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HolobiomicsLab

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1. ▌
   Replicate Spectrum Concatenation 2 · holobiomicslab

   Use when after extracting raw MS/MS spectra from mzML files for individual features (identified by precursor m/z and retention time) and you have multiple replicate spectra for the same feature that need to be pooled for consensus analysis.
   0 installs
2. ▌
   Retention Time Index Calibration 2 · holobiomicslab

   Use when you have acquired a bottom-up proteomics LC-MS/MS run (e.
   0 installs
3. ▌
   Retention Time Window Extraction 2 · holobiomicslab

   Use when you have loaded sqMass files containing pre-extracted transition group chromatograms and need to isolate chromatographic traces within a specific retention time interval—either defined by OpenSwath feature metadata (apex retention time ± margin) or by manual user selection.
   0 installs
4. ▌
   Runtime Performance Benchmarking 2 · holobiomicslab

   Use when when you have implemented or adopted a new clustering or analysis tool and need to validate that it meets stated runtime claims on a representative production-scale dataset. Particularly important when the tool uses hardware acceleration (GPU) and the claimed speedup is a core contribution;
   0 installs
5. ▌
   Scan Index Filtering By Ms Level 2 · holobiomicslab

   Use when when you have generated a scan index from rawrr::readIndex() on a Thermo .
   0 installs
6. ▌
   Singularity Container Deployment 3 · holobiomicslab

   Use when you have a Nextflow workflow (e.g., Nextflow4MS-DIAL) that currently runs under Docker or bare metal, and you need to execute it on an HPC cluster that lacks Docker support or enforces Singularity as the container runtime.
   0 installs
7. ▌
   Small Molecule Compound Indexing 2 · holobiomicslab

   Use when when you have retention order predictions from multiple ensemble members (e.g., ROASMI_1 through ROASMI_5) for a set of candidate compounds and need to assign a per-compound uncertainty score that reflects how consistently the ensemble members rank that compound relative to others.
   0 installs
8. ▌
   Software Testing Unit Validation 2 · 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.
   0 installs
9. ▌
   Spectral Data Import And Parsing 2 · holobiomicslab

   Use when you have raw mass spectrometry data in one or more supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, or JSON) and need to convert it into a standardized in-memory representation that can be processed, validated, and compared using matchms.
   0 installs
10. ▌
    Spectral Feature Standardization 2 · holobiomicslab

    Use when after peak-picking stage completes on centroided mzML or netCDF raw LC-MS data via any of the three wrapped algorithms (Centwave, FeatureFinderMetabo, ADAP), when you need to pass the detected features to downstream SLAW stages (alignment, isotope/adduct grouping, gap-filling, MS2.
    0 installs
11. ▌
    Spectral Fragment Ion Annotation 2 · holobiomicslab

    Use when you have an MS/MS spectrum (m/z and intensity arrays) and a known or hypothesized peptide sequence (optionally with post-translational modifications in ProForma 2.
    0 installs
12. ▌
    Spectral Prediction Model Fusion 3 · holobiomicslab

    Use when you have pre-trained MLP and GNN spectral prediction models evaluated on the same ESI/LC-MS test dataset, and you seek to improve average rank performance beyond either baseline model alone.
    0 installs
13. ▌
    Spectral Roi Boundary Definition 3 · holobiomicslab

    Use when when you have identified a spectral window of interest in a 1H NMR spectrum from a complex biological sample (serum, urine, CSF, tissue, saliva, or sweat) and need to systematically retrieve all metabolites from HMDB whose reference proton NMR chemical shifts fall within that window.
    0 installs
14. ▌
    Spectrum Annotation Augmentation 2 · holobiomicslab

    Use when you have a TCN-predicted training set of MS/MS spectra with formula annotations and need to prepare it for Siamese rescore model training.
    0 installs
15. ▌
    Structured Data Element Checking 2 · 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.
    0 installs
16. ▌
    Structured Inventory Compilation 2 · holobiomicslab

    Use when when you need to understand the modular composition of a multi-component research software project, particularly before onboarding, refactoring, or deploying it.
    0 installs
17. ▌
    System Environment Configuration 2 · holobiomicslab

    Use when you need to execute a complex computational chemistry workflow (QCxMS2) that depends on multiple external semiempirical and ab initio quantum chemistry packages.
    0 installs
18. ▌
    Tool Initialization Verification 2 · holobiomicslab

    Use when after completing Docker installation and container build steps for CloMet, before attempting substantive data analysis or pipeline execution.
    0 installs
19. ▌
    Transformation Method Comparison 2 · holobiomicslab

    Use when when you have paired microbiome (16S rRNA or functional) and metabolome (LC-MS/MS or similar) data and must decide between compositional transformations (CLR, RA, or others) before training a predictive model.
    0 installs
20. ▌
    Usi Spectrum Identifier Encoding 2 · holobiomicslab

    Use when you have a Universal Spectrum Identifier (USI) string referencing a spectrum in a supported metabolomics repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, MassIVE, or MS2LDA) and need to create an embeddable, scannable reference for publication or data integration that.
    0 installs
21. ▌
    Wasserstein Distance Computation 2 · holobiomicslab

    Use when when you have both an observed NMR mixture spectrum and a candidate reconstructed spectrum (each represented as intensity distributions across chemical shift bins), and you need a scalar similarity metric to evaluate how closely the reconstruction matches the observed data.
    0 installs
22. ▌
    Xcms Output Replacement Workflow 2 · holobiomicslab

    Use when xCMS has produced aligned LC-MS features but alignment quality is suspected to be poor—especially when analyzing hundreds of samples, data acquired over extended periods (>1 week), or when individual m/z bins show inconsistent RT shifts.
    0 installs
23. ▌
    Molecular Structure Encoding 2 · holobiomicslab

    Use when you have molecular structures (SMILES strings or molecular graphs) that need to be input to a transformer model for property prediction (e.g., Collision Cross Section), and the model requires tokenized or embedded representations rather than raw chemical notation.
    0 installs
24. ▌
    Backend Performance Comparison 2 · holobiomicslab

    Use when you have execution-time metrics (from a benchmark table or profiling logs) across multiple visualization backends for the same set of plots (e.
    0 installs
25. ▌
    Calibration Quality Assessment 2 · holobiomicslab

    Use when after applying polynomial m/z domain recalibration using a reference peak list (e.g., SRFA.ref) to a Bruker FT-ICR dataset. Use this skill to verify that calibration has converged and that mass error statistics support reliable downstream annotation.
    0 installs
26. ▌
    Column Header Keyword Matching 2 · holobiomicslab

    Use when importing a new delimited data file (CSV, semicolon-separated, or other formats) into Punc'data that contains high-resolution mass spectrometry results.
    0 installs
27. ▌
    Data Ingestion Pipeline Design 2 · holobiomicslab

    Use when when building a platform that must accept raw MS data files (e.g., .raw, .mzML, .mzXML) from instrument runs or external sources as the first stage of an automated omics workflow.
    0 installs
28. ▌
    Feature Alignment Metabolomics 2 · holobiomicslab

    Use when you have detected multiple ion peaks from replicate injections of the same sample in untargeted metabolomics and need to consolidate them into a single feature table.
    0 installs
29. ▌
    Hash Function Parameterization 2 · holobiomicslab

    Use when when you have normalized or vectorized mass spectrometry spectral data (m/z and intensity pairs converted to feature vectors) and need to construct an LSH index for fast nearest-neighbor retrieval of similar spectra.
    0 installs
30. ▌
    Lexer Tokenizer Implementation 2 · holobiomicslab

    Use when when you need to parse a domain-specific query language (like MassQL) into an abstract syntax tree (AST), and the query strings must be decomposed into discrete lexical units before syntactic analysis.
    0 installs
31. ▌
    Mass Spectrum Query Processing 2 · holobiomicslab

    Use when you have an unknown mass spectrum (as m/z and intensity arrays) and need to identify candidate compounds by matching against a mass spectral library.
    0 installs
32. ▌
    Metabolomic Feature Imputation 2 · holobiomicslab

    Use when when a preprocessed metabolomic feature table (e.g., MS-Dial output) retains features and samples that passed filtering for missingness thresholds and m/z validity, but still contain scattered missing values (NA). This skill is appropriate after sample-level filtering (e.
    0 installs
33. ▌
    S4 Class Extension Development 2 · holobiomicslab

    Use when you need to create a new backend for the Spectra package that provides MS data from a new source (file format, database, or computational resource) not covered by existing backends (MsBackendMzR, MsBackendMemory, MsBackendSql, etc.).
    0 installs
34. ▌
    Spectral Peak Fitting Gaussian 2 · holobiomicslab

    Use when you have 1D MS signal data (extracted ion chromatograms, arrival time distributions, or intensity profiles) and need to resolve overlapping or closely-spaced peaks with accurate position, height, and width estimates.
    0 installs
35. ▌
    Spectrum Feature Vectorization 3 · holobiomicslab

    Use when you have raw mass spectrometry spectra (peak lists or intensity arrays) that must be fed into a pre-trained deep learning model for substance classification (e.g., PS²MS for NPS detection).
    0 installs
36. ▌
    Biochemical Annotation Mapping 2 · holobiomicslab

    Use when you have loaded MSI data into napari, defined one or more ROIs of biological interest (e.g., tumor margin, specific tissue layer), extracted mean or summed intensity spectra from those regions, and need to identify the putative biochemical compounds corresponding to detected m/z peaks.
    0 installs
37. ▌
    Image Visualization Formatting 2 · holobiomicslab

    Use when you have loaded a normalized or raw pixel array (NumPy format) with associated metadata from MSI line-scan data, and need to generate publication-quality ion images with controlled intensity scaling, smoothing, and optional ratio or fractional abundance comparisons across multiple m/z.
    0 installs
38. ▌
    Model Checkpoint Serialization 2 · holobiomicslab

    Use when after successfully training a spectrum prediction model (FFN encoder, GNN encoder, intensity predictor, or fragment generator) to completion or at intermediate milestones, and before using that model for inference on test sets, structural elucidation queries, or transfer learning.
    0 installs
39. ▌
    Adduct Specific Model Fine Tuning 2 · holobiomicslab

    Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
    0 installs
40. ▌
    C Sharp Wrapper Invocation From R 2 · holobiomicslab

    Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings are unavailable or impractical. Use this when the target assembly requires Windows/.
    0 installs
41. ▌
    Composite Mass Track Construction 3 · holobiomicslab

    Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you need to detect peaks across the entire cohort.
    0 installs
42. ▌
    Compound Class Annotation Parsing 2 · holobiomicslab

    Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
    0 installs
43. ▌
    De Novo Precursor Mass Annotation 2 · holobiomicslab

    Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting without access to spectral libraries.
    0 installs
44. ▌
    Derivatizing Matrix Configuration 3 · holobiomicslab

    Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for metabolite annotation, and the matrix is not yet configured in your Met-ID installation.
    0 installs
45. ▌
    Feature Grouping By Molecular Ion 2 · holobiomicslab

    Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
    0 installs
46. ▌
    Library Analogue Search Branching 2 · holobiomicslab

    Use when when you need to reconstruct or validate the control-flow architecture of a spectral search system that must handle both exact-match library lookups and analogue discovery in a single pass, particularly when the system uses pre-computed embeddings for efficiency and machine learning for.
    2 installs
47. ▌
    Mb Vip Feature Importance Ranking 2 · holobiomicslab

    Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify which features drive model performance and warrant further statistical validation or biological interpretation.
    0 installs
48. ▌
    Metabolite Ratio Batch Correction 2 · holobiomicslab

    Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with measured ion areas for compounds and assigned internal standards.
    0 installs
49. ▌
    Metabolomics Data Format Handling 3 · holobiomicslab

    Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into MetaboAnalystR 4.0 for unified LC-MS1 feature detection and MS/MS spectra processing.
    0 installs
50. ▌
    Metabolomics Data Quality Metrics 2 · holobiomicslab

    Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high technical variability or signal degradation before proceeding to statistical analysis or interpretation of.
    0 installs
51. ▌
    Metadata Structure Transformation 2 · holobiomicslab

    Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be deposited into a structured online repository like Metabolomics Workbench, but the raw format does not conform to the.
    0 installs
52. ▌
    Ms Instrument Type Classification 3 · holobiomicslab

    Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS Imaging) is covered by at least one processing module.
    0 installs
53. ▌
    Neutral Loss Composition Matching 2 · holobiomicslab

    Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries from a MotifDB reference database.
    0 installs
54. ▌
    R6 Reference Semantics Comparison 2 · holobiomicslab

    Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it.
    0 installs
55. ▌
    Sample Relationship Visualization 2 · holobiomicslab

    Use when after generating aligned MS2 fingerprints (sample-by-fingerprint matrices) from metabolomics data when you need to visually inspect sample clustering, identify sample similarities, or detect batch effects and RT shifts across different LC methods or mass spectrometer technologies.
    0 installs
56. ▌
    Spectral Clustering Density Based 2 · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically when clustering bottom-up proteomics data with the goal of grouping spectra from the same peptide sequence or when you.
    0 installs
57. ▌
    Spectral Library Entry Generation 2 · holobiomicslab

    Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for a known metabolite.
    0 installs
58. ▌
    Spectrum Peak To Fragment Mapping 2 · 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.
    0 installs
59. ▌
    Assembly Version String Retrieval 2 · holobiomicslab

    Use when when you need to validate that a .NET assembly (such as ThermoFisher.CommonCore.RawFileReader) is correctly installed and accessible before attempting data reading operations.
    0 installs
60. ▌
    Atom Feature Extraction Chemistry 2 · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical database (e.
    0 installs
61. ▌
    Beam Search Decoding Optimization 2 · holobiomicslab

    Use when using Casanovo for de novo peptide sequencing on high-stakes datasets (immunopeptidomics, paleoproteomics, or monoclonal antibody discovery) where missing the correct sequence in the top-1 prediction is costly.
    0 installs
62. ▌
    C Sharp Wrapper Method Validation 2 · holobiomicslab

    Use when when integrating an R package that wraps a compiled .NET assembly (such as rawrr), you need to verify that the internal dispatch mechanism between the R layer and the C# layer is operational before attempting to read actual raw data files.
    0 installs
63. ▌
    Calibration Curve Fitting Ms Data 2 · holobiomicslab

    Use when you have raw mass spectrometry intensity data from targeted analytes and a set of calibration standard measurements with known concentrations.
    0 installs
64. ▌
    Ccs Calibration Tunemix Execution 3 · holobiomicslab

    Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5) with known CCS values spanning a wide m/z range (e.g., 118.086–1522 m/z) and need to establish a CCS calibration model to convert experimental drift times or collision cross sections for downstream analysis.
    0 installs
65. ▌
    Cheminformatics Database Querying 2 · holobiomicslab

    Use when you have a list of identified or suspected chemical compound names (e.g., from GC-MS Match.
    0 installs
66. ▌
    Chemodiversity Metric Calculation 2 · holobiomicslab

    Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment groups (e.g., inoculated vs. control samples).
    0 installs
67. ▌
    Chromatography Data Preprocessing 3 · holobiomicslab

    Use when you have raw spectra files from a liquid chromatography experiment (in-house or external database) and need to adapt a pretrained GNN-RT model to predict retention times for your molecules. Preprocessing is the mandatory first step before any model training or transfer learning can proceed.
    0 installs
68. ▌
    Command Line Interface Invocation 2 · holobiomicslab

    Use when when you have installed a Python package and need to verify that its command-line entry point is accessible, or when you need to discover available commands and options for NMR data processing workflows without consulting external documentation.
    2 installs
69. ▌
    Conditional Dependency Resolution 2 · holobiomicslab

    Use when a Python library exposes functionality that depends on external packages (like sqlalchemy, pandas, or lxml) that are not required for core operations.
    0 installs
70. ▌
    Cross Domain Masst Output Parsing 2 · holobiomicslab

    Use when you have executed batch searches against one or more domain-specific MASST tools and received multiple output files (_microbe.html, _plant.html, _tissue.html, _microbiome.html, _food.html, _matches.tsv, _library.tsv, _datasets.tsv, _count_*.
    0 installs
71. ▌
    Cross Tool Performance Comparison 2 · holobiomicslab

    Use when when you have raw tandem MS metabolomics data in vendor formats (.
    0 installs
72. ▌
    Cross Workflow Format Translation 2 · holobiomicslab

    Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) or GNPS2 (https://gnps2.org) and need to parse spectra (spectra.mgf), molecular family networks (molecular_families.tsv), spectral library annotations (annotations.
    0 installs
73. ▌
    Dataframe Lazy Loading Comparison 2 · holobiomicslab

    Use when when designing or optimizing an MsBackend implementation (or similar columnar data structure) you must decide whether to pre-allocate all known columns in the backing DataFrame at initialization or defer column creation until first access.
    0 installs
74. ▌
    Dotnet Assembly Path Verification 2 · holobiomicslab

    Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass spectrometry data extraction operations.
    0 installs
75. ▌
    Empirical Compound Pre Annotation 3 · holobiomicslab

    Use when after feature detection from mzML files (e.g., via Asari) when you have a feature table with m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
    0 installs
76. ▌
    Environment Dependency Management 3 · holobiomicslab

    Use when when deploying Galaxy-M or similar multi-component metabolomics platforms that depend on heterogeneous runtime environments (Python, R, MATLAB, WINE) across multiple operating systems (Ubuntu 14.
    0 installs
77. ▌
    File Format Compliance Validation 2 · holobiomicslab

    Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification before integration into a production workflow, data repository, or downstream analysis pipeline.
    0 installs
78. ▌
    Fragmentation Spectrum Extraction 2 · holobiomicslab

    Use when you have raw or peak-detected mass spectrometry data (mzXML, mzML, or netCDF format) from untargeted metabolomics or exposomics studies and need to separate composite fragmentation spectra into individual constituent spectra for annotation.
    0 installs
79. ▌
    Ion Species Annotation Assignment 2 · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across time-resolved MS scans, but before final candidate validation. Apply this skill when you need to distinguish between competing ion-species hypotheses (e.
    0 installs
80. ▌
    Isotope Pattern Spectral Matching 2 · holobiomicslab

    Use when when you have LC/MS feature data with observed m/z and intensity values across multiple peaks (monoisotopic and isotopologues) and need to narrow candidate annotations from a metabolite database.
    0 installs
81. ▌
    Isotopologue Abundance Correction 2 · holobiomicslab

    Use when you have LC-MS data from isotope labeling experiments where FAM measurements must be transformed to MDV values. Specifically, apply this when: (1) you have measured fractional abundances of isotopologues (FAM) in XLSX format from a high-resolution instrument (e.g., Orbitrap);
    0 installs
82. ▌
    Lcms Metabolomics Data Processing 3 · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .
    0 installs
83. ▌
    Lcms Peak Detection And Alignment 2 · holobiomicslab

    Use when you have one or more raw mzXML or mzML LCMS data files (from DDA, DIA, or fullscan acquisition) and need to extract quantitative metabolite features for multi-sample comparative analysis.
    0 installs
84. ▌
    Mass Spectrometry Data Extraction 3 · holobiomicslab

    Use when you have native Thermo Fisher RAW mass spectrometry files and need to extract scan-level metadata (retention time, total ion current, scan mode), MS1/MS2 peak lists with m/z and intensity arrays, or instrument/LC/MS method details for downstream computational analysis, QC, or cross-sample.
    0 installs
85. ▌
    Mass Spectrometry Data Validation 2 · holobiomicslab

    Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and post-filter counts of spectra and fragments at each major step (TIC cutoff, intra-spectrum grouping, frequency-based labeling).
    0 installs
86. ▌
    Mass Spectrometry Feature Mapping 2 · holobiomicslab

    Use when you have (1) aligned LC-MS/MS feature quantification matrix (features × fractions with m/z and RT for each feature), (2) bioassay activity measurements across the same fractions, and (3) need to assign bioactivity values to individual molecular network nodes to identify bioactive compounds.
    0 installs
87. ▌
    Mass Spectrum Prediction Modeling 2 · holobiomicslab

    Use when you have a collection of molecular structures (SMILES or chemical graphs) with paired experimental tandem mass spectra and want to build or benchmark a predictive model.
    0 installs
88. ▌
    Memory Profiling And Benchmarking 2 · holobiomicslab

    Use when when designing or optimizing backends that handle large MS datasets (mzML, mzXML, CDF files via MsBackendMzR), to verify that claimed memory advantages of on-disk or chunked approaches actually materialize in practice.
    0 installs
89. ▌
    Metabolite Feature Column Mapping 2 · holobiomicslab

    Use when you have peak-picked LC-MS metabolomics data in a tabular format (R data frame) with columns for mass-to-charge ratio, retention time, feature identifiers, adduct annotations, and sample measurements, but the column names do not follow a standard naming convention.
    0 installs
90. ▌
    Metabolite Mass Database Matching 2 · holobiomicslab

    Use when after features have been grouped into empirical compounds (empCpds) with inferred molecular formulas and adduct assignments by khipu, and you need to assign putative metabolite identities at the formula level.
    0 installs
91. ▌
    Metabolite Set Annotation Mapping 2 · holobiomicslab

    Use when you have a metabolomics peak intensity matrix with feature IDs (m/z, retention time, or arbitrary peak identifiers) and need to assign these peaks to standardized metabolite databases or spectral groupings (KEGG compounds, ChEBI IDs, GNPS Molecular Families, or MS2LDA Mass2Motifs) before.
    0 installs
92. ▌
    Metabolomics Data Standardization 2 · holobiomicslab

    Use when you have raw 1D NMR spectral data (urine, worm, or other biological samples) that needs to be converted into peak tables for metabolite identification and quantification.
    0 installs
93. ▌
    Molecular Network Node Annotation 2 · holobiomicslab

    Use when you have a GNPS-generated molecular network (classical or feature-based workflow) and corresponding MS2LDA LDA experiment results (Mass2Motif assignments and/or chemical class predictions), and you need to propagate those annotations to individual network nodes to support visual and.
    0 installs
94. ▌
    Shiny App Initialization 2 · holobiomicslab

    Use when you have developed an R-based workflow (e.g., data processing, peak detection, quality review) that is complex enough to warrant interactive parameter tuning and visual feedback, and you need to distribute it to collaborators or end-users who prefer a graphical interface over scripting.
    0 installs
95. ▌
    Similarity Matrix Export 2 · holobiomicslab

    Use when after computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular fingerprint-based, or metadata-related assessments), use this skill to persist the resulting similarity matrix to a named output file.
    0 installs
96. ▌
    Similarity Score Sorting 2 · holobiomicslab

    Use when after a deep-learning model has predicted structural similarity scores between an unknown metabolite's MS/MS spectrum and all known metabolites in a reference database.
    0 installs
97. ▌
    Smiles String Formatting 2 · holobiomicslab

    Use when you have a set of chemical structures (as SMILES strings or convertible to SMILES) and need to submit them programmatically to the NP Classifier /classify endpoint for batch or automated classification.
    0 installs
98. ▌
    Spectral Data Validation 2 · holobiomicslab

    Use when when raw spectra have been imported from common MS/MS file formats but contain inconsistent, missing, or malformed metadata fields that could compromise spectral similarity comparisons or cause downstream pipeline failures.
    0 installs
99. ▌
    Spectral Image Rendering 2 · holobiomicslab

    Use when when you have parsed and validated spectral data (jcamp, RAW, or mzML format) from NMR/IR/MS instruments and need to create visual representations with peak annotations for inspection, annotation, or publication.
    0 installs
100. ▌
     Spectral Peak Validation 2 · holobiomicslab

     Use when before feeding a peak list into the NMRformer model or other transformer-based spectral assignment frameworks.
     0 installs