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HolobiomicsLab

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1. ▌
   Blank Contamination Filtering · holobiomicslab

   Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.
   2 installs
2. ▌
   Chemical Formula Tokenization · holobiomicslab

   Use when you have collections of chemical formulae (e.g., from SIRIUS decomposition or subformula labeling) derived from MS/MS spectra and need to feed them into a transformer encoder.
   1 install
3. ▌
   Chemical Metadata Integration · holobiomicslab

   Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared structural features or chemical families across spectral clusters.
   1 install
4. ▌
   Clustering Tool Orchestration · holobiomicslab

   Use when you have raw tandem MS metabolomics data (in mzML or MGF format) and wish to compare the clustering performance of two or more MS clustering tools on the same dataset.
   1 install
5. ▌
   Consensus Taxonomy Generation · holobiomicslab

   Use when when you have structural annotations from multiple sources (in silico predictions via SIRIUS/CANOPUS and GNPS spectral library matches) for the same molecular features and need a single authoritative taxonomy assignment.
   1 install
6. ▌
   Corpus Preparation Validation · holobiomicslab

   Use when when you have raw LC-MS-MS fragmentation spectra in MGF format and need to convert them into a corpus JSON file before running topic modeling.
   2 installs
7. ▌
   Covariance Matrix Computation · holobiomicslab

   Use when after normalization (Step 7) is complete and you have a clean feature matrix ready for multivariate statistical analysis.
   1 install
8. ▌
   Cross Sample Feature Matching · holobiomicslab

   Use when you have detected feature tables from two or more LC-IMS-MS/MS samples and need to establish correspondence between features across samples to enable quantitative comparison, statistical analysis, or consensus feature calling.
   2 installs
9. ▌
   Cross View Similarity Scoring · holobiomicslab

   Use when you have an experimental mass spectrum (query) and a set of molecular candidate structures, and you need to rank the candidates by how well their predicted spectral features match the query spectrum.
   4 installs
10. ▌
    Dda Acquisition Data Handling · holobiomicslab

    Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators) to serve as input to the DNMS2Purifier customized model training workflow, or to prepare data for purification of.
    2 installs
11. ▌
    Decision Tree Path Extraction · holobiomicslab

    Use when you have a trained shallow decision tree on ChemEcho feature vectors (sparse, high-dimensional representations of tandem mass spectra peaks and neutral losses) and need to convert it into an interpretable, deployable query for a domain-specific language like MassQL.
    1 install
12. ▌
    Eic Data Extraction From Xcms · holobiomicslab

    Use when after running XCMS getEIC() to generate xcmsEIC objects and fillPeaks() to produce a filled xcmsSet object, before computing the 12 peak-quality metrics (Apex Max-Boundary Ratio, Elution Shift, FWHM2Base, Jaggedness, Modality, Symmetry, Sharpness, Gaussian Similarity, Retention-Time.
    2 installs
13. ▌
    Feature Extraction Untargeted · holobiomicslab

    Use when when you have raw untargeted LC/MS data in mzML or mzXML format and need to detect and quantify metabolite signals across mass-to-charge and retention time dimensions without prior knowledge of instrument parameters, batch effects, or optimal detection thresholds.
    2 installs
14. ▌
    Feature Gap Filling Recursion · holobiomicslab

    Use when after sample alignment has established consensus m/z and retention time coordinates, and after grouping of isotopologues and adducts is complete.
    2 installs
15. ▌
    Feature Hashing Vectorization · holobiomicslab

    Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
    0 installs
16. ▌
    Feature Identifier Assignment · holobiomicslab

    Use when after constructing MetaboSet objects from Excel-formatted LC-MS peak tables and before drift correction or quality flagging.
    0 installs
17. ▌
    Feature Table Filtering Logic · holobiomicslab

    Use when when you have a quantitative feature table (peak intensities across samples) and need to isolate molecular features that show differential abundance between defined sample groups within a specified fold-change range.
    0 installs
18. ▌
    Feature Table Format Handling · holobiomicslab

    Use when transitioning feature intensity data between pipeline stages (e.
    1 install
19. ▌
    Feature Table Quality Control · holobiomicslab

    Use when when you have a feature intensity matrix (samples × compounds) from untargeted LC–MS/MS or GC–MS analysis and accompanying sample-type metadata (blank, curve, QC, unknown classifications), and you need to remove features with high measurement variability, low QC detection rates, high blank.
    0 installs
20. ▌
    Feature Table Standardization · holobiomicslab

    Use when you have feature tables from external metabolomics software (MS-DIAL, XCMS, vendor tools) in CSV format and need to integrate them into JPA for cross-sample alignment and metabolite annotation.
    0 installs
21. ▌
    Formula Sampler Configuration · holobiomicslab

    Use when you need to generate a set of candidate chemical formulas for LC-MS/MS simulation—specifically when you want to populate a virtual mass spectrometer with realistic chemical structures drawn from a reference database (HMDB) or a uniform m/z distribution, and you need to apply m/z filtering.
    2 installs
22. ▌
    Fragment Ion Library Matching · holobiomicslab

    Use when you have peak-picked experimental MS/MS data (m/z, retention time, intensity) from UHPLC-HRMS/MS instruments (Orbitrap or Q-TOF from Agilent, Bruker, SCIEX, or similar vendors) and need to annotate detected features with specific lipid identifications using in-silico fragmentation.
    0 installs
23. ▌
    Fragment Ion Mass Calibration · holobiomicslab

    Use when when comparing experimental spectra to reference library spectra and fragment ion m/z values show systematic drift or measurement noise that could distort neutral loss peaks or cosine similarity scores.
    2 installs
24. ▌
    Global Similarity Aggregation · holobiomicslab

    Use when after computing pairwise cosine similarities between all spectra across two LC-MS/MS datasets when you need a single scalar summary of dataset-level resemblance rather than individual spectrum matches.
    1 install
25. ▌
    Gradient Performance Encoding · holobiomicslab

    Use when when you have extracted retention times from the top detected MS1 features in a LC-MS run and need to evaluate whether the gradient spreads those compounds efficiently across the available chromatographic time window—particularly during iterative gradient optimization where you need a.
    3 installs
26. ▌
    Graph Based Identity Transfer · holobiomicslab

    Use when when you have spectral library matches (seed identities with high confidence scores) mapped to initial candidate structures from in silico fragmentation, and you want to propagate those identities to related structures in the fragmentation candidate graph to improve annotation coverage.
    2 installs
27. ▌
    Hdf5 Hierarchical Data Access · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format (from Agilent .d, Bruker .d with ion mobility, Thermo .
    4 installs
28. ▌
    In Silico Compound Annotation · holobiomicslab

    Use when after feature filtering and clustering have been completed in MS-CleanR and you have a cleaned feature set with m/z, retention time, and MS/MS spectra data ready for structural assignment. Use it when you need to identify unknown compounds by querying multiple chemical databases (e.
    2 installs
29. ▌
    In Silico Fragment Prediction · holobiomicslab

    Use when you have a collection of compound structures in SDF format (e.g., DNA adduct structures) and need to systematically generate predicted fragment spectra across a defined ionization level and mass range to populate a reference spectral database or validate experimental fragmentation patterns.
    2 installs
30. ▌
    Ion Target Quality Monitoring · holobiomicslab

    Use when you have MS1 data from multiple samples and need to assess whether particular ion targets (e.g., internal standards, biomarkers, or metabolites of interest) maintain consistent quality across the cohort. Trigger on: (1) suspicion of sample-to-sample variability in ion signal;
    1 install
31. ▌
    Irt Peptide Standard Matching · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file from an LC-MS run containing a spiked iRT peptide standard mix (e.
    0 installs
32. ▌
    JSON File Parsing And Loading · holobiomicslab

    Use when after generating a structured JSON result file from a prior computational step (e.g., gensim LDA model output in myexp.ldaresult.json format) and needing to store it in PostgreSQL for web application access, visualization, or further analysis.
    4 installs
33. ▌
    Large Scale Spectral Matching · holobiomicslab

    Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all-pairs or many-to-many spectrum similarity to identify related compounds, build spectral libraries, or perform large-scale library searching.
    3 installs
34. ▌
    Lc Ms Eic Plot Interpretation · holobiomicslab

    Use when after executing TARDIS in screening_mode = TRUE on centroided .mzML files with a defined target compound list.
    2 installs
35. ▌
    Lc Ms Feature Quality Scoring · holobiomicslab

    Use when immediately after peak detection and feature table generation from LC-MS data, when you need to rank or filter features by confidence before annotation or statistical analysis.
    2 installs
36. ▌
    Lcms Peak Intensity Filtering · holobiomicslab

    Use when after XCMS peak picking, alignment, and grouping when you have identified putative incorporations (via PuInc_seeker) or base-peak isotopologue candidates and need to exclude low-intensity peaks that are likely noise or instrument artifacts.
    2 installs
37. ▌
    Lcms Retention Time Alignment · holobiomicslab

    Use when when XCMS-aligned LC-MS data shows coefficient of variation (CV) above expected thresholds for known features, or when analyzing long-duration experiments (>1 week) or large cohorts (>100 samples) where global warping functions are known to fail due to compound-specific RT drift structures.
    4 installs
38. ▌
    Lipid Structure Specification · holobiomicslab

    Use when you have identified lipid species unique to your sample type (e.
    2 installs
39. ▌
    M Z Tolerance Window Matching · holobiomicslab

    Use when when you have detected features with m/z, drift time, and retention time dimensions and need to associate peaks into isotopic groups (e.g., monoisotopes with C13 substitutions) or align features across multiple LC-IMS-MS/MS samples.
    2 installs
40. ▌
    Mass Range Window Restriction · holobiomicslab

    Use when you have loaded an MsmsSpectrum object and need to focus analysis on a biologically or chemically relevant mass window.
    1 install
41. ▌
    Mass Spectral Data Formatting · holobiomicslab

    Use when when you have raw mass spectral data in .mgf, .msp, .mzML, or .lbm2 file formats and need to search against a spectral library using entropy similarity or Flash Entropy Search. Also apply this skill before building spectral library indices or computing entropy-based compound identification.
    4 installs
42. ▌
    Mass Spectral Peak Annotation · holobiomicslab

    Use when you have centroided MS2 spectra (in mzML format from data-dependent acquisition) and a list of known or suspect PFAS diagnostic fragment masses, and you need to systematically flag which detected features contain fragments characteristic of PFAS compounds (e.
    2 installs
43. ▌
    Metabolite Annotation Scoring · holobiomicslab

    Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) from MS/MS spectra or external tools (SIRIUS, GNPS), sample metadata linking samples to organisms, and you need to prioritize candidates by both annotation quality AND biological.
    4 installs
44. ▌
    Metabolite Feature Annotation · holobiomicslab

    Use when after MS1 feature extraction from mzXML files when you have: (1) a feature table with m/z, retention time, and intensity values; (2) DDA (Data-Dependent Acquisition) mzXML files containing MS2 fragmentation spectra; and (3) a reference spectral library in MSP format.
    1 install
45. ▌
    Metaboset Object Manipulation · holobiomicslab

    Use when when you have read LC-MS peak table data from Excel (or equivalent) into R and need to organize it into a structured object that tracks feature abundances, sample information (injection order, QC status), and feature metadata (mass, retention time, Feature_ID) simultaneously.
    2 installs
46. ▌
    Molecular Fingerprint Parsing · holobiomicslab

    Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract the predicted molecular fingerprint representation and associated scoring metrics for compound identification or CANOPUS.
    1 install
47. ▌
    Molecular Formula Calculation · holobiomicslab

    Use when you have user-specified lipid class constraints (e.
    2 installs
48. ▌
    Molecular Fragment Prediction · holobiomicslab

    Use when when you have an experimental tandem mass spectrum (m/z peaks and intensities) and a chemical formula, and need to identify the true molecular structure from a candidate library (e.g., PubChem).
    0 installs
49. ▌
    Ms Ms Spectral Interpretation · holobiomicslab

    Use when you have acquired MS/MS spectral data (in mzML, mzXML, or equivalent format) for unknown compounds and need to identify the most probable metabolite structure.
    2 installs
50. ▌
    Multi Tool Results Comparison · holobiomicslab

    Use when you have feature identification outputs from two or more DIA-MS search tools (e.g., DIA-NN and OpenSwath result files) and need to assess their agreement on analyte detection, quantification, and scoring.
    2 installs
51. ▌
    Mzml Format Output Validation · holobiomicslab

    Use when after executing smiter.synthetic_mzml.write_mzml to generate synthetic LC-MS/MS runs from nucleoside or peptide fragmentation models.
    4 installs
52. ▌
    Mzml Metabolomics Data Import · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in mzML or ABF format that needs to be processed through a reproducible pipeline. Use this skill when: (1) you have public or proprietary .mzML LC-MS datasets (e.g. from MetaboLights, MassIVE, or PRIDE);
    1 install
53. ▌
    Neural Network Model Training · holobiomicslab

    Use when you have downloaded LC-MS spectral peak data (DOI 10.25345/C5FD2F or equivalent) and need to build a supervised deep neural network classifier to distinguish peak classes in mass spectrometry data.
    4 installs
54. ▌
    Numerical Equivalence Testing · holobiomicslab

    Use when you need to confirm that omitting an optional input parameter (such as secondaryAssay in buildExperiment) produces the expected mathematical result—specifically, when a default value should neutralize a transformation (e.
    1 install
55. ▌
    Parameter Search Space Design · holobiomicslab

    Use when when beginning an untargeted LC-MS analysis and either (1) the dataset characteristics (sample complexity, instrument platform, or polarity) differ from previously optimized cohorts, (2) multiple peak-picking algorithms (Centwave, FeatureFinderMetabo, ADAP) are available and their relative.
    0 installs
56. ▌
    Polarity Aware Data Filtering · holobiomicslab

    Use when when performing targeted peak detection on LC-MS data where compounds have been assigned expected ionization polarities (positive or negative mode) in the target list, and you want to prevent false peak assignments from the opposite polarity and avoid manual pre-filtering of raw data by.
    4 installs
57. ▌
    Pre Trained Model Fine Tuning · holobiomicslab

    Use when you have a small training dataset for molecular property prediction (e.g., <500 samples from PredRet or MoNA databases) and a pre-trained GNN model is available that was trained on a related, larger molecular corpus.
    4 installs
58. ▌
    Precursor And Noise Filtering · holobiomicslab

    Use when you have loaded raw tandem MS spectra (in MGF, mzML, or similar format) and need to prepare them for peptide identification, spectral library matching, or intensity-based analysis.
    1 install
59. ▌
    Precursor M Z Based Filtering · holobiomicslab

    Use when you have an unknown MS/MS query spectrum with a known or measured precursor m/z value and need to search a spectral library (local or public: GNPS, MASSBANK, DrugBANK) to annotate the compound.
    1 install
60. ▌
    Precursor Mz Window Filtering · holobiomicslab

    Use when when preparing augmented training data for Siamese or contrastive learning architectures in mass spectrometry, specifically when you need to generate hard negative examples that are spectrally distinct but mass-similar to positive examples.
    1 install
61. ▌
    Quantitation Table Generation · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a defined list of m/z, retention time, or other identifiers for which you need to extract and quantify peak abundances across one or more samples.
    2 installs
62. ▌
    R Data Structure Manipulation · holobiomicslab

    Use when when xcms has produced misaligned feature groups and you need to extract raw LC-MS profiles from source files into a structured format acceptable by ncGTW's realignment functions.
    2 installs
63. ▌
    Raw Ms Data Format Conversion · holobiomicslab

    Use when you have raw UPLC-HRMS data from ThermoFisher or Agilent instruments and need to feed it into MSThunder for nontargeted pollutant identification. Your input is a vendor binary format (.raw or .d) that MSThunder cannot directly ingest. Environment constraints (e.
    2 installs
64. ▌
    Rawrr Spectral Data Retrieval · holobiomicslab

    Use when you have Thermo Orbitrap .raw files and need to access raw spectral data (individual MS1 or MS2 scans, base-peak values, chromatogram traces, retention times, or scan-level metadata) for custom analysis, visualization, or integration into an R-based pipeline.
    4 installs
65. ▌
    Rdkit Molecular Featurization · holobiomicslab

    Use when you have molecular structure data (SMILES strings or MOL files) from an in-house chemical database and need to prepare it as input for a graph neural network that predicts liquid chromatography retention times for small molecule identification.
    0 installs
66. ▌
    Replicate Spectrum Comparison · holobiomicslab

    Use when you have multiple MS/MS spectra (replicates) for a single metabolic feature (same m/z and RT window) and need to identify which fragments are reproducibly detected across replicates versus noise.
    4 installs
67. ▌
    Retention Time Mass Alignment · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to identify which features in one dataset correspond to features in the other.
    4 installs
68. ▌
    Run Order Dependency Modeling · holobiomicslab

    Use when your feature table includes QC (quality control) sample replicates distributed throughout the analytical run sequence, and you observe systematic intensity variation correlated with sample injection order or batch identifier—typical indicators of instrumental drift in untargeted LC-MS.
    1 install
69. ▌
    Signal Residual Deconvolution · holobiomicslab

    Use when analyzing 1D signal arrays (e.g., extracted ion chromatograms, arrival time distributions, or MS1 spectra intensity profiles) where multiple peaks may overlap or where peak shape information (amplitude, position, width) is required beyond simple local-maximum detection.
    0 installs
70. ▌
    Spectra Object Manipulation R · holobiomicslab

    Use when when you have extracted and concatenated MS/MS spectra from multiple replicates for a set of metabolomic features (stored in a preprocessed list), and need to apply intensity-based filtering (e.
    0 installs
71. ▌
    Spectral Data Standardization · holobiomicslab

    Use when you have completed a GNPS1 (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING) or GNPS2 (classical_networking_workflow, feature_based_molecular_networking_workflow) molecular networking job and need to access its output files in a standardized format for.
    2 installs
72. ▌
    Spectral Embedding Generation · holobiomicslab

    Use when you have a collection of pre-processed MS/MS spectra (binned, intensity-normalized) and a trained MS2DeepScore base network, and you need to compute structural similarity scores between spectrum pairs or visualize spectra in chemical space via dimensionality reduction (e.g., UMAP).
    4 installs
73. ▌
    Spectral Match Interpretation · holobiomicslab

    Use when you have obtained search results from one or more domain-specific MASST web applications (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) for a query mass spectrum and need to consolidate, rank, and visualize those matches to infer the identity and biological source of.
    2 installs
74. ▌
    Spectral Metadata Integration · holobiomicslab

    Use when after isotopologue and adduct grouping has been completed and you need to associate MS2 spectra with consolidated feature groups in DDA LC-MS experiments.
    0 installs
75. ▌
    Spectral Noise Classification · holobiomicslab

    Use when you have MS/MS spectra contaminated with noise ions and need to improve compound identification accuracy.
    3 installs
76. ▌
    Spectral Noise Peak Filtering · holobiomicslab

    Use when when working with raw or partially processed tandem mass spectrometry (MS/MS) spectra that contain low-intensity background noise peaks.
    2 installs
77. ▌
    Spectrum Embedding Clustering · holobiomicslab

    Use when after embedding MS/MS spectra into 32-dimensional GLEAMS vectors, when you need to group spectra by the same peptide origin.
    4 installs
78. ▌
    Spectrum Vector Serialization · holobiomicslab

    Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
    1 install
79. ▌
    Structural Similarity Scoring · holobiomicslab

    Use when when you have a collection of mass spectra with annotated chemical structures (SMILES/InChI) and need to generate structural similarity labels to train or validate a model that predicts molecular similarity from spectral pairs.
    3 installs
80. ▌
    Structure Selection Filtering · holobiomicslab

    Use when when you have an unknown metabolite's predicted structural similarity scores (from a deep learning model such as DeepMASS) against all known metabolites in a reference database, and need to identify which known metabolites are most likely structurally related to the unknown to guide.
    4 installs
81. ▌
    Synthetic Spectrum Generation · holobiomicslab

    Use when when you need to create benchmark LC-MS/MS datasets with controlled, known composition for testing MS analysis algorithms, validating retention-time or fragmentation predictions, or predicting co-elution and co-fragmentation challenges before conducting real experiments.
    1 install
82. ▌
    Tandem Mass Spectrum Decoding · holobiomicslab

    Use when when you have raw predictions from a trained fragment generation or intensity prediction neural network model and need to convert those predictions into a standard spectrum file format (m/z–intensity pairs) for comparison against experimental spectra or for structural elucidation workflows.
    4 installs
83. ▌
    Taxonomy String Normalization · holobiomicslab

    Use when when preparing a metadata table (TSV format with species, genus, and family columns) for natural product metabolomics analysis where the Literature Component score must query known compounds by taxon.
    2 installs
84. ▌
    Total Ion Current Calculation · holobiomicslab

    Use when after loading all MS1 scans from a raw or intermediate mass spectrum file (e.
    2 installs
85. ▌
    Train Test Split Verification · holobiomicslab

    Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to confirm that the change produces the documented training/test split counts.
    2 installs
86. ▌
    Transfer Learning Fine Tuning · holobiomicslab

    Use when you have collected liquid chromatography (LC) spectra and retention time labels for your in-house molecular database, and you want to leverage a pretrained GNN-RT model rather than train from scratch.
    2 installs
87. ▌
    Transition Group Peak Picking · holobiomicslab

    Use when you have loaded extracted ion chromatogram (XIC) data from DIA mass spectrometry and need to identify peak boundaries for peptide precursor transitions.
    3 installs
88. ▌
    Bruker Nmr Spectral Data Import · 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.
    1 install
89. ▌
    Cnn Spectral Feature Extraction · holobiomicslab

    Use when you have preprocessed 1D NMR spectra (¹H and/or ¹³C) and need to extract spectral features for molecular structure inference on molecules with up to 19 heavy atoms. The skill is necessary as the first stage before fragment assembly or connectivity prediction;
    2 installs
90. ▌
    J Coupling Multiplet Generation · 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.
    2 installs
91. ▌
    Metabolite Structure Prediction · holobiomicslab

    Use when you have a parent compound (or set of compounds) in SMILES, MOL, or SDF format and need to predict plausible metabolite structures and pathways in a specific biological context (mammalian Phase I/II metabolism, human gut microbiota, or soil/aquatic microbial degradation).
    1 install
92. ▌
    Neural Network Model Deployment · holobiomicslab

    Use when you have LC-MS feature tables (m/z and retention time columns) and corresponding .mzXML or .mzML files, and you need to automatically classify whether extracted ion chromatograms represent genuine metabolomic features or false positives.
    3 installs
93. ▌
    Nmr Spectral Feature Extraction · holobiomicslab

    Use when when you have raw or preprocessed 1H NMR spectral tensors from flavor or chemical mixtures and need to generate high-level feature representations that capture both fine-grained local patterns (e.g., peak multiplet structure, coupling constants) and global spectral context (e.
    0 installs
94. ▌
    Nmr Workflow Pipeline Execution · holobiomicslab

    Use when you have raw 1D NMR spectra (FID or processed spectrum files) and need to extract peak parameters (chemical shift, intensity, linewidth) in a tabular format for downstream metabolomic or structural analysis.
    0 installs
95. ▌
    Restful API Endpoint Invocation · holobiomicslab

    Use when you have NMR peak data (1H and 13C chemical shift values) and need to obtain SMART 3 classification predictions from the DeepSAT service.
    4 installs
96. ▌
    Spectral Connectivity Filtering · holobiomicslab

    Use when you have picked peaks (coordinates and intensities) from an INADEQUATE NMR spectrum and need to cluster them into networks representing individual compounds.
    3 installs
97. ▌
    Spectral Intensity Thresholding · holobiomicslab

    Use when you have loaded raw INADEQUATE NMR spectrum data and need to distinguish true molecular peaks from noise and instrumental artifacts.
    0 installs
98. ▌
    Spectral Modality Preprocessing · holobiomicslab

    Use when you have downloaded raw spectroscopic data files (NMR, HSQC, COSY, IR modalities) from the Zenodo repositories and need to convert them into the standardized multi-modal input format required by the MultiModalSpectralTransformer before inference or retraining.
    1 install
99. ▌
    Structure Similarity Comparison · holobiomicslab

    Use when after executing a molecular structure prediction model on spectroscopic input data and obtaining predicted molecular structures in a standardized format (e.g., SMILES, MOL, SDF).
    2 installs
100. ▌
     Structure Similarity Evaluation · holobiomicslab

     Use when after an NMR-based structure prediction model has generated predicted molecular structures (formula and connectivity) for a test set of molecules with up to 19 heavy atoms.
     0 installs