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HolobiomicsLab

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1. ▌
   Formula Ranking Accuracy Evaluation 3 · holobiomicslab

   Use when use this skill after training or fine-tuning a chemical formula transformer model on annotated tandem MS/MS spectra, when you need to measure whether the model's ranked formula candidates match ground truth.
   9 installs
2. ▌
   Multidimensional Scaling Embedding 2 · holobiomicslab

   Use when after computing a pairwise sample distance matrix from aligned MS2 fingerprint vectors and you need to visualize sample relationships, clustering, or separation by group identity in 2D space.
   5 installs
3. ▌
   Spectral Fingerprint Vectorization 2 · holobiomicslab

   Use when you have MS2 fragmentation spectra from multiple metabolomics samples and need to compare them in a retention time-agnostic manner, especially when samples are chemically diverse, acquired with different LC methods or mass spectrometer technologies (e.
   6 installs
4. ▌
   Spectral Library Candidate Ranking 2 · holobiomicslab

   Use when after MS2Deepscore has selected the top 2000 candidate spectra from a library based on spectral similarity, and you need to re-rank these candidates to surface the single match (either exact or analogue) rather than rely on raw spectral similarity alone.
   6 installs
5. ▌
   Spectral Search Logic Control Flow 2 · holobiomicslab

   Use when when you need to understand or modify how MS2Query routes query spectra through its dual-pathway architecture, or when integrating MS2Query into another tool and need to trace how spectral similarity scores (MS2Deepscore) feed into library-match versus analogue-search branches with.
   2 installs
6. ▌
   Tandem Mass Spectra Interpretation 2 · holobiomicslab

   Use when you have an unknown MS/MS spectrum (tandem mass spectrum) with a measured precursor m/z and fragment peaks, and you need to assign the most likely molecular formula and ionization adduct (e.g., [M+H]+, [M+Na]+, [M+K]+).
   7 installs
7. ▌
   Usi Spectrum Retrieval And Loading 2 · holobiomicslab

   Use when you have a USI accession (e.g., 'mzspec:MSV000082283:f07074:scan:5475' or 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') pointing to a publicly deposited tandem mass spectrometry scan in a GNPS or ProteomeXchange repository, and you need to retrieve and instantiate.
   6 installs
8. ▌
   Adduct Based Feature Consolidation 3 · holobiomicslab

   Use when after accurate mass searching has assigned multiple detected m/z features to the same metabolite via positive and negative adduct libraries, and before sample-level feature merging.
   3 installs
9. ▌
   Batch Normalization Implementation 3 · holobiomicslab

   Use when apply batch normalization after dense hidden layers (but not the final embedding layer) in a deep neural network trained on MS/MS spectral data, particularly when the network processes high-dimensional binned spectra (9948-dimensional vectors) and you need to stabilize gradient flow across.
   5 installs
10. ▌
    Cardinal Imaging Object Conversion 2 · holobiomicslab

    Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
    6 installs
11. ▌
    Categorical Ion Status Aggregation 3 · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object when you need to understand the distribution of ions across filter status categories (passed vs. failed filters) and want to visualize or report the count and percentage composition of each status group.
    8 installs
12. ▌
    Chromatographic Feature Extraction 3 · holobiomicslab

    Use when you have centroided mzML files from LC- or GC-HRMS instruments (acquired in data-dependent mode with ddMS2) and need to systematically identify chromatographic peaks, measure their mass and retention time coordinates, and quantify their intensities before applying PFAS-specific.
    6 installs
13. ▌
    Lc Ms Roi Annotation Interpretation 2 · holobiomicslab

    Use when when you have extracted LC-MS ROI windows (m/z × retention time snippets) from raw mzML data and need to distinguish genuine metabolite peaks from noise or artifacts.
    5 installs
14. ▌
    Mass Accuracy Tolerance Calibration 3 · holobiomicslab

    Use when you have experimental fragment m/z values from HRMS/MS instruments (Q-Exactive orbitrap, Q-TOF) in CSV or mzML-derived peaklist format, and need to match them against a library of 500,000+ in-silico fragmented lipid species.
    6 installs
15. ▌
    Mass Spectrometry Data File Parsing 3 · holobiomicslab

    Use when you receive raw MS data files from LC-MS, LC-IMS-MS, direct infusion, or DDA/DIA experiments and need to extract ion chromatograms, mobility heatmaps, quality metrics, or perform spectral matching.
    6 installs
16. ▌
    Mass Spectrometry Fragment Matching 3 · holobiomicslab

    Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table formats) and need to assign lipid identities using untargeted or targeted tandem MS data.
    6 installs
17. ▌
    Metabolite Library Entry Generation 3 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (from MassBank or your own acquisition) and need to create a standardized library entry with ranked fragment ions for use in MetaboAnnotatoR or other fragment-based annotation pipelines.
    4 installs
18. ▌
    Metabolite Lipid Annotation Ranking 2 · holobiomicslab

    Use when you have LC–MS All-ion fragmentation chromatograms processed through xcms and RamClustR, a feature table with unknown identities, and you want to recover lipid annotations by matching observed spectra against lipid fragment libraries (e.g., LipidPos).
    5 installs
19. ▌
    Metabolomics Feature Transformation 3 · holobiomicslab

    Use when when you have a feature intensity table (samples × compounds) from targeted or non-targeted metabolomics and need to prepare it for statistical modeling or multivariate analysis.
    5 installs
20. ▌
    Mgf Metadata Completion From Smiles 3 · holobiomicslab

    Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL import or polarity-based separation workflows.
    8 installs
21. ▌
    Molecular Family Graph Construction 2 · holobiomicslab

    Use when you have downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING for GNPS1, or classical_networking_workflow/feature_based_molecular_networking_workflow for GNPS2) and need to construct a queryable molecular family graph.
    6 installs
22. ▌
    Motif Database Lookup And Retrieval 2 · holobiomicslab

    Use when after completing the MS2LDA LDA modeling step when you have a JSON-serialized inferred motifset (Mass2Motifs with fragment and neutral-loss patterns) and need to annotate those motifs by comparing them against a curated MotifDB reference database to identify known structural subpatterns.
    6 installs
23. ▌
    Peak Area And Intensity Measurement 2 · holobiomicslab

    Use when when you have vendor-format GC-CI-MS or LC-MS data from stable isotope labeling experiments, a target list of compounds with known monoisotopic m/z, retention time, and elemental formula, and you need per-isotopologue area and intensity values for quantification or downstream statistical.
    6 installs
24. ▌
    Peak Data Extraction And Formatting 2 · holobiomicslab

    Use when when you have initialized an MsBackend subclass (e.
    5 installs
25. ▌
    Retention Time Alignment Clustering 2 · holobiomicslab

    Use when you have two or more nontargeted LCMS feature tables from the same analytical method and need to establish matched feature correspondences across datasets, then consolidate redundant features.
    5 installs
26. ▌
    Retention Time Mz Intensity Mapping 2 · holobiomicslab

    Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to rapidly detect instrumental drift, retention time shifts, or.
    7 installs
27. ▌
    Root Mean Squared Error Calculation 2 · holobiomicslab

    Use when when you have paired predictions and ground-truth structural similarity labels (e.g., predicted Tanimoto scores from a neural network and reference Tanimoto scores from RDKit Daylight fingerprints) and need to report a single scalar metric of model prediction error across all pairs.
    6 installs
28. ▌
    Similarity Threshold Interpretation 3 · holobiomicslab

    Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide which matches are sufficiently confident to include in per-motif annotation output.
    6 installs
29. ▌
    Fdr Aware Psm Retention Strategy 2 · holobiomicslab

    Use when rescoring PSMs with machine learning or statistical models where: (1) you want to consider multiple candidate PSMs per spectrum (e.
    6 installs
30. ▌
    HTML Bundle Rendering In Browser 2 · holobiomicslab

    Use when you have a dashboard_data.json file (JSON export from the msFeaST pipeline) and need to interactively explore quantification tables, metadata, and spectral data on a desktop machine (macOS, Linux, or Windows).
    4 installs
31. ▌
    Lipid Species Abundance Counting 3 · holobiomicslab

    Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type categories present.
    8 installs
32. ▌
    M Z Intensity Feature Extraction 2 · holobiomicslab

    Use when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to inspect peak structure, verify instrument performance, or generate baseline visualizations before downstream peak annotation or statistical analysis.
    5 installs
33. ▌
    Mass Spectrometry Quantification 2 · holobiomicslab

    Use when you have measured MS intensity data from unknown samples and known-concentration standard compounds, and you need to convert sample intensities into predicted concentrations. Specifically applicable when intensity drift is observed across the measurement sequence (e.
    5 installs
34. ▌
    Metabolite Annotation Validation 2 · holobiomicslab

    Use when after running in silico annotation tools (SIRIUS, ISDB) or spectral library matching on your feature table, when you need to retain only annotations meeting a minimum confidence threshold.
    7 installs
35. ▌
    Missing Value Imputation For Pca 2 · holobiomicslab

    Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple standard deviation thresholds (e.g., 3 SD, 4 SD, 5 SD) on principal component scores.
    8 installs
36. ▌
    Missing Value Imputation With Na 3 · holobiomicslab

    Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which ones are explicitly stored in your backend.
    7 installs
37. ▌
    Msconvert Workflow Configuration 2 · holobiomicslab

    Use when when you need to convert vendor-specific raw mass spectrometry files (.raw) to the open mzML format using imzML Writer, and msconvert is not yet installed or its location is not recognized by the system.
    6 installs
38. ▌
    Proteomics Data Structure Design 2 · holobiomicslab

    Use when when building a mass-spectrometry analysis pipeline that must support multiple vendor and open formats (mzML, mzXML, Thermo, Agilent, Bruker, etc.) and you need to shield downstream tools from format-specific parsing logic.
    9 installs
39. ▌
    Proteomics Output Record Parsing 2 · holobiomicslab

    Use when after the Proteomics_Data_Processor tool has completed analysis of raw mass spectrometry files and returned structured output records.
    4 installs
40. ▌
    Pubchem Structure Lookup By Name 2 · holobiomicslab

    Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
    5 installs
41. ▌
    Software Testing Unit Validation 3 · holobiomicslab

    Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request. The skill is essential before pushing feature branches to the repository or merging changes into master.
    7 installs
42. ▌
    Spectral Data Integrity Checking 2 · holobiomicslab

    Use when after converting mass-spectrometry data from an existing format (mzML, mzXML, or vendor-specific formats) into mzPeak using command-line tools or API calls.
    8 installs
43. ▌
    Structured Data Element Checking 3 · holobiomicslab

    Use when you have generated or received a mass spectrometry data file in a structured format (e.g., mzPeak, Parquet-based archive) and need to verify it conforms to the published specification before use in analysis pipelines, sharing with collaborators, or publishing.
    7 installs
44. ▌
    Test Driven Database Development 2 · holobiomicslab

    Use when when you have an existing tool or library with file-based storage (JSON, CSV, binary formats) that needs to support efficient querying across large datasets, and you want to migrate to a relational database without breaking existing functionality or performance expectations.
    6 installs
45. ▌
    Spectral Intensity Normalisation 3 · holobiomicslab

    Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
    6 installs
46. ▌
    Spectral Intensity Normalization 3 · holobiomicslab

    Use when after removing precursor and noise peaks from an MsmsSpectrum object when the spectrum contains peaks with highly variable intensities (e.g., one or two dominant peaks with many weaker fragments).
    5 installs
47. ▌
    Web Application Endpoint Mapping 3 · holobiomicslab

    Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that spectrum to the appropriate domain-specific MASST application for searching.
    6 installs
48. ▌
    Deep Learning Model Assembly 2 · holobiomicslab

    Use when you have transformer encoder components and a prediction head specification, and need to wire them into a single trainable model that maps molecular structure inputs (SMILES, molecular graphs, or feature vectors) to scalar or vector molecular property predictions.
    7 installs
49. ▌
    Adduct Mass Difference Ranking 2 · holobiomicslab

    Use when you have computed a histogram of mass differences from all pairwise mass comparisons in your MALDI-MS imaging dataset and need to prioritize which mass differences are most frequent and likely represent genuine molecular adducts (e.g., metabolite + matrix ions) rather than noise.
    4 installs
50. ▌
    Batch Effect Visualization Pca 2 · holobiomicslab

    Use when after applying CordBat batch correction to a log2-transformed metabolite matrix from multi-batch metabolomics data, you want to quantitatively and visually assess whether the correction successfully reduced batch effects.
    7 installs
51. ▌
    Command Line Interface Testing 2 · holobiomicslab

    Use when after installing a Python package or before running a computational workflow for the first time, to verify that the CLI entry point is properly configured, the Python environment is correctly set up, and to discover available command-line arguments and their defaults (e.
    8 installs
52. ▌
    Cross Dataset Feature Matching 3 · holobiomicslab

    Use when you have two or more feature tables in HDF5 format with detected features characterized by m/z, drift time, retention time, and intensity, and you need to match corresponding features across samples to account for systematic shifts caused by instrument variation or tuning differences.
    6 installs
53. ▌
    Docker Container Orchestration 3 · holobiomicslab

    Use when your analysis requires msconvert or another ProteoWizard tool on macOS, but native installation is infeasible or licensing-restricted. You need to convert vendor raw mass spectrometry files (.raw) to the open mzML format without installing ProteoWizard directly on your system.
    5 installs
54. ▌
    Execution Time Metric Analysis 2 · holobiomicslab

    Use when you have computation-time metrics from a gallery or benchmark suite comparing multiple plotting backends on the same data types (e.
    6 installs
55. ▌
    Feature Intensity Thresholding 2 · holobiomicslab

    Use when after feature extraction from mzML/mzXML files when you have identified candidate peaks in breath spectrometry data but need to separate true VOC signals from instrument noise.
    5 installs
56. ▌
    Ftms Mass Calibration Workflow 2 · holobiomicslab

    Use when when you have a processed Bruker Solarix FT-ICR mass spectrum object (from ReadBrukerSolarix) and a reference peak list file (SRFA.
    5 installs
57. ▌
    Github Actions API Integration 3 · holobiomicslab

    Use when when you need to verify that a GitHub Actions workflow (such as a development build or release pipeline) executes without fatal errors and produces expected artifacts. Use this skill when the workflow is already configured in a repository (e.g., a .yml file in .
    7 installs
58. ▌
    Lipid Identifier Normalization 2 · holobiomicslab

    Use when when you have a list of lipids identified by different database identifiers (e.
    5 installs
59. ▌
    Log Transformation Application 2 · holobiomicslab

    Use when apply log-transformation immediately after loading a raw metabolomics featuredata matrix (metabolite peak intensities as rows=samples, columns=metabolites) and before normalization.
    5 installs
60. ▌
    Spectral Molecular Family Linking 2 · holobiomicslab

    Use when when you have pre-processed genomic data (GCFs from AntiSMASH/BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to systematically score and rank putative relationships between biosynthetic gene clusters and their.
    8 installs
61. ▌
    Spectral Peak Annotation Proforma 2 · holobiomicslab

    Use when you have an annotated or raw tandem mass spectrometry spectrum and need to identify which observed peaks correspond to expected peptide fragment ions from a known or predicted peptidoform. Use it before spectrum visualization if you want highlighted, labeled fragment matches;
    4 installs
62. ▌
    Spectrum Peak To Fragment Mapping 3 · holobiomicslab

    Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks correspond to expected b-ion and y-ion fragments, in order to validate peptide identification or annotate spectrum quality.
    6 installs
63. ▌
    Spectrum Relevance Classification 2 · holobiomicslab

    Use when you have a collection of MS/MS spectra from reference standards representing your compounds of interest (e.g., flavonoids, prenylated chalcones) and a set of MS/MS spectra from non-target or other compounds.
    6 installs
64. ▌
    Structure Prediction From Spectra 3 · holobiomicslab

    Use when you have experimental mass spectrometry spectra (LC–QTOF or similar format) from unknown compounds and need to predict their molecular structures.
    7 installs
65. ▌
    Tensorflow Model Layer Inspection 2 · holobiomicslab

    Use when after converting or downloading a pre-trained Keras model to HDF5 TensorFlow 2.3.0 format, particularly when integrating the model into a fixed-interface pipeline (e.g., NP Classifier) that expects specific named input/output layers.
    7 installs
66. ▌
    Thermo Raw Binary Data Extraction 2 · holobiomicslab

    Use when you have acquired .raw files from a Thermo mass spectrometer (e.g., Q Exactive, Orbitrap) and need to expose their contents—scan numbers, retention times, m/z values, intensities, and precursor information—for downstream nontargeted LCMS feature detection and alignment.
    4 installs
67. ▌
    Vectorized Operation Verification 2 · holobiomicslab

    Use when when implementing or auditing S4 replacement methods (e.
    7 installs
68. ▌
    Biomolecular Class Annotation 2 · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to label experimental features by biomolecular class before performing CCS calibration or validation.
    6 installs
69. ▌
    Molecular Descriptor Indexing 2 · holobiomicslab

    Use when when you have a collection of molecular structures (SMILES or SDF format) and need to generate a queryable database of collision cross section values for high-throughput mass spectrometry workflows, or when you want to organize pre-computed CCS predictions with conformer metadata into a.
    5 installs
70. ▌
    Confidence Score Interpretation 3 · 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.
    8 installs
71. ▌
    Cross Language Interface Design 3 · holobiomicslab

    Use when when you have domain-specific functionality (e.g., spectral similarity scoring, peak detection algorithms) implemented in one language (Python) but need to make it callable and composable within an R-based analytical pipeline (Spectra objects);
    7 installs
72. ▌
    Feature Table Format Conversion 2 · holobiomicslab

    Use when you have raw feature tables exported from NPP tools (XCMS, MZmine 2, MS-DIAL, OpenMS, etc.) in their native formats and need to compare their peak detection and alignment performance against a mzRAPP benchmark dataset.
    9 installs
73. ▌
    Igzip Header Structure Encoding 3 · holobiomicslab

    Use when when implementing an igzip parser, decoder, or validator that must interpret the custom header format; when debugging igzip file corruption or encoding errors; or when extending pymzML's igzip support to handle new index schemes.
    5 installs
74. ▌
    Lipid Type Category Enumeration 3 · holobiomicslab

    Use when when you have downloaded or cloned a lipidomics library repository (such as LipidMatch) and need to audit the breadth of lipid-type coverage to ensure the library meets minimum requirements for your analysis scope (e.g., ≥60 distinct lipid categories).
    5 installs
75. ▌
    Mass2motif Network Construction 3 · holobiomicslab

    Use when after MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative annotation, or integration with external tools. Use this skill when you have motifset.json or motifset_optimized.
    6 installs
76. ▌
    Ion Image Embedding Optimization 3 · holobiomicslab

    Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions (representation collapse) during contrastive learning—specifically when optimizing for maximized similarity between augmentations.
    5 installs
77. ▌
    Batch Correction Quality Assessment 2 · holobiomicslab

    Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have been attenuated without loss of data dimensionality or sample information.
    7 installs
78. ▌
    Biomolecular Class Label Assignment 3 · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or databases).
    7 installs
79. ▌
    Charge State Specific Peak Matching 3 · holobiomicslab

    Use when you have peak-picked features with m/z, drift_time, retention_time, and intensity columns, and you need to identify monoisotopic peaks and their charge-state-specific isotopologue members (e.g., singly charged C13-substituted species).
    5 installs
80. ▌
    Chemical Formula Ranking Evaluation 2 · holobiomicslab

    Use when after running formula inference on a benchmark dataset with known formula and adduct ground truth (e.g., NPLIB1, NIST20, or CASMI 2022). Apply this skill when you need to quantify ranking performance, isolate the contribution of specific model features (e.
    4 installs
81. ▌
    Fragment Mass Tolerance Calibration 2 · holobiomicslab

    Use when when implementing fragment ion annotation in proteomics workflows and needing to determine whether neutral loss annotation (e.g., H2O: -18.010565, NH3: -17.026549) should be enabled to maximize peak interpretation.
    4 installs
82. ▌
    Genome Annotation Format Comparison 2 · holobiomicslab

    Use when when running metabologenomic RiPP detection pipelines (MetaMiner) on the same genomic dataset but with different input sequence formats (e.g., contigs.fasta vs. antiSMASH .final.gbk output), or when unexpected null results occur and input format choice is a plausible cause.
    6 installs
83. ▌
    Irt Peptide Calibration And Scoring 2 · holobiomicslab

    Use when when you need to assess whether retention times measured on a given LC-MS run follow the expected linear relationship defined by iRT peptide standards (e.g., Pierce or Biognosys iRT peptides).
    7 installs
84. ▌
    Mass Spectrometry Query Formulation 2 · holobiomicslab

    Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and intensity pairs), and you seek to generate candidate molecular structures for an unknown metabolite that may not be in.
    8 installs
85. ▌
    Metabolite Annotation Result Export 2 · holobiomicslab

    Use when after running the annotateRC function on LC-MS All-ion fragmentation (AIF) features and obtaining a populated annotations object with ranked candidate matches, use this skill when you need to persist results to disk for archival, sharing, or downstream interpretation (e.
    6 installs
86. ▌
    Metabolomics Feature Table Curation 3 · holobiomicslab

    Use when you have a raw feature table (TSV/CSV) derived from LC-MS peak detection (e.
    7 installs
87. ▌
    Multidimensional Feature Annotation 3 · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic signatures to distinguish monoisotopic peaks from isotopologues, reduce feature redundancy, and support multi-dimensional.
    5 installs
88. ▌
    Nmr Spectrum To Structure Inference 2 · holobiomicslab

    Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph without manual peak interpretation or exhaustive combinatorial search.
    8 installs
89. ▌
    Permutation Test P Value Estimation 2 · holobiomicslab

    Use when after computing Multi-Block Variable Importance in Projection (MB-VIP) scores on a fitted MB-PLS discriminant model, when you need to distinguish signal features from noise by establishing empirical significance thresholds rather than relying on parametric assumptions.
    4 installs
90. ▌
    Retention Time Alignment Validation 2 · holobiomicslab

    Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
    7 installs
91. ▌
    Spectral Feature Vector Generation 2 · holobiomicslab

    Use when you have a collection of MS/MS spectra in standard formats (mzML, MGF) and need to perform rapid similarity search, clustering, or joint analysis across millions of spectra without repeated peptide database searches.
    4 installs
92. ▌
    Spectral Library Format Conversion 3 · holobiomicslab

    Use when when you have mass spectral libraries from multiple sources (NIST, MoNA, RIKEN, GNPS) in disparate formats (MSP, MGF, MOL folder structures) or with misaligned metadata (e.
    6 installs
93. ▌
    Spectral Library Schema Validation 2 · holobiomicslab

    Use when after harmonizing MS/MS spectra and metadata fields (compound identifiers, adduct annotations, collision energies, instrument types) to a common schema, and before exporting the spectral library to standardized formats (mzML, mzTab, or repository-native format).
    6 installs
94. ▌
    Spectral Similarity Scoring Cosine 2 · holobiomicslab

    Use when you have a collection of preprocessed and cleaned mass spectrometry spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to compute all-pairs or targeted spectral similarity scores to identify related spectra, perform spectral library searches, or build a similarity network.
    8 installs
95. ▌
    Technical Specification Tabulation 2 · holobiomicslab

    Use when when you need to verify whether a specific mass spectrometry instrument platform (vendor and model), acquisition mode (e.g., targeted, ddMS2-topN, AIF, direct infusion, imaging), or file format is compatible with a lipidomics or proteomics software tool;
    6 installs
96. ▌
    Top K Retrieval Ranking Evaluation 2 · holobiomicslab

    Use when when you have deployed a trained embedding or similarity model on a test set of tandem mass spectra and need to measure its ability to rank correct library compounds near the top of retrieved candidates.
    6 installs
97. ▌
    Vendor Raw File Format Recognition 2 · holobiomicslab

    Use when you have a directory containing mass spectrometry data files from multiple instrument vendors (Thermo, AB Sciex, Agilent, Bruker, etc.) and need to convert them to a common format (Aird or mzML).
    4 installs
98. ▌
    Arrival Time To Ccs Conversion 3 · holobiomicslab

    Use when when you have raw TWIM-MS arrival-time data and need to transform it into absolute CCS values for downstream biomolecular class assignment or comparative analysis.
    8 installs
99. ▌
    Biomolecular Class Ccs Mapping 3 · holobiomicslab

    Use when after biomolecular class labels have been assigned to features in a TWIM-MS dataset and you have raw ion mobility arrival time measurements. Use it when you need to convert arrival times to standardized CCS values where calibration accuracy depends critically on the biomolecular class (e.
    7 installs
100. ▌
     Class Specific Ccs Calculation 3 · holobiomicslab

     Use when when you have multi-omic TWIM-MS data (raw or processed arrival-time records) and have already assigned features or detected ion features to biomolecular classes (e.
     5 installs