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HolobiomicsLab

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1. ▌
   Workflow Configuration And Parameterization 2 · holobiomicslab

   Use when when preparing to execute the Nextflow4MS-DIAL workflow on raw LC-HRMS metabolomics data (.mzML or .
   1 install
2. ▌
   Adduct Formation Prediction For Metabolites 2 · holobiomicslab

   Use when when you have unidentified LC/MS features (m/z, retention time, intensity) and need to disambiguate which metabolites they represent by accounting for the fact that observed m/z values may correspond to different adduct forms (e.
   4 installs
3. ▌
   Chemical Type Classification And Annotation 2 · holobiomicslab

   Use when after identifying query chemicals from GC-MS data (via Match.
   0 installs
4. ▌
   Constraint Based Flux Sampling And Analysis 2 · holobiomicslab

   Use when when you have constraint-based metabolic models for multiple samples or cell lines, and you want to determine whether integrating multiple omics constraint types (nutrient availability, extracellular metabolite ratios, gene expression) produces distinct and biologically meaningful.
   0 installs
5. ▌
   Cross Dataset Score Distribution Comparison 2 · holobiomicslab

   Use when when you have applied multiple scoring functions (e.g., strain correlation and IOKR) to rank genomic-metabolomic (GCF-MF or BGC-spectrum) links and need to verify that: (1) standardisation produces zero mean and unit variance across all links;
   1 install
6. ▌
   Cross Language Implementation Compatibility 2 · holobiomicslab

   Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.
   1 install
7. ▌
   Dataframe Construction From Backend Sources 2 · holobiomicslab

   Use when when implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
   0 installs
8. ▌
   Deep Learning Model Architecture Validation 2 · holobiomicslab

   Use when after converting or loading a Keras model to HDF5 TensorFlow 2.3.0 format, especially when the model will be served through a pipeline (e.g., NP Classifier) that expects specific input/output layer names.
   0 installs
9. ▌
   Dotnet Framework Installation In Containers 2 · holobiomicslab

   Use when you need to containerize a C# application (e.g., AirdPro) that targets .NET Framework 4.8 and must run on Linux hosts via Docker, but the application was originally built for Windows. Use this skill when you are building multi-stage Docker images from a Ubuntu 22.
   0 installs
10. ▌
    Latent Dirichlet Allocation Topic Inference 2 · holobiomicslab

    Use when you have a preprocessed corpus of mass spectrometry spectra converted to bag-of-fragments format (with neutral losses extracted and noise filtered), and you seek to discover recurring fragmentation patterns or substructures that characterize multiple spectra without prior knowledge of the.
    0 installs
11. ▌
    Mass Accuracy Collision Energy Optimization 2 · holobiomicslab

    Use when you have defined a set of lipid targets (species, adducts, chain compositions) for PRM or MRM analysis and need to generate precursor-to-fragment transition rules that will maximize signal intensity and specificity on your mass spectrometer (Thermo QExactive HF, Agilent QTOF, or.
    0 installs
12. ▌
    Mass Spectrometry Data Visualization Pandas 2 · holobiomicslab

    Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV) loaded into a Pandas DataFrame with columns for m/z, retention time, ion mobility, or intensity values, and you need to render spectrum plots, chromatograms, mobilograms, or 2D peak maps.
    0 installs
13. ▌
    Ondiskmsnexp Object Manipulation And Export 2 · holobiomicslab

    Use when you have raw CE-MS data and need to (1) transform migration time values to effective mobility using two calibration markers (e.
    1 install
14. ▌
    Pfas Characteristic Fragment Identification 2 · holobiomicslab

    Use when you have centroided data-dependent acquisition (ddMS2) mzML spectra from LC- or GC-HRMS and need to prioritize putative PFAS features.
    0 installs
15. ▌
    Principal Component Analysis Interpretation 2 · holobiomicslab

    Use when when you have normalized MS1 ion intensity features from multiple samples and need to assess overall data quality, detect systematic batch effects or instrumental drift, or identify which samples deviate significantly from the cohort norm in an omics-agnostic manner (metabolomics.
    0 installs
16. ▌
    Untargeted Metabolomics Dataset Integration 2 · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) from independent untargeted metabolomic experiments or replicates and need to establish one-to-one feature correspondence across them to compare abundances, detect shared metabolites, or merge datasets.
    1 install
17. ▌
    Gpu Accelerated Nearest Neighbor Indexing 2 · holobiomicslab

    Use when when searching unknown mass spectra against large high-resolution spectral libraries for open modification identification and you need to reduce search latency from seconds to milliseconds while maintaining sensitivity and specificity.
    0 installs
18. ▌
    Lipidomics Experiment Object Construction 2 · holobiomicslab

    Use when when you have lipidomics quantitation data (lipid abundances across samples) that you need to load into a unified, annotated R object for analysis—either from public Metabolomics Workbench studies via API, Skyline mass spectrometry software exports, or a custom numerical matrix with.
    1 install
19. ▌
    Mass Spectrometry Data Structure Decoding 2 · holobiomicslab

    Use when when you have a mzPeak file (uncompressed ZIP archive containing Parquet tables) and need to access decoded spectral data arrays (m/z, intensity), spectrum metadata (scan descriptors, precursors), or chromatogram data in a form suitable for Python/R analysis pipelines.
    0 installs
20. ▌
    Mass Spectrometry Target List Preparation 2 · holobiomicslab

    Use when you have a raw .xlsx or tabular file listing candidate compounds with theoretical or measured m/z values, expected retention times, and ionization polarities, and you need to feed this into TARDIS or another targeted LC–MS analysis pipeline.
    0 installs
21. ▌
    Neural Network Module Architecture Design 2 · holobiomicslab

    Use when when building an end-to-end deep learning model that must predict multiple correlated peptide properties (charge, isotope count, retention time) simultaneously from mass spectrometry data, and you need a principled way to merge learned representations from separate task-specific branches.
    1 install
22. ▌
    Metabolite Detection Frequency Estimation 2 · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative ionization modes) into an AnnData object, and before filtering metabolites or performing cross-modal integration.
    1 install
23. ▌
    Metabolite Level Expression Summarization 2 · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative mode files) into an AnnData object and before filtering or integrating with spatial transcriptomics.
    0 installs
24. ▌
    Msms Spectrum Data Structure Manipulation 2 · holobiomicslab

    Use when you have raw or downloaded MSMS spectra (from online resources via Universal Spectrum Identifier, or from local mzML/mzXML files) that require standardization, cleaning, and fragment assignment before visualization, statistical comparison, or machine-learning feature extraction.
    1 install
25. ▌
    Formula Transformer Architecture Application 2 · holobiomicslab

    Use when you have tandem mass spectra (MS/MS) with unknown precursor formulas and need to rank chemical formula candidates conditioned on observed fragment m/z values and precursor mass. Use this skill when fragmentation tree computation (e.
    0 installs
26. ▌
    Fragmentation Pattern Extraction And Ranking 3 · holobiomicslab

    Use when you have a collection of MS/MS spectra (≥2 spectra) and wish to identify fragmentation signatures common to subsets of those spectra.
    0 installs
27. ▌
    Graph Based Metabolite Similarity Assessment 3 · holobiomicslab

    Use when you have a collection of MS/MS spectra (stored as Spectrum2 objects in an ms2Lib class) and need to identify which spectra share identical fragmentation patterns—particularly when coupled to a GNPS molecular network to focus on explaining network components (connected components, cliques.
    1 install
28. ▌
    Metabolite Structural Annotation Integration 2 · holobiomicslab

    Use when after statistical analysis (e.g., MB-PLS with permutation testing) has identified a subset of significant LC-MS features (p < 0.05 or similar threshold) that require structural interpretation.
    1 install
29. ▌
    Quality Control Metric Distribution Analysis 4 · holobiomicslab

    Use when after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
    1 install
30. ▌
    Sequential Tool Integration And Data Routing 2 · holobiomicslab

    Use when when you have raw LC-HRMS metabolomics data in .mzML or .
    0 installs
31. ▌
    Spectral Scoring And Significance Assessment 2 · holobiomicslab

    Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) against a chemical structure database of known natural products, and you need to: (1) identify which pipeline(s).
    1 install
32. ▌
    Component Candidate Prioritization Filtering 2 · holobiomicslab

    Use when after generateComponents has assigned candidate TP features to parent features and computed similarity metrics (spectrum similarity, fragment matches, neutral loss matches, retention time differences), use this skill to narrow the candidate pool to high-confidence parent–TP pairs that.
    0 installs
33. ▌
    Converter Pipeline Integration And Execution 2 · holobiomicslab

    Use when when you have a .msp mass spectra file with incomplete or missing chemical metadata fields (SMILES, InChI, CAS number, formula, InChIKey, IUPAC name) and need to populate those fields by querying multiple external chemical identifier services and local cheminformatics tools in parallel.
    1 install
34. ▌
    Cross Dataset Feature Correspondence Mapping 2 · holobiomicslab

    Use when you have two or more nontargeted LCMS feature tables from the same analytical method (same column, ionization mode, and acquisition parameters) and need to identify which features in one dataset correspond to features in another.
    1 install
35. ▌
    Feature Annotation With Chemical Descriptors 2 · holobiomicslab

    Use when you have a feature list (m/z values, retention times, and optionally molecular formulas or neutral masses) from LC- or GC-HRMS data and need to rapidly identify features matching characteristic chemical signatures (e.
    0 installs
36. ▌
    Feature Table Generation From Chromatography 2 · holobiomicslab

    Use when after retention-time correction and alignment of centroided mzML or mzXML LC-MS files across a sample cohort.
    0 installs
37. ▌
    Mass2motif Probability Distribution Learning 2 · holobiomicslab

    Use when when you have preprocessed MS/MS spectra converted to a bag-of-fragments format (fragments and neutral losses extracted, noise filtered) and you seek to discover recurring fragmentation patterns without prior compound identification.
    0 installs
38. ▌
    Metabolite Feature Association Across Labels 2 · holobiomicslab

    Use when after PuInc_seeker has identified putative incorporations (m/z features showing significant fold-change and p-value signals between labeled and unlabeled sample groups) and you need to assign base peaks—the most intense isotopologue signals—and validate isotope-pair mass gaps match.
    0 installs
39. ▌
    Metabolomics Feature Intensity Normalization 2 · holobiomicslab

    Use when after peak detection and feature table construction (rows = features, columns = samples with intensity values) and before applying intensity-based filters (e.g., fold-change, phenotype score) or when preparing data for dashboard visualization.
    0 installs
40. ▌
    Microbe Metabolite Prediction Neural Network 2 · holobiomicslab

    Use when you have paired microbiome (16S or metagenomic taxonomy/functions at genus or finer level) and metabolome (LC-MS or similar profiled metabolites) data from the same samples and want to: (1) predict unobserved metabolite abundances from microbiome composition;
    0 installs
41. ▌
    Molecular Formula Computation From Structure 2 · holobiomicslab

    Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings. The computed formulas are required before combining libraries or writing them to msp format for MS-DIAL compatibility.
    0 installs
42. ▌
    Ms2 Spectral Library Matching Post Denoising 2 · holobiomicslab

    Use when after frequency-based denoising of MS/MS spectra, when you need to validate that denoising improves metabolite identifications and quantify the trade-off between signal retention and annotation confidence. Specifically: (1) you have denoised MS/MS spectra from replicate measurements;
    1 install
43. ▌
    Multi Component Weighted Ranking Aggregation 2 · holobiomicslab

    Use when you have completed LC–MS/MS feature detection and annotation (via MZmine2/3 and GNPS/SIRIUS/CANOPUS), have compiled a taxonomically annotated metadata table, and need to rank extracts by their likelihood of containing novel chemistry.
    0 installs
44. ▌
    Neural Network Layer Metadata Interpretation 2 · holobiomicslab

    Use when after deploying a TensorFlow-backed classification service, you need to verify that the model's input layer names ('input_2048' and 'input_4096') and output layer name ('output') are correctly configured before constructing inference requests.
    1 install
45. ▌
    Olden Method Feature Attribution Calculation 2 · holobiomicslab

    Use when after training multiple MLPNN models (via cross-validation) on paired microbiome and metabolome data when you need to extract interpretable feature importance scores from network weights to identify which microbes drive metabolite predictions and group them into co-functional modules.
    0 installs
46. ▌
    Peak List Simulation With Controlled Effects 3 · holobiomicslab

    Use when you need to validate batch correction or normalization algorithms, require ground-truth condition/batch effect annotations for method benchmarking, or want to systematically evaluate how different batch types (linear, random) and condition allocations affect feature recovery in metabolomic.
    1 install
47. ▌
    Performance Threshold Filtering And Analysis 2 · holobiomicslab

    Use when when a trained model produces probabilistic or ensemble predictions and you need to achieve a specific target accuracy metric (e.g., RMSE ≤ 0.1) or minimize error on a test set, but the unfiltered model does not meet that target.
    0 installs
48. ▌
    Spectral Match Scoring Algorithm Development 2 · holobiomicslab

    Use when when building or extending MS/MS library search tools that must re-rank top candidate spectra (e.g., top 2000 from MS2Deepscore) to identify the analogue or exact match.
    0 installs
49. ▌
    Spectral Similarity Prediction Deep Learning 2 · holobiomicslab

    Use when when you have paired MS/MS spectra (unknown and known metabolites) with annotated structural similarity labels, and you need to rank candidate structures for metabolite identification.
    0 installs
50. ▌
    Word Embedding Aggregation For Spectral Data 4 · holobiomicslab

    Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular networking that correlate better with structural similarity than cosine-based methods.
    1 install
51. ▌
    Word Embedding Based Spectrum Representation 3 · holobiomicslab

    Use when when comparing large numbers of MS/MS spectra against spectral libraries or in molecular networking, particularly when molecules differ by multiple structural modifications and cosine-based scores produce excessive false positives.
    0 installs
52. ▌
    Conditional Threshold Logic Implementation 2 · holobiomicslab

    Use when when visualizing numeric columns with unknown or highly variable ranges, and the visualization quality depends on parameter selection tied to data statistics. Specifically: after loading a numeric column (e.
    0 installs
53. ▌
    Dotnet Framework Compilation In Containers 2 · holobiomicslab

    Use when you have a C# GUI application targeting .NET Framework 4.8 (Windows-only) and need to execute it on macOS or Linux hosts without modifying the source code. The application requires compilation from source and GUI display support via X11 forwarding or headless CLI execution.
    0 installs
54. ▌
    Machine Learning Cross Validation Training 2 · holobiomicslab

    Use when you have a labeled dataset (e.g., mass spectra with molecular structures, SIRIUS 6 fingerprint annotations) that you wish to train a supervised deep learning model on, and you need to estimate generalization performance and reduce variance from a single train–test split.
    0 installs
55. ▌
    Multivariate Feature Importance Extraction 2 · holobiomicslab

    Use when you have a preprocessed peak table (feature matrix: samples × peaks) with known class labels or phenotype groupings, and you want to identify which individual peaks contribute most to classification or discrimination between groups.
    0 installs
56. ▌
    Quality Control Sample Metadata Extraction 2 · holobiomicslab

    Use when you have txt files exported from Sciex MultiQuant (>v3.0.
    0 installs
57. ▌
    XML Parsing And Element Tree Serialization 2 · holobiomicslab

    Use when when spectrum or chromatogram data is stored as serialized XML strings in a database or file system and must be converted into pymzML Spectrum or Chromatogram objects for programmatic access.
    0 installs
58. ▌
    Mass Spectrometry Data Matrix Construction 2 · holobiomicslab

    Use when you have raw spatial metabolomics imzML files (paired with .ibd binary data files) that need to be loaded into a unified AnnData format for integration with spatial transcriptomics data or for cross-modal spatial pattern identification in single or multiple sample datasets.
    0 installs
59. ▌
    Isotopologue Adduct Cross Assay Link Encoding 2 · holobiomicslab

    Use when after structural cluster assignment and correlation clustering are complete, and you need to represent the full set of structural relationships (isotopologues, adducts, cross-assay links, and correlation co-membership) in a single unified graph for interactive visualization, network.
    1 install
60. ▌
    Mass Spectrometry Data Loading And Formatting 2 · holobiomicslab

    Use when you have raw or curated mass spectrometry data (MS1, MS2, or MSMS) in mzML, mzXML, CDF, MGF, MSP formats, or from a MassBank/MetaboLights repository, and need to convert it into an in-memory or on-disk spectral object that supports filtering, comparison, and annotation workflows.
    1 install
61. ▌
    Metabolite Quantification Accuracy Assessment 2 · holobiomicslab

    Use when you have executed mzExacto() on a preprocessed GC-MS dataset and need to verify that the returned dataframe correctly matches query chemicals to their m/z peaks, retention times, and quantitative measurements (area values).
    1 install
62. ▌
    Peak Annotation Quantification And Comparison 2 · holobiomicslab

    Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
    0 installs
63. ▌
    Pfas Characteristic Mass Difference Detection 3 · holobiomicslab

    Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
    0 installs
64. ▌
    Root Mean Squared Error Regression Evaluation 2 · holobiomicslab

    Use when you have a trained regression model (e.g., a neural network or similar predictor) and a held-out test set with ground-truth continuous labels, and you need to measure whether the model's predictions match the true values.
    1 install
65. ▌
    Structural Similarity Ground Truth Validation 2 · holobiomicslab

    Use when you have a spectral library with structural ground truth (InChIKey or SMILES annotations for ≥50% of spectra) and want to benchmark whether a new or existing spectral similarity scorer ranks structurally related compounds higher than unrelated ones.
    1 install
66. ▌
    Vendor Mass Spectrometry File Format Handling 2 · holobiomicslab

    Use when you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird format for batch processing, cloud deployment, or integration with downstream analysis tools.
    0 installs
67. ▌
    Background Distribution Threshold Calibration 2 · holobiomicslab

    Use when when you have trained a predictive model (e.g., neural network or regression model) that outputs continuous scores (such as Spearman correlation coefficients) for individual features (e.
    0 installs
68. ▌
    Centered Log Ratio Transformation Application 2 · holobiomicslab

    Use when apply CLR transformation when working with microbiome or metabolomic relative abundance tables that will be input to multivariate regression or neural network models.
    0 installs
69. ▌
    Cross Dataset Model Generalization Assessment 2 · holobiomicslab

    Use when you have trained a neural network or regression model on one paired microbiome-metabolome dataset and wish to test whether it can predict metabolite abundances in an independent, externally-sourced dataset collected from different patient cohorts or study populations.
    0 installs
70. ▌
    Documentation Mining For Project Architecture 2 · holobiomicslab

    Use when you have access to a multi-component research software repository (e.
    0 installs
71. ▌
    Feature Table Annotation With Sample Metadata 2 · holobiomicslab

    Use when your input is a feature intensity table (CSV or R data frame) with features as columns and samples as rows, and you have accompanying sample metadata (batch identifiers, QC/study sample labels, run order, sample phenotypes, collection dates).
    0 installs
72. ▌
    Isotopologue Distribution Matrix Construction 2 · holobiomicslab

    Use when when you have measured fractional abundances of isotopologues (FAM) from LC-MS in an isotope labeling experiment and need to correct them to obtain true mass distribution vectors (MDV) that reflect only the labeling contribution, accounting for background from naturally occurring isotopes.
    5 installs
73. ▌
    Large Scale All Pairs Similarity Benchmarking 4 · holobiomicslab

    Use when you have multiple competing spectral similarity scoring methods (e.
    0 installs
74. ▌
    Mass Spectrometry Spectral Embedding Learning 2 · holobiomicslab

    Use when when you have preprocessed MS/MS spectral pairs (peak intensities and m/z values) and need to predict molecular structural similarity scores, or when you want to project spectra into a learned chemical embedding space for visualization (e.g., via UMAP) or downstream similarity searches.
    0 installs
75. ▌
    Message Passing Neural Network Implementation 2 · holobiomicslab

    Use when when you have molecular input data (SMILES strings or graph representations) and need to predict molecular properties or spectra using graph neural networks. Apply this skill specifically when the base chemprop MPNN must be extended with new feature modules (e.
    0 installs
76. ▌
    Molecular Fingerprint Generation And Encoding 2 · holobiomicslab

    Use when when you have paired tandem MS spectra and corresponding molecular structures (as SMILES strings or InChI keys) and need to train a model that jointly embeds spectra and structures for structure annotation by database lookup.
    1 install
77. ▌
    Multi Criterion Score Combination And Ranking 2 · holobiomicslab

    Use when you have generated hypothetical links (e.g., GCF–MF pairs) and computed multiple independent scoring functions on them (e.g., strain co-occurrence, IOKR structural fingerprint matching), but individual scores show incomplete discrimination power.
    0 installs
78. ▌
    Neural Network Ensemble Inference Via Dropout 2 · holobiomicslab

    Use when when you have a trained neural network and need to quantify prediction uncertainty or improve accuracy by filtering low-confidence predictions. Particularly useful when input spectra pairs have variable quality or when downstream tasks (e.
    0 installs
79. ▌
    Probabilistic Modeling Convergence Assessment 2 · holobiomicslab

    Use when during the LDA training phase when you need to decide whether the model has learned a stable representation of Mass2Motifs.
    0 installs
80. ▌
    R Workflow Scripting For Analytical Chemistry 3 · holobiomicslab

    Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration times, m/z values, peak intensities) by orchestrating multiple R packages in a controlled, documented sequence.
    0 installs
81. ▌
    Retention Time Mass Correspondence Resolution 2 · holobiomicslab

    Use when you have two LC-MS untargeted metabolomic feature tables (each containing m/z, retention time, and intensity columns) and need to establish which features in dataset A correspond to which features in dataset B, typically for comparative metabolomics, batch effect correction, or.
    1 install
82. ▌
    S4 Class Extension For Backend Implementation 2 · holobiomicslab

    Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly into workflows that use the Spectra package.
    0 installs
83. ▌
    Spectral Annotation And Overlay Visualization 2 · holobiomicslab

    Use when after correlation testing has validated putative parent–adduct ion pairs (e.g., via corrPairsMSI() on a massdiff object annotated with adductMatch results), use this skill to annotate and visualize the mass spectrum plot to confirm that identified pairs exhibit expected overlap—e.
    0 installs
84. ▌
    Tabular Data Parsing And Structure Conversion 2 · holobiomicslab

    Use when you have a txt or tabular export file from a liquid chromatography–mass spectrometry (LC-MS) instrument (e.g., Sciex MultiQuant > v3.0.
    0 installs
85. ▌
    Targeted Dia Data Extraction From Raw Spectra 3 · holobiomicslab

    Use when when you have raw diaPASEF mzML files, a transition list with target analytes (protein, peptide, charge state), and search results (DIA-NN, OpenSwath output) containing feature metadata (retention time, ion mobility, m/z coordinates), and you need to isolate and visualize signal for.
    1 install
86. ▌
    Url Validation And Accessibility Verification 2 · holobiomicslab

    Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
    0 installs
87. ▌
    Word2vec Embedding Training Mass Spectrometry 4 · holobiomicslab

    Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture fragmentation patterns and neutral loss relationships.
    0 installs
88. ▌
    Msi Data Visualization And Spatial Analysis 2 · holobiomicslab

    Use when when you have imzML-format MSI data and need to identify biochemical species in specific tissue regions or anatomical structures.
    0 installs
89. ▌
    Network Component Identification And Filtering 3 · holobiomicslab

    Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
    1 install
90. ▌
    Peak Map Rendering Retention Time Mz Intensity 3 · holobiomicslab

    Use when when you have loaded mass spectrometry data (from mzML or Bruker .
    1 install
91. ▌
    Probabilistic Topic Modeling Mass Spectrometry 2 · holobiomicslab

    Use when you have preprocessed tandem mass spectrometry spectra converted into a bag-of-fragments representation (with fragments and neutral losses extracted and noise filtered) and your goal is to discover recurring fragmentation patterns or substructures across a large spectral dataset without.
    0 installs
92. ▌
    Ribosomally Synthesized Peptide Identification 2 · holobiomicslab

    Use when you have LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and corresponding genomic sequence data (raw FASTA nucleotide sequences or genome mining tool outputs like antiSMASH .final.
    0 installs
93. ▌
    Spectral Batch Submission To Networking Server 2 · holobiomicslab

    Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and perform structured chemical similarity analysis.
    0 installs
94. ▌
    Peak Classification Validation 2 · holobiomicslab

    Use when after training or loading a NeatMS neural network model, before applying it to filter false positive MS1 peaks in a new dataset.
    0 installs
95. ▌
    Precursor Product Mass Pairing 2 · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment masses.
    0 installs
96. ▌
    Spectral Corpus Representation 2 · holobiomicslab

    Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
    0 installs
97. ▌
    Spectral Feature Consolidation 2 · holobiomicslab

    Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint data into a single matrix for comparative analysis.
    1 install
98. ▌
    Spectral Library Matching Ripp 2 · holobiomicslab

    Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by matching experimental spectra against a database of predicted post-translationally modified RiPP structures derived from.
    0 installs
99. ▌
    Substructural Motif Annotation 2 · holobiomicslab

    Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to associate each network node with its constituent substructural motifs and visualize which motifs are shared between.
    0 installs
100. ▌
     Targeted Metabolite Extraction 2 · holobiomicslab

     Use when you have centroided LC-MS data (.mzML format) and a curated list of targeted metabolites or lipids (with m/z, retention time, and polarity) that you want to quantify and quality-assess across multiple analytical runs, and you need both per-run AUC values and averaged QC metrics for each.
     0 installs