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HolobiomicsLab

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1. ▌
   JSON Document Enrichment 2 · holobiomicslab

   Use when when your project JSON document contains public identifiers (genome IDs, biosample accessions, etc.) that lack human-readable or linked metadata, and you need to populate those fields programmatically before storage or publication to enable full-text search, validation, or cross-linking.
   0 installs
2. ▌
   Lc Ms Data Preprocessing 2 · holobiomicslab

   Use when you have raw mzML files and corresponding feature tables (CSV format, mzmine-formatted) from untargeted LCMS experiments, and you need to convert them into uniformly-shaped peak matrices (2 × 120 per peak: margin + signal regions) as input for neural network classification of MS1 peak.
   2 installs
3. ▌
   Matlab Package Execution 2 · holobiomicslab

   Use when you have two separate LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to establish feature-to-feature correspondence between them.
   0 installs
4. ▌
   Peak Matrix Construction 2 · holobiomicslab

   Use when when you have raw mzML files and a corresponding feature table (CSV format, e.g., from mzmine) and need to generate peak matrices with fixed dimensions (e.g., 2 × 120) that encode margin vs. peak signal regions for training a neural network classifier to filter false positive LCMS peaks.
   4 installs
5. ▌
   Precursor Mass Filtering 2 · holobiomicslab

   Use when after retrieving top-scoring library candidates from a full MS2Deepscore comparison, but before or during final re-ranking.
   0 installs
6. ▌
   Build Badge Verification 2 · holobiomicslab

   Use when you need to validate that a repository's automated build and publish pipeline is functioning correctly on a release or target branch, particularly when assessing the reliability of release artifacts or the health of a CI/CD workflow.
   0 installs
7. ▌
   Code Repository Analysis 2 · holobiomicslab

   Use when you have a published research article describing a new FT-ICR MS analysis tool and need to verify which analytical and visualization features are actually implemented (not just claimed).
   0 installs
8. ▌
   Coeluting Ion Separation 2 · holobiomicslab

   Use when raw GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks—i.e., when multiple analytes elute at similar retention times and produce composite mass spectra with ambiguous m/z signals.
   0 installs
9. ▌
   Ensemble Model Inference 2 · holobiomicslab

   Use when you have a set of compounds (as SMILES strings or molecular structures) that need retention order predictions in a reversed-phase liquid chromatography (RPLC) system at eluent pH ~2.7, and you want to quantify prediction uncertainty rather than relying on a single model's output.
   0 installs
10. ▌
    File Format Writing Mzml 2 · holobiomicslab

    Use when after completing an Environment simulation or replay with scan-level MS2 acquisition control, and evaluation data has been collected in memory.
    0 installs
11. ▌
    HTTP API Endpoint Design 2 · holobiomicslab

    Use when when you need to expose a multi-step spectral processing workflow (parse → extract → render → annotate → compress) as a web service endpoint that accepts jcamp/RAW/mzML spectral files and must return coordinated output artifacts (modified JCAMP files, peak tables, and PNG images) in a.
    0 installs
12. ▌
    Interoperability Testing 2 · holobiomicslab

    Use when when a new file format specification exists as a living document (e.
    0 installs
13. ▌
    Ionization Mode Handling 2 · holobiomicslab

    Use when your MZmine MGF and CSV input files contain mixed or ambiguous ionization modes, or when your experimental design specifies separate negative (NEG) and positive (POS) ionization mode acquisitions that must be processed independently before merging.
    0 installs
14. ▌
    Isf Feature Table Export 2 · holobiomicslab

    Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have an ISFrag analysis results object containing identified ISF features and need to save them as a portable, tabular file for external analysis, reporting, or integration with other metabolomics.
    0 installs
15. ▌
    JSON Response Validation 2 · holobiomicslab

    Use when after sending HTTP requests to API endpoints (such as /classify or /model/metadata on an NP-Classifier server) to verify that the response is parseable JSON and contains the expected output fields and metadata before attempting to extract or process the data programmatically.
    0 installs
16. ▌
    Lipid Candidate Matching 2 · holobiomicslab

    Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
    0 installs
17. ▌
    Mass To Charge Filtering 2 · holobiomicslab

    Use when after generating theoretical B/Y ion spectra or after importing experimental MS/MS scans when your analysis goal requires restricting the ion population to a specific m/z window (e.g., m/z < 2000).
    0 installs
18. ▌
    Mass Tolerance Filtering 2 · holobiomicslab

    Use when when you have observed fragment peak m/z values from tandem mass spectra and need to assign chemical subformulae to them.
    0 installs
19. ▌
    Metabolic Model Curation 2 · holobiomicslab

    Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
    0 installs
20. ▌
    Ms Ms Ion Interpretation 2 · holobiomicslab

    Use when when you have two MS/MS spectra (each with a precursor m/z and a list of fragment ion m/z values) and need to identify which fragment ions correspond between them, especially when structural differences make simple monotonic alignment unreliable.
    0 installs
21. ▌
    Mwtab To JSON Conversion 2 · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and data blocks that need to be converted to JSON for integration with REST APIs, web applications, or downstream tools that expect JSON input.
    0 installs
22. ▌
    Mzml File Format Parsing 2 · holobiomicslab

    Use when when you have mass spectrometry raw data in mzML format and need to execute MassQL queries, perform batch analysis across a directory of spectra files, or programmatically access MS1 and MS2 scan data with retention time, m/z, and intensity metadata.
    0 installs
23. ▌
    Mzml File Format Writing 2 · holobiomicslab

    Use when you have peak properties (mass, intensity, retention time) for biomolecules, selected noise and fragmentation models, and instrument parameters (e.
    0 installs
24. ▌
    Mzml XML Deserialization 2 · holobiomicslab

    Use when your input is an mzML file (XML-based mass spectrometry data format) and you need to expose spectral metadata, scan information, and ion data in a structured, programmatic form for alignment, clustering, drift correction, or quantification within the BMXP pipeline.
    0 installs
25. ▌
    Numpy Array Manipulation 2 · holobiomicslab

    Use when when you have raw MS/MS peak lists that need to be loaded, analyzed for intensity frequency patterns, or filtered based on noise characteristics.
    0 installs
26. ▌
    Peak Pairwise Comparison 2 · holobiomicslab

    Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover biochemical transformations without prior knowledge of reaction networks.
    0 installs
27. ▌
    Peak Property Validation 2 · holobiomicslab

    Use when after converting a CSV file of molecule definitions into a peak properties dictionary using csv_to_peak_properties, or after loading a serialized peak properties dictionary from pickle/JSON storage, before passing it to SMITER simulation functions (e.g., smiter.synthetic_mzml.write_mzml).
    0 installs
28. ▌
    Peak Table Deconvolution 2 · holobiomicslab

    Use when your peak table contains ions with similar retention time and mass-to-charge ratios that likely represent isotopic patterns incorrectly split during preprocessing or detector artifacts.
    0 installs
29. ▌
    Python Environment Setup 3 · holobiomicslab

    Use when when you have cloned a scientific Python repository (e.g., ROIAL-NMR) and need to verify that the documented dependencies can be installed and the main entrypoint is invokable without errors. Use this skill before attempting to run the application's core analysis workflows.
    0 installs
30. ▌
    Qiime2 Artifact Handling 2 · holobiomicslab

    Use when you have raw mass-spectrometry files (MGF, BIOM, mzXML, mzML) or feature abundance tables from external tools (MZmine2, peak detection software) and need to convert them into QIIME 2's typed artifact format before running downstream plugins like q2-qemistree, diversity analyses, or.
    0 installs
31. ▌
    R Data Frame Aggregation 2 · holobiomicslab

    Use when when you have extracted multiple spectral attributes (e.g., base-peak m/z, intensity, retention time, scan index) from individual MS scans via accessor functions and need to organize them into a single rectangular data frame for batch analysis, filtering, or export to external tools.
    0 installs
32. ▌
    Retention Time Alignment 2 · holobiomicslab

    Use when after peak detection in untargeted metabolomics when you have identified ion signals across mass-to-charge and retention-time dimensions from replicate injections of the same samples, and you need to group peaks from different runs that represent the same metabolite before building a.
    0 installs
33. ▌
    Retention Time Filtering 3 · holobiomicslab

    Use when working with GCIMS datasets where retention time spans a wide range (e.g., 0–1500 s) but your analytes of interest are confined to a narrower window (e.g., 0–1100 s).
    1 install
34. ▌
    Pytest Test Suite Execution 2 · holobiomicslab

    Use when after installing a package in development mode (e.g., via `pip install -e .[dev]`) to verify the package functions as intended, or before submitting pull requests to confirm no regressions were introduced by code changes.
    0 installs
35. ▌
    Python Source Code Analysis 2 · holobiomicslab

    Use when you have a Python webservice codebase (e.g., a Flask, Django, or FastAPI application) and need to document its HTTP API surface (endpoints, methods, parameters, schemas, authentication) for integration, testing, or specification generation.
    0 installs
36. ▌
    R Data Structure Conversion 3 · holobiomicslab

    Use when you have preprocessed MSI data in Cardinal format (post-peakBin) and need to apply mass2adduct's adduct-detection workflow, OR you have exported MSI intensity data as CSV from third-party software (SCiLS, MSiReader) and must convert it into a standardized R object for downstream analysis.
    0 installs
37. ▌
    R Data Structure Processing 3 · holobiomicslab

    Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100 s) and drift time (5–16 ms) ranges, or when you need to apply smoothing, decimation, or baseline correction to raw GCIMS.
    0 installs
38. ▌
    Reactant Ion Peak Exclusion 3 · holobiomicslab

    Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion source) would otherwise be misidentified as an analyte peak, causing false positives in the peak list.
    0 installs
39. ▌
    Repository Backend Dispatch 2 · 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.
    0 installs
40. ▌
    Repository History Analysis 2 · holobiomicslab

    Use when when you need to understand how a complex feature or architectural pattern was implemented in a codebase, particularly when the current README or documentation does not fully explain the control flow, decision criteria, or parameter passing between subsystems.
    0 installs
41. ▌
    Retention Time Mz Alignment 3 · 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.
    0 installs
42. ▌
    Rust Build System Execution 2 · holobiomicslab

    Use when you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library. Use this skill when the source includes a Cargo.
    0 installs
43. ▌
    Smiles Structure Annotation 3 · holobiomicslab

    Use when you have LC–QTOF mass spectra from real environmental or biological samples (e.g., wastewater, complex mixtures) and need to assign molecular structures to spectra where traditional library matching fails or reference compounds are unavailable.
    0 installs
44. ▌
    Software Plugin Development 2 · holobiomicslab

    Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel reagent, derivatizing matrix, or analytical method (e.
    0 installs
45. ▌
    Sparsity Metric Computation 2 · holobiomicslab

    Use when when you have loaded a dataset of molecular fingerprint vectors (such as biosynfoni fingerprints from a Zenodo deposit) and need to quantify how sparse the bit-representations are—that is, what fraction of bit positions are zero across the fingerprint collection.
    0 installs
46. ▌
    Spectral Data Serialization 2 · holobiomicslab

    Use when after completing MS/MS spectra detection and peak recognition on tandem MS breath samples.
    0 installs
47. ▌
    Spectral Data Visualization 2 · 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.
    0 installs
48. ▌
    Spectral Feature Annotation 2 · holobiomicslab

    Use when after auto-deconvolution has resolved co-eluting GC-MS peaks into individual component spectra.
    2 installs
49. ▌
    Spectral Peak Deconvolution 2 · holobiomicslab

    Use when you have a raw 1D NMR spectrum (FID or processed format) from urine, worm, or other biological samples and need to extract peak positions, intensities, and linewidths as a tabular peak list.
    0 installs
50. ▌
    Spectral Peak Visualization 2 · 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.
    0 installs
51. ▌
    Tabular Data Io And Masking 2 · 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.
    1 install
52. ▌
    Tic Based Intensity Scaling 2 · holobiomicslab

    Use when after feature detection when you have a metabolomics feature table with intensity values across multiple samples and observe evidence of inter-sample intensity bias (e.g., batch effects, variable ionization efficiency, or instrument drift).
    0 installs
53. ▌
    Tima Entry Point Validation 2 · holobiomicslab

    Use when when you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.
    0 installs
54. ▌
    Transformer Model Inference 2 · holobiomicslab

    Use when you have electron ionization mass spectrum data (m/z and intensity pairs) and a pre-trained transformer model checkpoint, and you need to predict molecular weight directly from the spectrum without manual feature engineering or rule-based methods.
    0 installs
55. ▌
    Twim Ms Calibration Mapping 2 · holobiomicslab

    Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.
    0 installs
56. ▌
    Two Dimensional Tic Folding 2 · holobiomicslab

    Use when immediately after acquiring raw GCxGC-MS data in NetCDF format (.cdf files) and before any signal enhancement (smoothing, baseline correction) or alignment steps.
    0 installs
57. ▌
    Uhplc Hrms Ms Data Matching 2 · holobiomicslab

    Use when you have peak-picked UHPLC-HRMS/MS data (from Q-Exactive orbitrap, Agilent, Bruker, or SCIEX Q-TOF instruments) with both MS1 and MS/MS fragment spectra, and you need to assign lipid identities to detected features using in-silico fragmentation patterns.
    0 installs
58. ▌
    Vendor Data Standardization 3 · holobiomicslab

    Use when you have raw MS data files directly from a vendor instrument (Thermo .raw, Agilent .d, Waters .ms, etc.) and need to process them through AriumMS or any other metabolomics pipeline that accepts only .mzXML or .mzML formats.
    0 installs
59. ▌
    YAML Configuration Handling 2 · holobiomicslab

    Use when when initializing a MolNotator project with user-defined parameters for ionization modes, adduct tables, database selections, output directories, and tool-specific thresholds.
    0 installs
60. ▌
    Ccs Bias Quantification 3 · holobiomicslab

    Use when you have IM-MS lipidomics data acquired on samples spiked with fully labeled U13C lipid standards (e.g., U13C yeast extract), and you need to assess whether systematic CCS deviation exists between your instrument's measured values and the DT CCS N2 reference library for U13C labeled lipids.
    0 installs
61. ▌
    Data Structure Validation 2 · holobiomicslab

    Use when after converting or filtering objects (e.g., transformation products to suspect lists, feature groups through componentization) and before passing them to downstream functions like screenSuspects or generateComponents.
    0 installs
62. ▌
    Indexed Gzip File Parsing 2 · holobiomicslab

    Use when you have compressed mzML.gz files and need to retrieve specific spectra by numeric identifier without decompressing the entire file.
    0 installs
63. ▌
    Isotope Pattern Detection 2 · holobiomicslab

    Use when you have MS1-format mass spectrometry files and need to determine the isotope count for peptide features without manual inspection or expert parameter tuning.
    0 installs
64. ▌
    Kendrick Mass Calculation 2 · holobiomicslab

    Use when you have uploaded m/z values from a high-resolution mass spectrometry analysis of a complex sample (e.g., crude oil, natural organic matter) and need to visualize homolog series trends.
    0 installs
65. ▌
    Mrm Data Format Ingestion 2 · holobiomicslab

    Use when you have raw MRM lipidomics export files in vendor-specific formats (e.g., TSV or CSV from a mass spectrometry instrument) and need to convert them into a standardized tabular format before performing lipid identification, statistical analysis, or visualization.
    0 installs
66. ▌
    Proforma Notation Parsing 2 · holobiomicslab

    Use when when peptide identifications from a search engine (MaxQuant, MSGFPlus, Sage, etc.) contain custom or engine-specific modification notation that must be converted to a standardized format before rescoring, or when different search engines use incompatible modification label schemes that.
    0 installs
67. ▌
    Raw Spectral Data Reading 2 · holobiomicslab

    Use when you have Thermo Orbitrap .raw files and need to extract specific spectral features (base-peak m/z, intensity values, chromatographic traces, scan-level metadata) for downstream statistical analysis or visualization in R. Use this skill when you want to avoid lossy format conversion (e.
    0 installs
68. ▌
    Rendering Speed Profiling 2 · holobiomicslab

    Use when when you have implemented the same visualization (e.g., chromatogram, spectrum, peakmap, mobilogram) across multiple plotting backends in pyOpenMS-viz and need to determine which backend minimizes rendering latency.
    0 installs
69. ▌
    Retention Time Clustering 2 · holobiomicslab

    Use when you have an XCMS CentWave feature extraction output table containing multiple features with near-identical m/z values and retention times (e.
    0 installs
70. ▌
    Software Tool Enumeration 2 · holobiomicslab

    Use when a software package claims to bundle or install a specific number of tools (documented or approximate) but the tool names, versions, and sources are not enumerated in the primary README or documentation.
    0 installs
71. ▌
    Spectral Library Indexing 2 · holobiomicslab

    Use when you have large spectral libraries (thousands to millions of spectra) and need to search query spectra against them for peptide identification with tolerance for post-translational modifications.
    0 installs
72. ▌
    Spectral Signal Detection 2 · holobiomicslab

    Use when you have mzML mass spectrometry data and a list of predicted candidate metabolites (with known mass-to-charge ratios and retention times) for a drug of interest, and you need to determine which candidates actually appear in the observed spectra rather than treating all predictions as.
    0 installs
73. ▌
    Threshold Based Filtering 2 · holobiomicslab

    Use when after computing pairwise similarity scores between query molecular embeddings and a reference database, apply this skill when you need to distinguish high-confidence candidate matches from spurious matches.
    0 installs
74. ▌
    Training Dataset Assembly 2 · holobiomicslab

    Use when when you have a large list of SMILES strings but lack corresponding experimental mass spectra, and you need to generate 30,000+ training pairs to train a deep learning model for molecular structure prediction.
    0 installs
75. ▌
    Xcms Parameter Estimation 2 · holobiomicslab

    Use when you have raw untargeted metabolomics data (at least 3 samples in mzML, mzXML, or CDF format) from qTOF, orbitrap, or Fourier transform ion cyclotron resonance mass analyzers and need to obtain optimized XCMS processing parameters tailored to your specific instrument and dataset rather than.
    0 installs
76. ▌
    Anndata Object Annotation 2 · holobiomicslab

    Use when after loading or merging spatial metabolomics data into an AnnData object (via read_sm_csv_as_anndata, read_sm_imzml_as_anndata, or merge_sm_pos_neg), and before filtering or normalization steps.
    0 installs
77. ▌
    Overlapping Ion Detection 2 · holobiomicslab

    Use when when annotating matrix-related ions in MSI datasets where two or more ions share identical or near-identical m/z values (isobaric ions) or exhibit overlapping spatial distributions across imaging pixels.
    0 installs
78. ▌
    CI CD Pipeline Orchestration 2 · holobiomicslab

    Use when you need to automate testing and quality checks on code changes—specifically when pull requests or commits are made to a repository and you want to verify that builds succeed, test suites pass, and code quality metrics meet project standards before merging.
    0 installs
79. ▌
    Feature Annotation Filtering 2 · holobiomicslab

    Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among thousands of detected features.
    0 installs
80. ▌
    Filter Output Interpretation 2 · holobiomicslab

    Use when after applying a filter function (filter_mispicked_ions(), filter_group(), filter_cv(), filter_insource_ions()) to an mpactr object, use this skill to inspect and document which features were retained versus removed.
    0 installs
81. ▌
    Fragmentation Motif Learning 2 · holobiomicslab

    Use when you have preprocessed mass spectrometry fragmentation data (neutral losses and fragment masses extracted and noise-filtered) and want to discover hidden structural motifs across a spectral dataset in an unsupervised manner.
    0 installs
82. ▌
    Gc Ms Spectral Deconvolution 3 · holobiomicslab

    Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be resolved by simple peak picking.
    0 installs
83. ▌
    Installation Troubleshooting 2 · holobiomicslab

    Use when when setting up matchms for the first time in a new environment, after upgrading Python or conda, when switching between package managers (pip vs conda), or when distributing matchms to end users to confirm functionality across supported installation channels.
    0 installs
84. ▌
    Instrumental Drift Detection 2 · holobiomicslab

    Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex Multiquant software (v3.0.
    0 installs
85. ▌
    Library Integration Workflow 2 · holobiomicslab

    Use when you have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library, and you want to include them as matching candidates in your UHPLC-HRMS/MS fragment m/z matching workflow without modifying.
    0 installs
86. ▌
    Molecular Formula Validation 2 · holobiomicslab

    Use when when you have a feature list from HRMS with tentatively assigned molecular formulas (from in silico tools or databases) and need to assess formula plausibility before applying downstream PFAS-specific filters.
    0 installs
87. ▌
    Multi Omics Data Integration 2 · holobiomicslab

    Use when when you have matched transcriptomics (RNA-seq read counts), intracellular metabolomics (LC-MS abundance data), and extracellular flux measurements (YSI bioanalyzer or similar) from multiple biological samples or cell lines, and you need to determine whether differences in metabolic enzyme.
    0 installs
88. ▌
    Multiblock Pls Model Fitting 2 · holobiomicslab

    Use when you have split multi-assay LC-MS intensity data into training (90%) and test (10%) subsets with assay-specific column prefixes, and you need to fit a discriminant or regression model that respects the block structure (separate assays) while jointly predicting a phenotypic outcome (e.
    0 installs
89. ▌
    Pairwise Spectral Comparison 2 · holobiomicslab

    Use when you have a collection of preprocessed mass spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to quantify similarity relationships across all pairs—for instance, to identify redundant spectra in a library, cluster related compounds, or perform spectral library searches.
    0 installs
90. ▌
    Peak Filtering Noise Removal 2 · holobiomicslab

    Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library matching.
    0 installs
91. ▌
    Phylogenetic Tree Validation 2 · holobiomicslab

    Use when after generating a Chemical Feature Tree from q2-qemistree (or any tree artifact) and before using it for alpha-diversity or beta-diversity phylogenetic analyses.
    0 installs
92. ▌
    Polarity Mode Filtering Lcms 2 · holobiomicslab

    Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run acquired in a specific polarity mode.
    0 installs
93. ▌
    Session Object Serialization 2 · holobiomicslab

    Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data object containing t-SNE embeddings (based on ms2deepscore similarity scores) and associated spectral metadata.
    0 installs
94. ▌
    Siamese Architecture Scoring 2 · holobiomicslab

    Use when after a TCN-based formula prediction model has generated initial formula candidates from MS/MS spectra, apply this skill to rescore and refine those candidates when you need to improve ranking accuracy.
    0 installs
95. ▌
    Spectral Data Format Parsing 2 · holobiomicslab

    Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for downstream spectral analysis, fragmentation tree computation, or metabolite identification.
    0 installs
96. ▌
    Spectral Feature Engineering 2 · holobiomicslab

    Use when you have molecular structures (SMILES or graph representations) and need to predict or analyze infrared spectral properties using message passing neural networks.
    0 installs
97. ▌
    Spectral Workflow Validation 2 · holobiomicslab

    Use when after implementing or modifying a cross-language integration layer that wraps Python mass spectrometry functions (e.g., spectral matching, peak detection, normalization from matchms or spectrum_utils) as R-callable functions within Spectra workflows.
    0 installs
98. ▌
    Spectrum Metadata Extraction 2 · holobiomicslab

    Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including scan information, precursor m/z and charge, and ion selection parameters—into a queryable, vendor-agnostic tabular schema.
    0 installs
99. ▌
    Alignment Quality Assessment 2 · holobiomicslab

    Use when after retention time and m/z-based clustering have been applied to group features across samples in a multi-sample metabolomics study.
    0 installs
100. ▌
     Analog Search Result Routing 2 · holobiomicslab

     Use when after MS2Query has ranked and scored library matches against query spectra, when you need to apply different confidence thresholds, interpretation strategies, or downstream workflows depending on whether the result is an exact match (precursor m/z difference ≈ 0) or a chemical analog.
     0 installs