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HolobiomicsLab

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1. ▌
   Spectral Topic Modeling Lda · holobiomicslab

   Use when when you have a collection of normalized mass spectrometry spectra (peak intensities or binned m/z representations) and seek to enrich neural network training signals for metabolite identification by discovering latent spectral patterns.
   6 installs
2. ▌
   Spectrum Embedding Indexing · holobiomicslab

   Use when you have pre-computed Word2vec embeddings of mass spectra and need to retrieve the k most similar spectra from a library of hundreds of thousands to millions of candidates.
   7 installs
3. ▌
   Tanimoto Similarity Scoring · holobiomicslab

   Use when when running iterative reaction network expansion (Pickaxe) and you need to reduce the combinatorial explosion of generated compounds by prioritizing those structurally similar to a reference set (e.g., known metabolites, drug targets, or desired scaffolds).
   4 installs
4. ▌
   Tensorflow Model Conversion · holobiomicslab

   Use when you have downloaded pre-trained Keras models and need to prepare them for deployment in a TensorFlow Serving container. Use this skill when you must convert legacy or freshly downloaded Keras model files to HDF5 format for compatibility with TensorFlow 2.3.0 serving infrastructure.
   6 installs
5. ▌
   Workflow Build System Usage · holobiomicslab

   Use when when you have a Nextflow workflow repository with a Makefile, and you need to execute the workflow for local testing or validation. Triggers include: (1) first-time setup of a downloaded workflow; (2) regression testing after code changes;
   6 installs
6. ▌
   Compound Ground Truth Matching · holobiomicslab

   Use when when you have pre-computed embeddings for query and reference MS/MS spectra, computed their cosine similarity matrix, and need to measure retrieval success by verifying whether the correct compound (identified by SMILES string) appears in the top-1, top-5, or top-10 ranked candidates from.
   4 installs
7. ▌
   Data Augmentation Metabolomics · holobiomicslab

   Use when you have preprocessed and normalized ROI feature data extracted from mzXML or mzML mass spectrometry files and seek to increase feature representation and robustness before statistical modeling or machine learning.
   5 installs
8. ▌
   Spatial Coordinate Mapping Msi · 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.
   5 installs
9. ▌
   Chromatogram Alignment Warping · holobiomicslab

   Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference chromatogram, and you need to align peak positions across both dimensions before joining multiple samples for multiway PCA or.
   6 installs
10. ▌
    Chromatographic Noise Modeling · holobiomicslab

    Use when you need to generate blank or background-only .mzML files for method validation, when you want to create synthetic negative controls with realistic instrumental noise but no analyte peaks, or when you need to simulate serum matrix background (e.
    6 installs
11. ▌
    Chromatography Data Decimation · holobiomicslab

    Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g., 5–16 ms) ranges and applying Savitzky-Golay smoothing. Use it as a preprocessing step before alignment operations.
    6 installs
12. ▌
    Cluster Statistics Integration · holobiomicslab

    Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did not yield detected peaks at certain cluster positions.
    6 installs
13. ▌
    Control Flow Diagram Synthesis · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on declared input type (LC, GC, IMS, or MS Imaging).
    4 installs
14. ▌
    Drift Retention Time Alignment · holobiomicslab

    Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature fluctuations or chromatographic column degradation, and you need to normalize sample positions before downstream peak.
    6 installs
15. ▌
    Gaussian Peak Shape Evaluation · holobiomicslab

    Use when after peak detection on a composite mass track has identified candidate peaks in a mass chromatogram, and before compiling the final feature table.
    5 installs
16. ▌
    Gc Ims Matrix Table Generation · holobiomicslab

    Use when after integratePeaks has been executed with a chosen integration method (e.g., fixed_size with RIP saturation threshold of 0.1) on a clustered, baseline-corrected GC-IMS dataset.
    4 installs
17. ▌
    Gcxgc Ms Multivariate Analysis · holobiomicslab

    Use when after preprocessing a set of aligned 2D-TIC (two-dimensional Total Intensity Chromatogram) matrices from GCxGC-MS experiments—when you have multiple samples across distinct biological groups (e.
    5 installs
18. ▌
    Imputation Algorithm Selection · holobiomicslab

    Use when you have a metabolomics dataset with left-censored missing values (e.g., below limit of quantification in LC/MS or GC/MS) and need to evaluate multiple imputation approaches.
    4 installs
19. ▌
    Mass Spectrometry Data Parsing · holobiomicslab

    Use when you have received raw or vendor-converted centroid mzML files from LC-MS, GC-MS, or DI-MS platforms and need to extract MS1 spectra before building mass tracks, performing peak detection, or constructing composite feature maps.
    8 installs
20. ▌
    Mona Metadata Field Extraction · holobiomicslab

    Use when when you have loaded a MoNA mass spectral library (GC-MS or LC-MS/MS) in MSP format and observe that SMILES strings are present in the Comment field rather than in a dedicated SMILES metadata field.
    6 installs
21. ▌
    Ranking Task Loss Optimization · holobiomicslab

    Use when you have multiple pre-trained neural network models (e.g., MLP and GNN) that produce overlapping predictions on the same set of candidates, and your evaluation metric is rank-based (average rank, Rank@K) rather than point-wise accuracy or RMSE.
    6 installs
22. ▌
    Workflow Routing Configuration · holobiomicslab

    Use when when you have raw mass spectrometry data files from multiple acquisition modalities (LC-MS, GC-MS, ion mobility, or imaging) and need to automatically route each to the correct downstream analysis module without manual intervention.
    6 installs
23. ▌
    Xcms Data Import Preprocessing · holobiomicslab

    Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass calibration (e.
    2 installs
24. ▌
    4d Lcimmsms Feature Extraction · holobiomicslab

    Use when you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values against a quantum chemistry calculation-assisted CCS prediction database.
    5 installs
25. ▌
    Annotation Object Manipulation · holobiomicslab

    Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate annotations per feature, visualize matched ions in ranked spectra, or export pseudo-MS/MS spectra for external analysis.
    7 installs
26. ▌
    Attention Mechanism Validation · holobiomicslab

    Use when after instantiating a transformer encoder module for mass spectrometry data processing (e.g., in IDSL_MINT), before training on large MS/MS datasets or running inference on test spectra.
    5 installs
27. ▌
    Automated Lipid Identification · holobiomicslab

    Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
    4 installs
28. ▌
    Blank Sample Feature Filtering · holobiomicslab

    Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data and your experimental design includes blank (negative control) samples.
    7 installs
29. ▌
    Chemical Coverage Optimization · holobiomicslab

    Use when your LC-MS feature table is incomplete or has low chemical coverage because traditional peak extraction algorithms (e.g., standard XCMS workflows) systematically miss features at m/z and retention time positions corresponding to known suspect compounds in your database.
    7 installs
30. ▌
    Chemical Similarity Clustering · holobiomicslab

    Use when you have untargeted LC-MS/MS metabolomic data (MS1 features with MS2 fragmentation spectra) preprocessed by MZmine2 into a feature table (BIOM format) and MGF file, and you want to construct a chemically-informed hierarchy of features for alpha/beta-diversity analysis or to group features.
    6 installs
31. ▌
    Clustering Metrics Computation · holobiomicslab

    Use when when you have executed multiple clustering tools on the same tandem-MS dataset and need to quantitatively compare their performance using normalized, comparable metrics rather than raw cluster assignments alone.
    4 installs
32. ▌
    Cnn Inference On Spectral Data · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) in memory or on disk, a trained CNN model checkpoint available, and you need to generate molecular embedding vectors for matching against a reference database of known metabolites.
    6 installs
33. ▌
    Cross Sample Feature Alignment · holobiomicslab

    Use when you have run mass detection and chromatogram building independently on each LC-MS/MS sample and produced per-sample feature lists with m/z, retention time, and intensity values.
    6 installs
34. ▌
    Cross Spectrum Negative Mining · holobiomicslab

    Use when when training a Siamese architecture rescore model for MS/MS-based molecular formula prediction and you have an imbalanced training set with far fewer negative than positive spectrum pairs.
    5 installs
35. ▌
    Cross Split Metric Aggregation · holobiomicslab

    Use when when you have a pre-trained model and need to report stable, generalizable performance on a fixed training set with multiple held-out test splits. Specifically: when you have 10 (or n) random query/reference splits on the same dataset (e.
    5 installs
36. ▌
    Data Format Conversion CSV Tsv · holobiomicslab

    Use when after completing data merging, cleanup, and batch correction steps in the FBMN-STATS pipeline, when you have a processed feature quantification table combined with sample metadata in memory (R data frame or Python pandas DataFrame) and need to preserve it for multivariate statistical.
    7 installs
37. ▌
    Deep Learning Model Evaluation · holobiomicslab

    Use when after training a Siamese neural network on MS/MS spectrum pairs, use this skill to quantify prediction performance on a disjoint test set (e.g., 3600+ spectra from 500 unseen compounds).
    4 installs
38. ▌
    Diagnostic Fragment Annotation · holobiomicslab

    Use when when you have centroided, data-dependent acquisition (ddMS2) spectra in mzML format with extracted precursor m/z values and associated fragment ion lists, and you need to discriminate PFAS features from background signals using characteristic fragmentation patterns.
    6 installs
39. ▌
    Dimensionality Reduction T Sne · holobiomicslab

    Use when you have computed high-dimensional embeddings (e.
    5 installs
40. ▌
    Feature Group Adduct Detection · holobiomicslab

    Use when you have a feature table from LC-MS analysis (containing m/z, retention time, and intensity values) and need to identify which detected features represent the same molecular species ionized under different adduction states.
    4 installs
41. ▌
    Feature Group Spectral Mapping · holobiomicslab

    Use when after sample alignment and isotopologue/adduct grouping are complete, when you need to associate MS2 spectral data (DDA-acquired) with the consolidated feature groups to enable MS/MS-based compound annotation or to bundle MS1 quantification with MS2 evidence.
    7 installs
42. ▌
    Feature List Format Validation · holobiomicslab

    Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic detection, or wishes to augment/replace pyOpenMS results with pre-processed features.
    2 installs
43. ▌
    Feature Statistical Annotation · holobiomicslab

    Use when after LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes. Use this skill when you have access to a reference list of molecules of interest (e.
    5 installs
44. ▌
    File Format Robustness Testing · holobiomicslab

    Use when when processing MS spectral data from multiple open mass spectra libraries (OMSLs) in mixed formats (MSP, MGF, JSON, CSV), especially when source data exhibits missing fields, malformed entries, inconsistent adduct representations, or non-standard format variants that may cause silent.
    7 installs
45. ▌
    Fragment Intensity Aggregation · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files but before consensus spectrum generation, when you observe high-resolution fragment lists where nearby peaks (within a specified mass tolerance, typically 0.
    5 installs
46. ▌
    Fragment Ion Database Matching · holobiomicslab

    Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment libraries (e.g., LipidPos for lipids).
    4 installs
47. ▌
    Fragment Ion Spectral Matching · holobiomicslab

    Use when after pointwise correlation analysis and exact mass difference refinement have identified candidate ion-species pairs that may share a common analyte origin.
    5 installs
48. ▌
    Full Scan Acquisition Strategy · holobiomicslab

    Use when you need to assess MS1-level ionization efficiency, peak detection sensitivity, and chromatographic separation without the overhead of MS/MS fragmentation. Use it to benchmark full-scan detection across chemically diverse samples (e.
    6 installs
49. ▌
    Ggplot2 Geom Treemap Rendering · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).
    5 installs
50. ▌
    Graph Based Feature Annotation · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and corresponding MS2LDA substructural feature assignments or chemical class predictions, and you want to systematically propagate these annotations to individual network nodes to enable feature-aware visualization and.
    6 installs
51. ▌
    Hierarchical Database Indexing · holobiomicslab

    Use when when you have a large combinatorial chemical space (e.g., all regioisomeric positions of lipid double bonds across carbon counts and saturation levels) and need to query it repeatedly against experimental mass spectrometry spectra.
    6 installs
52. ▌
    High Dimensional Data Indexing · holobiomicslab

    Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest neighbors efficiently.
    4 installs
53. ▌
    Instrument Type Filtering Gnps · holobiomicslab

    Use when you have a large, mixed-instrument GNPS spectral dataset and need to create an instrument-specific training set for FIDDLE or similar deep learning models. Use this skill when your configuration file specifies an instrument allowlist (e.
    6 installs
54. ▌
    Intensity Threshold Evaluation · holobiomicslab

    Use when you have processed LC-MS data (mzML or vendor format) and need to validate that internal standards and target analytes produce peak intensities within expected operational ranges.
    4 installs
55. ▌
    Inter Scan Interval Validation · holobiomicslab

    Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the scheduled method with correct temporal spacing.
    4 installs
56. ▌
    Interpretable Machine Learning · holobiomicslab

    Use when when you have tandem mass spectra data and need to predict a binary molecular property (e.g., presence of a functional group like a sulfo group) while maintaining full interpretability of the model's decision logic.
    6 installs
57. ▌
    Iokr Fingerprint Space Ranking · holobiomicslab

    Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a compound-class-agnostic method.
    2 installs
58. ▌
    Iokr Kernel Regression Scoring · holobiomicslab

    Use when when you have paired genomics (antiSMASH-detected BGCs with MIBiG homology assignments) and metabolomics data (MS2 spectra from GNPS), and you need to score BGC-spectrum links using molecular structure similarity rather than strain co-occurrence patterns.
    7 installs
59. ▌
    Ionization Mode Classification · holobiomicslab

    Use when when converting raw MS/MS spectral records (e.g. from .msp format) into metabolite fragment database entries for MetaboAnnotatoR, and the output filenames or library index must distinguish between positive and negative ionization modes to ensure correct library selection during annotation.
    6 installs
60. ▌
    Isotopic Enrichment Simulation · holobiomicslab

    Use when you have a peptide sequence and need to predict its theoretical m/z values under partial or complete isotopic enrichment (e.g., 1% natural 13C abundance, 50% 13C labeling, or other SIP conditions).
    6 installs
61. ▌
    Lc Ms Adduct Pattern Detection · holobiomicslab

    Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may represent the same compound ionized as different adducts (e.g., [M+H]⁺ vs. [M+Na]⁺).
    9 installs
62. ▌
    Lc Ms Peak Feature Engineering · holobiomicslab

    Use when you have LC-MS feature tables with m/z and retention time coordinates paired with raw .mzXML or .mzML data files, and you need to systematically assess which features correspond to genuine chromatographic peaks versus noise or artifacts.
    4 installs
63. ▌
    Lda Model Training Convergence · holobiomicslab

    Use when you have a preprocessed bag-of-fragments corpus derived from tandem mass spectrometry spectra and need to discover recurring fragmentation motifs without prior compound identification.
    5 installs
64. ▌
    Link Scoring Metcalf Algorithm · holobiomicslab

    Use when you have loaded GCFs (from AntiSMASH via BigScape clustering), GNPS spectra, and molecular families (from GNPS molecular networking), and need to compute pairwise scoring between genomic and metabolomic entities to identify putative gene cluster–metabolite associations.
    6 installs
65. ▌
    Mass Spectral Feature Grouping · holobiomicslab

    Use when you have untargeted metabolomics MS/MS spectra from multiple features and need to identify which features belong to the same molecular family or are related by biotransformation.
    10 installs
66. ▌
    Mass Spectrometry Data Loading · holobiomicslab

    Use when you have raw MS data files from supported instruments (Agilent, Thermo, Bruker, or mzML format) and need to ingest them into IonToolPack for visualization, quality control, targeted extraction, or spectral library matching.
    6 installs
67. ▌
    Mass Spectrum De Novo Analysis · holobiomicslab

    Use when you have an unknown MS/MS spectrum (m/z and intensity pairs) from positive-mode ionization and need to identify the most likely molecular formula and adduct type (e.g., [M+H]+, [M+Na]+) when no reference library match is available or desirable.
    4 installs
68. ▌
    Metabolights Dataset Retrieval · holobiomicslab

    Use when you have a MetaboLights dataset identifier (e.g., MTBLS1124) and need to download a specific mzML file (e.g., QC07.mzML) from the public repository for visualization, quality control assessment, or integration into a metabolomics workflow. The USI format mzspec:MTBLS1124:QC07.
    6 installs
69. ▌
    Metabolite Annotation At Scale · 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.
    4 installs
70. ▌
    Metabolite Intensity Alignment · 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.
    6 installs
71. ▌
    Metabolomics Sample Comparison · holobiomicslab

    Use when you have a MemoMatrix (sample-by-fingerprint matrix) from aligned MS2 spectra and need to visually compare sample similarity or clustering patterns, especially when samples show poor feature overlap, strong retention time shifts across different LC methods, or were acquired on different.
    9 installs
72. ▌
    Ms Dial Export Format Handling · holobiomicslab

    Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool. The skill is required whenever you are preparing MS-DIAL output for consumption by external analysis pipelines that expect standardized export formats.
    6 installs
73. ▌
    Ms Ms Spectrum Peak Annotation · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or local data) and need to identify significant fragment ions above noise, assign occurrence scores to peaks, and generate a CSV-formatted library entry for use in metabolite feature annotation pipelines.
    7 installs
74. ▌
    Ms2 Fingerprint Matrix Merging · holobiomicslab

    Use when you have two MemoMatrix objects generated from separate sample cohorts (e.
    5 installs
75. ▌
    Ms2lda Substructure Assignment · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected substructural motifs to identify shared fragmentation patterns and structural classes across molecular families.
    4 installs
76. ▌
    Multi Class Network Annotation · holobiomicslab

    Use when you have (1) metabolite-disease correlation matrices and protein association predictions generated by a deep learning module (e.
    5 installs
77. ▌
    Multi Panel Spectra Comparison · holobiomicslab

    Use when when you need to visually compare two or more spectra (MS1, MS2, or extracted ion chromatograms) across different retention times, m/z ranges, or ion mobility bins in a single figure. Apply this skill after extracting spectra arrays from MZA files (e.
    7 installs
78. ▌
    Multi Sample Cohort Assessment · holobiomicslab

    Use when when you have MS1 mass spectrometry data from multiple samples (a cohort) acquired across an instrument run or batch, and you need to identify which samples deviate from cohort norms or which ion targets show anomalous behavior.
    4 installs
79. ▌
    Multi Species Lipid Prediction · holobiomicslab

    Use when you have candidate lipid annotations from high-throughput spectral matching (e.
    6 installs
80. ▌
    Neural Network Scoring Ranking · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs), a set of candidate chemical formula–adduct pairs (enumerated via SIRIUS or another generator), and need to rank them by credibility without access to a spectrum library.
    4 installs
81. ▌
    Nextflow Profile Customization · holobiomicslab

    Use when you need to execute a Nextflow metabolomics workflow (e.
    4 installs
82. ▌
    Outlier Feature Classification · holobiomicslab

    Use when after peak picking by MS-DIAL and import into R, when the feature table contains m/z values with decimal components that fall within the [4, 8] interval (indicating instrumental artifacts or calibration errors).
    6 installs
83. ▌
    Peak And Neutral Loss Counting · holobiomicslab

    Use when when you have matchms-processed MS2 spectra from multiple samples and need to create comparable sample-level signatures for cross-sample analysis, particularly when samples are chemodiverse, have poor feature overlap, or exhibit strong retention time shifts across LC methods or MS.
    4 installs
84. ▌
    Qc Summary Table Extraction · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain a structured report of which ions passed or failed each filter.
    5 installs
85. ▌
    R6 Object Method Invocation · holobiomicslab

    Use when when working with large metabolomics peak tables (e.
    6 installs
86. ▌
    Repository Backend Dispatch · holobiomicslab

    Use when when you have a USI string (e.g., 'mzspec:GNPS:TASK-abc123:scan:1943') and need to retrieve the underlying spectrum data from its native repository without knowing a priori which backend stores it.
    2 installs
87. ▌
    Repository Code Integration · holobiomicslab

    Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public repository, and you need to apply that method to new experimental data (e.
    5 installs
88. ▌
    Retention Time Mz Alignment · holobiomicslab

    Use when processing raw LC/MS data (mzML or mzXML format) from multi-sample cohorts where retention time or intensity drift is suspected due to batch effects, instrument calibration drift, or variable run order.
    4 installs
89. ▌
    Retention Time Scan Mapping · holobiomicslab

    Use when when you have loaded an LC-MS spectrum file (mzML, mzXML, or equivalent) into the GNPS LCMS Visualization Dashboard and need to annotate extracted ion chromatograms with the precise retention time or scan ID positions where MS2 events occurred.
    8 installs
90. ▌
    Sample Metadata Integration · holobiomicslab

    Use when when you have LC-MS peak table data in Excel format (e.g., from MS-DIAL peak picking) with separate compartments for sample information, feature properties, and intensity values, and you need to construct a structured R object that enforces consistency between sample metadata (e.
    6 installs
91. ▌
    Scoring Module Unit Testing · holobiomicslab

    Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring logic into an existing MS2Query pipeline.
    3 installs
92. ▌
    Snr Based Signal Validation · holobiomicslab

    Use when after composite map peak detection has generated a full unfiltered peak list with SNR values computed for each candidate peak.
    6 installs
93. ▌
    Spec2vec Similarity Scoring · holobiomicslab

    Use when after discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation pattern against a pre-indexed spectral library using learned spectral embeddings.
    4 installs
94. ▌
    Spectral Data Serialization · holobiomicslab

    Use when after completing MS/MS spectra detection and peak recognition on tandem MS breath samples.
    7 installs
95. ▌
    Spectral Data Visualization · holobiomicslab

    Use when you have executed MassQL queries on mzML mass spectrometry data and need to communicate query results visually—particularly when comparing peak shapes across multiple files, assessing retention time distributions, or validating precursor/product ion matches.
    6 installs
96. ▌
    Spectral Mz Range Filtering · holobiomicslab

    Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment (e.g., 100–1400 m/z for typical tryptic peptides).
    5 installs
97. ▌
    Spectral Peak Visualization · holobiomicslab

    Use when you have a resolved mass spectrum (m/z values, intensities, and metadata) from a supported USI source (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA, or MassIVE) and need to create a publication-ready image that retains a link back to an interactive spectrum.
    4 installs
98. ▌
    Spectral Similarity Ranking · holobiomicslab

    Use when you have a query MS/MS spectrum and need to identify the -matching library spectrum from a large spectral database, particularly when the research goal requires distinguishing between exact matches and structural analogues without separate workflows.
    5 installs
99. ▌
    Spectrum Cluster Assignment · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters. Use this skill when: (1) you have a sparse similarity or distance matrix as input;
    6 installs
100. ▌
     Tabular Data Io And Masking · holobiomicslab

     Use when after generating a preliminary feature table from LC-MS data (e.g., via Asari), when experimental design includes blank samples or negative controls and you need to filter out features that are likely instrumental or chemical background rather than true biological signal.
     3 installs