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HolobiomicsLab

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1. ▌
   Biological Reactant Pair Mapping Kegg 2 · holobiomicslab

   Use when constructing or enriching a chemical formula database that must capture not just structural similarity (DBEdges) but also biological co-occurrence patterns.
   0 installs
2. ▌
   Chromatographic Resolution Evaluation 2 · holobiomicslab

   Use when when you have a feature table from LC-MS peak detection (e.g., output from MassCube's nontargeted peak segmentation step) and need to assess which features have adequate chromatographic separation from coeluting or nearby peaks.
   0 installs
3. ▌
   Compound Structure Comparison Metrics 2 · holobiomicslab

   Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
   0 installs
4. ▌
   Convolutional Neural Network Encoding 2 · holobiomicslab

   Use when you have pairs of augmented ion images from mass spectrometry imaging data and need to generate low-dimensional representation vectors that maximize similarity between augmentations of the same image while avoiding representation collapse.
   0 installs
5. ▌
   Cumulative Distribution Visualization 2 · holobiomicslab

   Use when when you have per-feature quality metrics (such as CV values from NMR or MS reproducibility analysis) and need to: (1) confirm that a specified proportion of features meet regulatory thresholds (e.g., 99% < 0.30, 92% < 0.15 for CV);
   0 installs
6. ▌
   Dda Mode Metabolomics Data Processing 2 · holobiomicslab

   Use when when you have LC-MS/MS data collected in DDA mode and suspect that MS/MS spectra contain chimeric (multiply-charged or co-fragmented) ion signals that will degrade downstream spectral matching, library searching, or metabolite identification.
   2 installs
7. ▌
   Deep Learning Spectral Language Model 2 · holobiomicslab

   Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format with mandatory PRECURSOR_MZ and IONMODE tags) and need to identify structurally related metabolites from a reference database.
   0 installs
8. ▌
   Distribution Statistics Summarization 2 · holobiomicslab

   Use when you have loaded a collection of molecular fingerprint vectors (such as biosynfoni fingerprints from a deposited dataset) and need to characterize their statistical and distributional properties before using them for machine learning, similarity searching, or method validation.
   0 installs
9. ▌
   Feature Group Fragment Classification 2 · holobiomicslab

   Use when you have a detected LC-MS feature table (with m/z, retention time, and intensity columns) and need to identify which features are derivatives of the same parent molecule rather than distinct metabolites.
   0 installs
10. ▌
    Feature Normalization Standardization 2 · holobiomicslab

    Use when after extracting and encoding molecular descriptors and structural features (atom types, bond connectivity, graph topology) from SMILES strings into a fixed-size numerical tensor, before passing the feature matrix to the PS2MS deep learning model for NPS prediction.
    2 installs
11. ▌
    Gaussian Peakshape Fitting Evaluation 2 · holobiomicslab

    Use when after peak detection on mass track segments using find_peaks, when you need to distinguish genuine chromatographic peaks from noise-induced false positives or irregular shapes.
    2 installs
12. ▌
    Intensity Threshold Filtering Ms Data 2 · holobiomicslab

    Use when when you have loaded aligned peak data (from a preceding molecular networking alignment task) as a structured table with peak intensity, m/z, retention time, and alignment quality metrics, and you need to reduce false positives, remove noise, or focus analysis on peaks above a.
    2 installs
13. ▌
    Intensity To Concentration Conversion 2 · holobiomicslab

    Use when you have raw mass spectrometry intensity measurements from sample analyses and need absolute quantitative concentrations.
    2 installs
14. ▌
    Ion Mobility Demultiplexing Algorithm 2 · holobiomicslab

    Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover conventional (non-multiplexed) IM-MS spectra with resolved mobility and mass dimensions.
    0 installs
15. ▌
    Landmark Peak Selection And Filtering 2 · holobiomicslab

    Use when when preparing mass tracks for retention-time (RT) alignment across multiple LC-MS samples.
    0 installs
16. ▌
    Mass Spectrometry Data Interpretation 2 · holobiomicslab

    Use when you have a set of ions already matched to a khipu instance (i.e., ions whose isotope and adduct assignments are known and positioned on the theoretical khipu grid), and you need to estimate the neutral mass of the parent compound.
    0 installs
17. ▌
    Mass Spectrometry Image Preprocessing 2 · holobiomicslab

    Use when you have raw or preprocessed single-channel (2D array) or multi-channel (spectral) ion images from mass spectrometry imaging (MSI) data and need to train a contrastive deep learning model.
    2 installs
18. ▌
    Mass Spectrometry Prediction Modeling 2 · holobiomicslab

    Use when when you have a collection of compound structures in SDF format (e.
    2 installs
19. ▌
    Memory Mapped File Selection Strategy 2 · holobiomicslab

    Use when initializing a Dataset object in NMRFx and must decide which storage backend to use for in-memory or memory-mapped file access.
    0 installs
20. ▌
    Metabolic Model Consensus Integration 2 · holobiomicslab

    Use when you have draft metabolic reconstructions in SBML or standard format for multiple organisms in a microbial community (e.
    0 installs
21. ▌
    Metabolomics Training Set Preparation 2 · holobiomicslab

    Use when when you have LC-MS/MS acquisitions in DDA mode and need to train a customized DNMS2Purifier model to purify chimeric MS/MS spectra specific to your experimental conditions, metabolite classes, or ionization settings.
    0 installs
22. ▌
    Missing Pattern Generation Validation 2 · holobiomicslab

    Use when you have a complete metabolomics data matrix (simulated or real abundance table) and need to create reproducible, controlled MNAR scenarios for evaluating imputation algorithm performance.
    0 installs
23. ▌
    Multi Head Attention Mechanism Design 2 · holobiomicslab

    Use when when building a transformer-based model to process mass spectrometry data (MS/MS spectra or fingerprints) where you need the model to learn multiple independent attention patterns across spectrum features simultaneously.
    0 installs
24. ▌
    Mzmine Batch Processing Configuration 2 · holobiomicslab

    Use when you have raw metabolomics data in mzML or mzXML format and need to extract ion features, align them across samples, and produce a normalized feature table for downstream statistical or chemotaxonomic analysis.
    2 installs
25. ▌
    Non Pathway Metabolite Classification 2 · holobiomicslab

    Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other non-pathway metabolite sets) by their activity levels across experimental contrasts.
    0 installs
26. ▌
    Normalization For Unequal Group Sizes 2 · holobiomicslab

    Use when when tabulating chemical annotation enrichment (e.g., GNPS spectral library matches) across sample groups stratified by metadata category (e.g., sample type, extraction method, ionization source), and the groups contain different numbers of files or samples.
    0 installs
27. ▌
    Precursor Mass Difference Calculation 2 · holobiomicslab

    Use when when comparing two MS/MS spectra using modified cosine similarity and the precursor m/z values differ, indicating potential neutral losses, adduct variations, or analogs with different substituents.
    2 installs
28. ▌
    Quality Control Threshold Application 2 · holobiomicslab

    Use when when you have a raw feature abundance matrix with missing values (NAs or zeros) and need to remove features with excessive sparsity before imputation or reproducibility analysis.
    0 installs
29. ▌
    Sinusoidal Positional Encoding Design 2 · holobiomicslab

    Use when you have variable-length lists of MS/MS peaks (m/z and intensity pairs) that need to be encoded into a fixed-dimensional representation compatible with transformer architecture.
    0 installs
30. ▌
    Spectral Fragmentation Motif Analysis 2 · holobiomicslab

    Use when when you have metabolomics intensity data with metabolites grouped by fragmentation spectral similarity (Molecular Families or Mass2Motifs) and need to rank or score these groups by their differential activity across experimental conditions, especially when traditional pathway databases.
    0 installs
31. ▌
    Spectral Library Matching And Scoring 2 · 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.
    0 installs
32. ▌
    Spectral Peak Detection Composite Map 2 · holobiomicslab

    Use when when you have aligned mass tracks (extracted ion chromatograms) across multiple LC-MS samples consolidated into a composite map and need to detect reproducible elution peaks (features) that will be tracked back to individual samples.
    0 installs
33. ▌
    Standalone Web Application Deployment 2 · holobiomicslab

    Use when you have cloned the GNPS_MASST codebase and need to instantiate a domain-specific MASST variant (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) to accept individual MS/MS spectra as input queries and perform searches against the corresponding curated reference.
    1 install
34. ▌
    Summarized Experiment Object Handling 2 · holobiomicslab

    Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS) with epidemiological confounders.
    0 installs
35. ▌
    Transformer Cnn Hybrid Model Training 2 · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data with compound labels and need to identify multiple compounds in a flavor mixture where both local spectral patterns (handled by CNN) and long-range spectral dependencies (handled by Transformer) are diagnostic.
    0 installs
36. ▌
    Two Dimensional Spectral Map Analysis 2 · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map with m/z values on one axis and retention time on the other, and you need to identify analyte signals and chemo-/biomarker features while minimizing false positive and false negative peak detections.
    0 installs
37. ▌
    Workflow Definition Schema Validation 2 · holobiomicslab

    Use when you have located a workflow definition file (YAML or JSON) in a versioned release or commit and need to verify that it conforms to the schema specification for that release version (e.g., v1.0.0).
    0 installs
38. ▌
    Embedding Space Representation 2 · holobiomicslab

    Use when you have pairs or triplets of MS/MS spectra with associated metadata (compound structural information, Tanimoto similarity scores) and want to learn embeddings that simultaneously preserve spectral similarity relationships and reconstruct peak intensities.
    0 installs
39. ▌
    Conformer Ensemble Energy Ranking 2 · holobiomicslab

    Use when after RDKit has generated a large set of 3D conformers for a molecule in SDF or XYZ format, and before submitting conformers to computationally expensive quantum-chemical methods (e.g., QUICK).
    1 install
40. ▌
    Qm Output Parsing And Aggregation 2 · holobiomicslab

    Use when you have completed parallel QUICK quantum calculations on multiple conformers filtered by ASE-ANI and need to extract electronic properties from the output logs and consolidate them into a single structured table for use in CCS calculations or metabolite annotation workflows.
    0 installs
41. ▌
    Chromatographic Baseline Estimation 2 · holobiomicslab

    Use when you have extracted ion chromatogram (EIC) candidate data from untargeted LC/HRMS files (mzXML, mzML, or netCDF format) and need to identify genuine peaks within each EIC.
    0 installs
42. ▌
    Duplicate Spectrum Detection Splash 2 · holobiomicslab

    Use when when processing large collections of mass spectra from multiple Open Mass Spectra Libraries (OMSLs) or databases that may contain redundant spectral records with identical m/z–intensity peak patterns but potentially different metadata annotations.
    2 installs
43. ▌
    Feature Table Export And Validation 2 · holobiomicslab

    Use when after executing an MZmine batch processing workflow on raw metabolomics data (mzML/mzXML format), when you need to convert the in-memory feature detection and alignment results into a shareable, schema-compliant tabular format suitable for downstream statistical analysis, figure.
    2 installs
44. ▌
    High Performance Metric Computation 2 · holobiomicslab

    Use when you have implemented or are evaluating an algorithmic or system optimization (e.g., MASST+) that claims to reduce execution time, and you need to quantify and statistically validate the speedup against a baseline system (e.g., MASST).
    0 installs
45. ▌
    Mass Accuracy Tolerance Application 2 · holobiomicslab

    Use when when you have generated in silico annotations (from GNPS ISDB, SIRIUS, or timaR) and need to distinguish true matches from false positives by enforcing a mass accuracy constraint. Apply this skill before computing novelty metrics (e.
    0 installs
46. ▌
    Mass Spectrometry Adduct Assignment 2 · holobiomicslab

    Use when when processing in-silico or experimental MS spectra records from databases with incomplete metadata, specifically when the adduct field is null or absent but the ionmode field (positive/negative polarity) is present.
    0 installs
47. ▌
    Metabolomic Peak Quality Assessment 2 · holobiomicslab

    Use when after peak detection in untargeted LC/HRMS workflows, when you have a list of candidate peaks with signal intensity profiles and need to filter them according to data quality thresholds (signal-to-noise ratio, peak width, baseline separation, and isotopic pairing consistency) before.
    2 installs
48. ▌
    Peak Annotation With Bounding Boxes 2 · holobiomicslab

    Use when you have isolated reference peaks from training chromatograms (ground-truth, single compounds per sample) and need to create a diverse, labelled training set large enough to train a CNN peak detector.
    0 installs
49. ▌
    Semantic Version Parsing Comparison 2 · holobiomicslab

    Use when before executing a bioinformatics pipeline that depends on multiple R packages with strict version constraints (e.g., DaDIA, which requires R ≥4.0, XCMS ≥3.11.4, and metaMS =1.25.1).
    0 installs
50. ▌
    Batch File Processing Orchestration 2 · holobiomicslab

    Use when when you have multiple CDF imaging files (e.g., from mass spectrometry imaging scans of biological samples) that need to be read into a single Matlab workspace with consistent structure and metadata (spectral intensity, m/z arrays, spatial coordinates).
    2 installs
51. ▌
    Contrastive Learning Encoder Design 2 · holobiomicslab

    Use when when you have mass spectrometry ion image data and need to learn meaningful low-dimensional representations through self-supervised contrastive learning.
    0 installs
52. ▌
    Metabolic Network Edge Construction 2 · holobiomicslab

    Use when when building a comprehensive chemical knowledge base for mass spectrometry formula assignment, particularly when you need to link chemical formulae across heterogeneous repositories (HMDB, ChEMBL, PubChem) and connect them through known metabolic transformations to improve annotation.
    2 installs
53. ▌
    Root Developmental Tissue Profiling 2 · holobiomicslab

    Use when you have CDF-format mass spectrometry imaging files from plant roots with accompanying MATLAB workspace files (.mat), and your research goal is to reproduce linear-axis intensity profiles, feature distributions, and spatial metrics reported in a prior publication (e.g., Sama et al. 2025).
    2 installs
54. ▌
    Binary Cross Entropy Loss Optimization 2 · holobiomicslab

    Use when you have a pre-trained TCN spectrum encoder, annotated MS/MS spectra paired with ground-truth molecular formulas, and you want to train only the formula ranking and rescoring components without retraining the spectrum feature extractor.
    2 installs
55. ▌
    Neutral Loss Annotation Interpretation 2 · holobiomicslab

    Use when when building Word2Vec or embedding-based spectral similarity models where you need to capture fragmentation patterns beyond individual peak positions.
    2 installs
56. ▌
    Baseline Noise Estimation Chromatogram 2 · holobiomicslab

    Use when after auditing and optionally rescaling a mass track (composite mass chromatogram) when you need to subtract background signal and set dynamic prominence thresholds for peak detection.
    2 installs
57. ▌
    Cardinal Peak Processing Snr Filtering 2 · holobiomicslab

    Use when when you have loaded an unprocessed Cardinal object from MS imaging data (e.g., from Zenodo or native formats) containing thousands of m/z features across many spectra, and you need to produce a curated peak list with known expected peak count (e.g., 687 cleaned peaks from PIGII_206).
    2 installs
58. ▌
    Chemical Structure Similarity Matching 2 · holobiomicslab

    Use when you have a set of query chemical compounds (as SMILES, names, or ChemMine objects) and a reference library organized into type groups (e.g., Type A–E chemical sets), and you need to assign each query compound to its -matching type based on structural similarity.
    0 installs
59. ▌
    Community Dependent Reaction Inference 2 · holobiomicslab

    Use when you have consensus metabolic reconstructions for multiple community members (e.g., plant-associated microbes or plant-microbial consortia) and those individual models contain incomplete or disconnected metabolic pathways.
    0 installs
60. ▌
    Metabolite Annotation At Scale 2 · holobiomicslab

    Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign putative metabolite identities using public structural databases.
    1 install
61. ▌
    Metabolite Intensity Alignment 2 · holobiomicslab

    Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE method (high-pressure liquid chromatography–mass spectrometry output) and need to prepare them for multivariate analysis to detect differential lipids and metabolites across biological samples (e.
    0 installs
62. ▌
    Modification Site Localization 2 · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally related modified (unknown) compound—and need to identify which atom(s) in the structure carry the modification.
    0 installs
63. ▌
    Organism Dictionary Enrichment 2 · holobiomicslab

    Use when after organism names have been cleaned and standardized (e.g., via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) but before final integration of organism, structure, and reference data. Use it when you have a cleaned organism table (interim/tables/2_cleaned/organism/cleaned.tsv.
    0 installs
64. ▌
    Pathway Level Activity Scoring 2 · holobiomicslab

    Use when you have a metabolite intensity matrix (samples × metabolites) with assigned annotations (peak IDs mapped to KEGG or ChEBI compound IDs), a metabolic pathway database, and need to rank pathways by activity level within experimental groups or comparisons.
    2 installs
65. ▌
    Pipeline Prerequisite Checking 2 · holobiomicslab

    Use when before launching the DaDIA metabolomics pipeline or any multi-package workflow, when you have an R environment with potentially mixed or unknown package versions and need to confirm that R ≥4.0, XCMS ≥3.11.4, metaMS ≥1.25.
    0 installs
66. ▌
    Plasma Serum Sample Comparison 2 · holobiomicslab

    Use when you have NMR-based metabolomics measurements from a cohort containing both plasma and serum samples with associated processing delay metadata (pre- and post-centrifugation times), and you need to determine whether metabolic parameter stability differs between the two sample types or to.
    0 installs
67. ▌
    Precursor Fragment Ion Pairing 2 · holobiomicslab

    Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo, Waters, or Bruker instruments) and a list of target compounds defined by precursor m/z values (and optionally retention time windows).
    0 installs
68. ▌
    Repository Metadata Extraction 2 · holobiomicslab

    Use when when you need to inventory a collection of related web applications or tools distributed across multiple repositories, discover their live deployment URLs, trace their associated publications, and verify accessibility and metadata completeness.
    0 installs
69. ▌
    Semantic Versioning Validation 2 · holobiomicslab

    Use when when you need to confirm that a generated or retrieved release artifact from a version control system (e.g., git tag v1.0.0) produces byte-for-byte or functionally equivalent outputs to the official release published on a platform (e.g., GitHub Releases) on a specific date.
    0 installs
70. ▌
    Signal Smoothing Preprocessing 2 · holobiomicslab

    Use when when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection. Smoothing is particularly needed when the signal-to-noise ratio is low or when gradient-based peak detection would be compromised by high-frequency noise.
    0 installs
71. ▌
    Sparse Feature Vector Handling 2 · holobiomicslab

    Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train an interpretable model (e.
    0 installs
72. ▌
    Spatial Coordinate Mapping Msi 2 · holobiomicslab

    Use when after loading and preprocessing a Cardinal MSImagingExperiment object (with normalized peaks and optional spatial segmentation results), and before conducting spatial statistical tests or co-localization analyses.
    0 installs
73. ▌
    Spectral Library Matching Gnps 2 · holobiomicslab

    Use when you have MS2 product-ion spectra in open formats (.mzML or .mzXML) from public mass spectrometry datasets (e.g., from MassIVE with a valid accession) and need to identify chemical compounds by comparing fragmentation patterns against the GNPS reference spectral library.
    0 installs
74. ▌
    Spectrum Feature Vectorization 2 · holobiomicslab

    Use when you have raw mass spectrometry spectra (peak lists or intensity arrays) that must be fed into a pre-trained deep learning model for substance classification (e.g., PS²MS for NPS detection).
    0 installs
75. ▌
    Taxonomic Metadata Integration 2 · holobiomicslab

    Use when after organism name cleaning and standardization (via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) has produced a cleaned organism table (interim/tables/2_cleaned/organism/cleaned.tsv.gz), apply this skill to map those cleaned names to Open Tree of Life (OTL) identifiers.
    1 install
76. ▌
    Theoretical Mz Grid Generation 2 · holobiomicslab

    Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of the same neutral compound.
    0 installs
77. ▌
    Scientific Task Formulation 2 · holobiomicslab

    Use when you encounter a published scientific article or software paper that makes claims about data processing, analysis, or results, but the reproducibility context is unclear, artifacts are scattered, or the connection between claims and outputs is not immediately evident.
    0 installs
78. ▌
    Conformer Generation Rdkit 2 · holobiomicslab

    Use when when you have ionized adduct structures (SMILES or MOL format) from an ionization-state determination step and need to create an ensemble of relaxed 3D geometries for each molecule prior to expensive conformation filtering (e.g., ASE-ANI or quantum methods).
    0 installs
79. ▌
    Consensus Mass Determination 2 · holobiomicslab

    Use when after constructing individual mass tracks from mzTree data bins and before alignment across samples.
    2 installs
80. ▌
    JSON Spectral Format Parsing 2 · holobiomicslab

    Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness, check for required metadata fields (SMILES, InChI, InChIKey, precursor m/z, adduct), and separate spectra by acquisition.
    0 installs
81. ▌
    Spectral Metadata Validation 2 · holobiomicslab

    Use when processing heterogeneous mass spectral datasets from multiple open libraries (e.g., MassBank, UNPD, GMD) where structural identifiers, precursor m/z, and adduct information are frequently incomplete or inconsistent across records.
    0 installs
82. ▌
    Linear Axis Spatial Analysis 2 · holobiomicslab

    Use when you have deposited mass spectrometry imaging datasets in NetCDF (CDF) format with accompanying MATLAB workspace files (.
    1 install
83. ▌
    Matlab Data Structure Design 2 · holobiomicslab

    Use when you have multiple CDF files containing mass spectrometry imaging data (spectra, m/z arrays, and spatial coordinates) that need to be ingested into MATLAB for the DIMPLE pipeline or similar linear-axis mass spectrometry imaging analysis.
    0 installs
84. ▌
    Random Missing Value Masking 2 · holobiomicslab

    Use when preparing ion image data for contrastive learning in mass spectrometry imaging (MSI), specifically when you need to augment single ion images into pairs of variants for encoder training in COL mode (co-localized ions) or as a base component of ISO mode (isotope ions).
    0 installs
85. ▌
    Spatial Filtering Ion Images 2 · holobiomicslab

    Use when preparing raw ion image data from mass spectrometry imaging for deep learning-based representation learning.
    0 installs
86. ▌
    Metabolite Set Activity Scoring 2 · holobiomicslab

    Use when you have log2-transformed, standardized peak intensity matrices with metabolite annotations (peak ID → KEGG/ChEBI IDs) and need to test whether groups of peaks co-vary systematically within known pathways or spectral groupings.
    0 installs
87. ▌
    Molecular Descriptor Extraction 2 · holobiomicslab

    Use when when you have validated SMILES strings or canonical molecule objects from RDKit and need to convert them into the fixed-size numerical tensor format expected by a deep learning model (e.g., PS2MS).
    0 installs
88. ▌
    Spectral Data Format Conversion 2 · holobiomicslab

    Use when you have raw LC–MS data in vendor-proprietary or uncorrected formats (e.g., .raw, .d) and need to perform targeted peak detection, retention-time correction, or automated quality metrics on identified compounds. The input files must be converted to .
    2 installs
89. ▌
    Spectral File Format Conversion 2 · holobiomicslab

    Use when when importing raw mass spectrometry data from instrument vendors or public repositories in one format (e.g., mzML, mzXML) and needing to export it in another format (e.
    0 installs
90. ▌
    Axis Label Format Customization 2 · holobiomicslab

    Use when when designing injection plate layouts in InjectionDesign and needing to display sample positions with clear, domain-appropriate labels on the y-axis (e.g., row identifiers, well coordinates, or sample indices).
    0 installs
91. ▌
    Biotransformation Rule Encoding 2 · holobiomicslab

    Use when you have untargeted metabolomics data with unknown metabolite structures and need to generate plausible candidate products by systematically applying known enzymatic or chemical transformation rules.
    0 installs
92. ▌
    Bruker Nmr Spectral Data Import 2 · holobiomicslab

    Use when you have raw Bruker NMR spectral files (from a Bruker instrument) in a directory and need to prepare them for automated metabolite identification and quantification using ASICS.
    2 installs
93. ▌
    Candidate Metabolite Prediction 2 · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in positive or negative ion mode and need to identify candidate metabolites from a structure database.
    2 installs
94. ▌
    Chromatographic Method Transfer 2 · holobiomicslab

    Use when you have retention time predictions from a source chromatographic method and need to predict retention times for a target chromatographic method, but have limited calibration data (10–100 molecules) measured on both methods.
    0 installs
95. ▌
    Confidence Score Interpretation 2 · holobiomicslab

    Use when after executing forward inference on preprocessed mass spectrometry spectra with a deep learning model (e.g., PS²MS), when you have per-spectrum predictions with associated confidence scores or per-class probabilities.
    2 installs
96. ▌
    Contrastive Loss Implementation 2 · holobiomicslab

    Use when training embeddings from MS/MS spectra and you need to simultaneously enforce: (1) discrimination between spectra with different structural properties via contrastive learning on peak information and metadata embeddings, and (2) accurate reconstruction of embeddings from peak features via.
    2 installs
97. ▌
    J Coupling Multiplet Generation 2 · holobiomicslab

    Use when you have parsed metabolite identities with known spin-system coupling constants (J-values) and chemical shifts, and need to generate the theoretical multiplet patterns that will form the basis of a simulated 1D or 2D NMR spectrum.
    0 installs
98. ▌
    Lipid Class Coverage Assessment 2 · holobiomicslab

    Use when when you have acquired a CCS reference library (such as DTCCSN2 for U13C labeled lipids) and need to verify that it contains the expected lipid classes, CCS values are physically plausible for ion mobility data, and coverage matches the library's advertised documentation before using it.
    0 installs
99. ▌
    Lipid Class Stratified Analysis 2 · holobiomicslab

    Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
    1 install
100. ▌
     Mass Spectral Feature Alignment 2 · holobiomicslab

     Use when when you have separate LC-MS peak tables for unlabeled (C12) and labeled (C13) isotope tracer experiments and need to identify which features correspond to the same metabolite across the two labeling conditions.
     2 installs