verification 2 · holobiomicslab

    Use when working with mass spectrometry spectral libraries (GNPS, MoNA, MTBLS1572, MassBank) that have been preprocessed by prior teams but may contain formatting errors or entries with missing/null SMILES fields.
    0 installs
16. ▌
    Compound Class Prediction From Spectra 2 · holobiomicslab

    Use when you have an unknown mass spectrometry spectrum (acquired experimentally or computationally) and need to assign it to a known drug class or identify candidate structures.
    0 installs
17. ▌
    Multivariate Lipid Metabolite Analysis 2 · holobiomicslab

    Use when you have integrated, normalized lipidomic and metabolomic feature tables from the Multi-ABLE method or similar concurrent multiomics workflows, with matched sample phenotypes (e.
    0 installs
18. ▌
    Reference Feature Combination Strategy 2 · holobiomicslab

    Use when when you have isolated, high-confidence reference chromatographic peaks (ground-truth) from reference LC-HRMS chromatograms that have been matched across multiple samples, and you need to train a CNN model to detect peaks in new chromatograms but lack sufficient labelled instances.
    2 installs
19. ▌
    Spectral Data Preprocessing Lipidomics 2 · holobiomicslab

    Use when you have raw lipidomic and metabolomic spectral data files from a Multi-ABLE barocycler-based concurrent multiomics experiment and need to normalize ion intensities, align retention times and m/z values across samples, and remove noise or low-signal features before statistical comparison.
    0 installs
20. ▌
    Structure Database Candidate Retrieval 2 · holobiomicslab

    Use when you have a mass spectrum of an unknown metabolite with a known or inferred precursor m/z, you have run a deep-learning semantic similarity model (e.
    0 installs
21. ▌
    Synthetic Training Instance Generation 2 · holobiomicslab

    Use when when you have a small set of matched reference features (isolated, high-quality chromatographic peaks from reference chromatograms that have been aligned to a ground-truth reference list) and need to train a CNN model for peak detection in LC-HRMS profile mode data.
    0 installs
22. ▌
    Colocalization Coefficient Computation 2 · holobiomicslab

    Use when you have two co-registered LA-ICP-MS element channel images and need to quantify whether their spatial distributions are statistically correlated or independent. Use it specifically when investigating whether two elements co-occur spatially (e.
    0 installs
23. ▌
    Mass Spectrometry Image Reconstruction 2 · holobiomicslab

    Use when you have paired .imzML (XML metadata) and .
    0 installs
24. ▌
    Multimodal Spot Correspondence Mapping 2 · 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
25. ▌
    Conda Environment Creation And Management 2 · holobiomicslab

    Use when when setting up a new computational workflow (e.g., ENPKG) that depends on pinned versions of Python packages and system libraries, or when collaborating across machines where package availability or versions may differ.
    0 installs
26. ▌
    Automated Feature Extraction From Spectra 2 · holobiomicslab

    Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication, sample scoring, or comparative profiling without manual inspection.
    2 installs
27. ▌
    Block Layout Analysis For Io Optimization 2 · holobiomicslab

    Use when when preparing NMR datasets for processing in NMRFx and the Dataset.createDataFile() method must choose among competing storage backends.
    2 installs
28. ▌
    Chemical Annotation Confidence Assessment 2 · holobiomicslab

    Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical explorer visualization, sample filtering, or comparative metabolomics).
    0 installs
29. ▌
    Chemical Structure Annotation Oracle Mode 2 · holobiomicslab

    Use when you have a known compound structure with validated MS/MS spectrum and a structural analog (modified version) with its own MS/MS spectrum, and you need to assess whether a modification site prediction method correctly identifies which atoms were altered.
    1 install
30. ▌
    Chemical Structure Descriptor Computation 2 · holobiomicslab

    Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or molecular geometry files, and you need to train or apply a machine-learning model to predict an instrument-dependent.
    0 installs
31. ▌
    Chimeric Spectrum Detection And Filtering 2 · holobiomicslab

    Use when you have acquired LC-MS/MS data in Data-Dependent Acquisition (DDA) mode for untargeted metabolomics and suspect contamination from chimeric (co-fragmented) MS/MS spectra.
    0 installs
32. ▌
    Compound Annotation Confidence Assessment 2 · holobiomicslab

    Use when you have MS/MS spectra matched to a reference library via both identity search (exact or high-similarity matches) and fuzzy/analog search (structurally related compounds with similar fragmentation), and you need to prioritize which annotations to trust for downstream reporting, validation.
    0 installs
33. ▌
    Contrastive Learning Encoder Construction 2 · holobiomicslab

    Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or isotope discovery.
    0 installs
34. ▌
    Convolutional Neural Network Layer Design 2 · holobiomicslab

    Use when you have 1H NMR spectral tensors as input and need to extract local features (e.g., peak patterns, signal neighborhoods) before applying attention-based or sequence-level processing.
    0 installs
35. ▌
    Decision Tree Training And Interpretation 2 · holobiomicslab

    Use when you have tandem mass spectra data and need to predict a discrete molecular property (e.g., presence/absence of a sulfo group) while maintaining full interpretability of the decision logic.
    0 installs
36. ▌
    Deep Learning Architecture Implementation 2 · holobiomicslab

    Use when you have two augmented versions of the same ion image (from mass spectrometry imaging data) and need to extract learnable 512-dimensional feature representations using a shared-weight encoder for contrastive loss optimization.
    0 installs
37. ▌
    Feature To Metabolite Network Propagation 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table (m/z, retention time, p-value from statistical test) but lack comprehensive metabolite identifications or MS/MS annotations.
    0 installs
38. ▌
    Functional Module Inference From Networks 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table (m/z and retention time columns) and a statistical test result (p-value) per feature, but lack confident metabolite identifications.
    0 installs
39. ▌
    Gaussian Process Regression Model Fitting 2 · holobiomicslab

    Use when after you have accumulated experimental MS data from ≥2 LC gradient trials, extracted separation efficiency metrics (retention time spacing) from each trial, and encoded each gradient as a feature vector.
    0 installs
40. ▌
    Injection Order Assignment And Scheduling 2 · holobiomicslab

    Use when designing multi-batch LC/GC-MS experiments where you need to control for batch effects (e.g., instrument drift, reagent lot variation) and have identified both a balance dimension (e.g., sample group, treatment condition) and a randomization dimension (e.
    0 installs
41. ▌
    M Z Database Matching With Mass Tolerance 2 · holobiomicslab

    Use when you have a set of observed m/z values extracted from a Cardinal MSImagingExperiment object, raw LC-MS data, or similar high-throughput MS dataset, and you need to assign them to known metabolites in a reference database (HMDB, Lipidmaps, etc.) with control over mass accuracy tolerance and.
    0 installs
42. ▌
    Mass Spectrometry Data Loader Integration 2 · holobiomicslab

    Use when you have mass spectrometry data available in multiple identifier formats (GNPS Task ID, Universal Spectrum Identifier, or Feature-Based Molecular Networking task reference) and need to route each format to its specific loader without manual preprocessing.
    0 installs
43. ▌
    Metabolite Signal Extraction From Lc Hrms 2 · holobiomicslab

    Use when you have raw untargeted LC/HRMS data (mzXML, mzML, or netCDF format) from population-scale studies (n > 500 samples) and need to extract a comprehensive peaklist with aligned features across all samples.
    0 installs
44. ▌
    Metabolomics Model Performance Comparison 2 · holobiomicslab

    Use when you have trained multiple machine learning classifiers (e.g., AdaBoost, SVM, Random Forest) on the same metabolomics peak-quality training set using k-fold cross-validation with repeated runs (e.
    0 installs
45. ▌
    Microbial Genome Annotation Harmonization 2 · holobiomicslab

    Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single consensus model per organism that reflects only metabolic capabilities agreed upon across the input reconstructions, or when.
    0 installs
46. ▌
    Molecular Network Clustering And Analysis 2 · holobiomicslab

    Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative molecular families.
    0 installs
47. ▌
    Nmr Metabolomic Quality Control Reporting 2 · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of plasma or serum samples, and you need to assess how processing delays affect metabolite concentrations and.
    0 installs
48. ▌
    Nmr Spectrum Tiling Format Interpretation 2 · holobiomicslab

    Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile) and the system must decide between multiple storage backends (SubMatrixFile, BigMappedMatrixFile, MappedSubMatrixFile, MappedMatrixFile). Triggers include: (1) dataset metadata specifies a cache-file flag;
    2 installs
49. ▌
    Pca Dimensionality Reduction Unsupervised 2 · holobiomicslab

    Use when you have a feature-by-sample matrix (rows = annotated chemical features such as m/z, retention time, GNPS spectral library matches;
    0 installs
50. ▌
    Probability Prediction Metric Computation 2 · holobiomicslab

    Use when after running ModiFinder's probability generation on a known compound–modified compound pair, you have a vector of per-atom modification probabilities and need to validate whether the predicted probability peaks align with the true modification sites.
    0 installs
51. ▌
    Retention Time Mass Tolerance Calibration 2 · holobiomicslab

    Use when you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct annotations, and you need to merge them into a single aligned feature matrix.
    2 installs
52. ▌
    Retention Time Prediction From Structures 2 · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) for which you need to predict retention time in liquid chromatography, especially when your target dataset contains fewer than ~500 annotated examples.
    2 installs
53. ▌
    Singular Value Decomposition Metabolomics 2 · 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.
    0 installs
54. ▌
    Statistical Filtering Metabolite Features 2 · holobiomicslab

    Use when when you have peak area tables (unlabeled C12 and labeled C13) from LC-MS metabolomics with sample metadata indicating case and control groups, and you need to distinguish true metabolic changes from instrumental noise or batch artifacts before attempting isotopic pairing.
    2 installs
55. ▌
    Tandem Mass Spectra Fragmentation Parsing 2 · holobiomicslab

    Use when when you have raw tandem mass spectra in mz/intensity format with precursor m/z values, and need to extract all fragmentation features (observed peaks and neutral losses) as a foundation for building interpretable machine learning models.
    0 installs
56. ▌
    Tissue Specific Metabolite Quantification 2 · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from multiple tissue samples and need to identify and quantify unsaturated sterol lipids at the isomer level (distinguishing double-bond position and stereochemistry).
    1 install
57. ▌
    Mass Grid Index Traversal And Retrieval 2 · holobiomicslab

    Use when when you have constructed a MassGrid (m/z-aligned mass tracks across multiple samples) and need to retrieve all sample-specific mass tracks for a given m/z value in order to sum their intensities, apply retention time calibration, or construct composite mass track objects for peak.
    0 installs
58. ▌
    Molecular Structure Tokenization Smiles 2 · holobiomicslab

    Use when when you have molecular structures encoded as SMILES strings and need to incorporate them into a multi-modal language model (such as BART) that also processes mass spectra.
    2 installs
59. ▌
    Multistage Neural Architecture Training 2 · holobiomicslab

    Use when you have paired mass spectra and molecular structure datasets and need to train a model that jointly understands both modalities for tasks like structure elucidation. Specifically, use it when: (1) you have large unlabeled or weakly-labeled pretraining data with both spectra and molecules;
    0 installs
60. ▌
    Cohort Stratified Metabolic Performance Analysis 2 · holobiomicslab

    Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR metabolomic measurements for a plasma or serum cohort, and you need to determine how processing delays impact metabolite.
    0 installs
61. ▌
    Composite Mass Track Assembly And Peak Detection 2 · holobiomicslab

    Use when after mass tracks have been aligned across all samples into a MassGrid (via sample-wise or centroid-based alignment), you have a unified set of m/z features tracked across the entire study.
    0 installs
62. ▌
    Confidence Score Extraction From Neural Networks 2 · holobiomicslab

    Use when when you have a trained deep learning model (e.g., PS2MS) and an evaluation dataset of compounds, and you need to assess how prediction confidence varies across structural novelty classes (e.g., training-similar vs. structurally novel NPS analogues).
    2 installs
63. ▌
    Dataset Object Serialization And Deserialization 2 · holobiomicslab

    Use when you have mass spectrometry data arriving through heterogeneous input formats (Task ID from GNPS, Universal Spectrum Identifiers, or Feature-Based Molecular Networking identifiers) and need to load, validate, and store them as a single standardized dataset object for interactive peak.
    0 installs
64. ▌
    Empirical Compound Annotation And Representation 2 · holobiomicslab

    Use when you have a tab-delimited feature table (m/z, retention time, intensities) from LC-MS preprocessing and need to group related ions (isotopologues, adducts, in-source fragments) into compound-level annotations with inferred neutral mass.
    0 installs
65. ▌
    Mass Spectrometry Reference Database Integration 2 · holobiomicslab

    Use when you have individual MS/MS spectra or batch .mgf files from untargeted metabolomics experiments and need to search them against domain-specific reference libraries (e.
    0 installs
66. ▌
    Quantum Chemistry Based Fragmentation Prediction 2 · holobiomicslab

    Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z values and intensities) to compare against experimental LC-IM-MS/MS data before performing CCS prediction or downstream.
    0 installs
67. ▌
    Retention Time Calibration Via Lowess Regression 2 · holobiomicslab

    Use when after mass track extraction and alignment across samples, when preparing to detect elution peaks on composite mass tracks. Use this when inter-sample retention time variation exceeds acceptable alignment tolerance (e.
    0 installs
68. ▌
    Sample Study Size Stratified Algorithm Selection 2 · holobiomicslab

    Use when when beginning mass alignment in a multi-sample LC-MS metabolomics study, before constructing the MassGrid.
    0 installs
69. ▌
    Spectral Tensor Representation And Preprocessing 2 · holobiomicslab

    Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT. Specifically: you have raw spectral data with variable peak counts and need fixed-size tensor inputs;
    0 installs
70. ▌
    Statistical Distribution Analysis Across Cohorts 2 · holobiomicslab

    Use when when you have prediction scores (softmax probabilities, uncertainties) from a trained deep learning model evaluated on a heterogeneous dataset and you need to determine whether prediction confidence or accuracy varies systematically across structurally distinct or novel compound.
    0 installs
71. ▌
    Systematic Mass Calibration And Drift Correction 2 · holobiomicslab

    Use when when processing multiple LC-MS samples in a cohort study and MassGrid construction reveals that anchor mass tracks (13C/12C isotope or Na/H adduct pairs) in non-reference samples deviate systematically from the reference sample's m/z values by >1 ppm.
    0 installs
72. ▌
    Transition List Formatting For Targeted Analysis 2 · holobiomicslab

    Use when you have generated or assembled a lipid spectral library with precursor m/z values, adduct information, and fragmentation patterns, and you need to import those spectra into Skyline for targeted data-independent or parallel-reaction-monitoring (PRM) analysis.
    0 installs
73. ▌
    Within Batch Randomization By Metadata Attribute 2 · holobiomicslab

    Use when you have already assigned samples to batches (inter-batch balance is fixed) and need to shuffle injection order within each batch to decorrelate sample properties from time-dependent instrumental effects. Use it when your metadata table includes a randomization dimension (e.
    0 installs
74. ▌
    Feature Property Refinement From Training Data 2 · holobiomicslab

    Use when you have a set of training LC-HRMS chromatograms (retention time × m/z matrix format) and a manually curated reference list of isolated single chromatographic peaks, and you need to update the reference peak properties (retention time, m/z, peak shape) to match the actual peak signatures.
    0 installs
75. ▌
    Marker Feature Visualization Retention Time Mz 2 · holobiomicslab

    Use when after NPFimg's automated detection algorithm has identified marker features from a two-dimensional MS map (m/z vs retention time), especially when you need to validate feature positions, inspect co-localization patterns, or communicate results to stakeholders.
    0 installs
76. ▌
    Redundant Node Removal And Edge Classification 2 · holobiomicslab

    Use when after network partitioning, when you have identified connected subnetworks of features matched by isotope or adduct patterns and need to sanitize and categorize the relationships before tree construction. Use it when redundant features (e.
    1 install
77. ▌
    Reproducibility Signal Detection Nonparametric 2 · holobiomicslab

    Use when when you have high-dimensional replicate experimental data (e.g., metabolomics, proteomics, genomics assays) where technical or biological variability threatens reproducibility, and you need to distinguish genuine reproducible signals from noise without assuming normality.
    0 installs
78. ▌
    Msi Metadata Harmonization Across Image Stacks 2 · holobiomicslab

    Use when you have processed and quantified MSI data from one or more imzML files in LipidQMap and need to export them as a unified, standards-compliant HDF5 container that preserves feature-by-pixel intensity matrices, per-feature lipid annotations (m/z, lipid class, adduct, neutral ID), per-pixel.
    2 installs
79. ▌
    Peak Intensity Normalization Weighted Aggregation 2 · holobiomicslab

    Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments without allowing a single dominant peak to overwhelm the learned word associations.
    2 installs
80. ▌
    Bayesian Meta Learning Chromatographic Projection 2 · holobiomicslab

    Use when you have experimental retention times (RTs) for a small set of calibration molecules (≥10) measured on both a source chromatographic method and a target method, and you need to predict RTs for candidate metabolites on the target method to rank annotation candidates.
    0 installs
81. ▌
    Biotransformation Rule Application To Metabolites 2 · holobiomicslab

    Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated database of biotransformation rules (e.g., from KEGG, RetroRules, or domain-specific repositories).
    0 installs
82. ▌
    Computational Resource Profiling And Benchmarking 2 · holobiomicslab

    Use when when evaluating a new or updated version of a data processing tool (especially asari or similar LC-MS workflows) before production deployment, or when verifying claims about scalability, memory efficiency, or throughput on specific hardware classes (e.g., ≤16 GB RAM single-core systems).
    0 installs
83. ▌
    Ion Mobility Mass Spectrometry Data Preprocessing 2 · holobiomicslab

    Use when when you have raw IM-MS data from drift tube (DT) or SLIM instruments in Agilent MassHunter (.
    0 installs
84. ▌
    Mass Spectrometry Annotation Engine Customization 2 · holobiomicslab

    Use when when you have baseline MS/MS peak annotations from a known compound but need to refine them using newly available structural information (e.
    0 installs
85. ▌
    Metabolomics Database Search And Formula Matching 2 · holobiomicslab

    Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time values.
    0 installs
86. ▌
    Nearest Neighbor Clustering For Mass Spectrometry 2 · holobiomicslab

    Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
    0 installs
87. ▌
    Internal Standardization Correction Lipidomes 2 · holobiomicslab

    Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and measured CCS values need bias assessment or correction.
    0 installs
88. ▌
    Machine Learning Based Conformation Filtering 2 · holobiomicslab

    Use when when you have generated multiple 3D conformations for a molecule or set of ionized adducts (e.g., via RDKit) and need to retain only the most energetically favorable structures before expensive quantum calculations.
    2 installs
89. ▌
    Preprocessing Pipeline Parameter Optimization 2 · holobiomicslab

    Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d) or UIMF format with jagged peaks and low-abundance ions that require signal enhancement, but you need to decide whether to apply smoothing, and at what strength, to avoid over-smoothing real signals or under-removing artifacts.
    0 installs
90. ▌
    Signal Quality Enhancement Low Abundance Ions 2 · holobiomicslab

    Use when you observe jagged or noisy peak profiles in low-abundance ions after loading raw IM-MS data (Agilent MassHunter .
    0 installs
91. ▌
    Chemical Formula Deduplication Across Databases 2 · holobiomicslab

    Use when you have retrieved chemical formulae and metadata from two or more of HMDB, ChEMBL, or PubChem and need to merge them into a single searchable database without formula duplication.
    0 installs
92. ▌
    Chromatographic Peak Detection Gradient Descent 2 · holobiomicslab

    Use when you have LC-HRMS profile-mode data (retention time × m/z matrix format) and need to automatically identify chromatographic peak locations and boundaries prior to feature extraction, reference matching, or training a peak-classification CNN model.
    1 install
93. ▌
    Coordinate System Normalization 1based Indexing 2 · holobiomicslab

    Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
    0 installs
94. ▌
    Internal Standard Ion Selection And Application 2 · holobiomicslab

    Use when after isotope correction has been applied to MSI ion images, when you have sprayed or identified a reference lipid standard of known amount (pmol/mm²) and need to normalize target lipid intensities against this standard to remove matrix effects and enable cross-pixel and cross-sample.
    0 installs
95. ▌
    Spatial Transcriptome Metabolome Coregistration 2 · holobiomicslab

    Use when you have paired spatial transcriptome and metabolome datasets (both as h5ad files with .obsm['spatial'] coordinate matrices and .
    2 installs
96. ▌
    Structure Organism Pair Counting And Deduplication 2 · holobiomicslab

    Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) in TSV or CSV format with separate 2D and 3D structure-organism pair tables, and need to produce authoritative headline counts of unique referenced pairs, unique curated structures, unique organisms, and source.
    0 installs
97. ▌
    Unknown Pollutant Identification Mass Spectrometry 2 · holobiomicslab

    Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a Windows environment with ≥16 GB RAM and ≥2 GB NVIDIA GPU, and you need compound identification with confidence scores and.
    2 installs
98. ▌
    Visual Pattern Recognition In Spectral Data 2 · holobiomicslab

    Use when after database search algorithms have scored unknown MS samples against reference species, and you need to visually inspect and confirm species assignments or identify ambiguous classifications.
    0 installs
99. ▌
    Ion Mobility Mass Spectrometry Data Processing 3 · holobiomicslab

    Use when you have IM-MS lipidomics samples spiked with U13C-labeled internal standards (e.
    2 installs
100. ▌
     Peak Apex Identification From Intensity Profiles 2 · holobiomicslab

     Use when after EIC candidate generation and peak detection have been completed on LC/HRMS data, when you need to extract the retention time and intensity values at peak maxima for each detected peak.
     2 installs