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HolobiomicsLab

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1. ▌
   SQL Query Optimization For Similarity Search 2 · holobiomicslab

   Use when when migrating spectral library data from file-based formats (JSON, CSV, binary) into a persistent store and need to support fast filtered queries on metadata and similarity computations against query spectra.
   6 installs
2. ▌
   Transformer Model Inference On Spectral Data 2 · holobiomicslab

   Use when you have a 1D 1H NMR spectrum represented as chemical shift vs. intensity values, a corresponding list of detected peak positions, and you need to assign metabolite identities to those peaks.
   11 installs
3. ▌
   Annotation Coverage Statistics Computation 3 · holobiomicslab

   Use when you have run MSMetaEnhancer's annotate_spectra() method on a .
   9 installs
4. ▌
   Cross Platform Software Capability Mapping 3 · holobiomicslab

   Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization features are already implemented in competing or complementary tools (e.
   8 installs
5. ▌
   M Z To Normalized Kendrick Mass Conversion 2 · holobiomicslab

   Use when you have uploaded peak list data containing m/z values and wish to construct a Kendrick mass plot where alkane homolog series (or other homologous families) are expected to appear as horizontal lines.
   9 installs
6. ▌
   Mass Spectrometry Plot Type Specialization 3 · holobiomicslab

   Use when you have a Pandas DataFrame containing mass spectrometry data (e.
   12 installs
7. ▌
   Class Imbalance Downsampling Ratio Adjustment 2 · holobiomicslab

   Use when after generating cross-spectrum negative examples via precursor m/z windowing and before training a rescore model (e.g., Siamese architecture in FIDDLE v2.0.0).
   9 installs
8. ▌
   Feature Table Generation From Aligned Spectra 2 · holobiomicslab

   Use when after retention-time and m/z-based peak alignment has been completed across a cohort of LC-MS samples, and you need to create a unified quantitative matrix for statistical testing, multivariate analysis, or annotation workflows.
   9 installs
9. ▌
   Multi Batch Experimental Design Understanding 3 · holobiomicslab

   Use when your metabolomics experiment includes samples acquired across multiple instrument runs, different preparation dates, or distinct sample cohorts.
   5 installs
10. ▌
    Spectrum Similarity Nearest Neighbor Indexing 2 · holobiomicslab

    Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise distance computation is computationally prohibitive.
    10 installs
11. ▌
    Composite Spectra Assembly From Fragment Ions 2 · holobiomicslab

    Use when you have DDA raw mass spectrometry data (mzML, mzXML, or netCDF format) and need to reconstruct composite fragmentation spectra by associating fragment ions with their parent precursor ions.
    9 installs
12. ▌
    Isotopologue Adduct Cross Assay Link Encoding 3 · 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.
    11 installs
13. ▌
    Mass Spectrometry Data Loading And Formatting 3 · 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.
    11 installs
14. ▌
    Neural Network Architecture Design Spectra 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectra pairs (unknown and known metabolites) with annotated structural similarity labels, and you need to learn a generalizable model that can rank candidate structures for novel unknowns by predicting their similarity to reference compounds in a database.
    11 installs
15. ▌
    Retention Time Agnostic Spectral Alignment 3 · holobiomicslab

    Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts between acquisitions, or use of different LC-MS platforms (e.g., Orbitrap vs. Q-ToF).
    9 installs
16. ▌
    Sodium Adduct Detection And Classification 4 · holobiomicslab

    Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in the range of ~20–25 Da (characteristic of Na adducts).
    8 installs
17. ▌
    Spectral Data Export And Format Conversion 2 · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-processed metabolomics data, export spectral data when you need to share clustered spectra with external annotation software (MSFinder, Sirius), perform spectrum matching against reference databases, or prepare results for collaborative analysis.
    13 installs
18. ▌
    Spectral Feature Clustering And Comparison 3 · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.
    8 installs
19. ▌
    Topic Modeling Hyperparameter Optimization 2 · holobiomicslab

    Use when when preparing to apply LDA to a new MS/MS spectral dataset in bag-of-fragments format, before running the full modeling pipeline.
    9 installs
20. ▌
    Spectral Quality Metrics Extraction 2 · holobiomicslab

    Use when you have multi-sample MS1 data (from Agilent, Thermo, Bruker, or mzML formats) and need to quantify ion-level quality attributes—such as signal consistency, noise characteristics, or chromatographic stability—to either flag outlier samples or validate data fitness for downstream.
    10 installs
21. ▌
    Ion Mobility Calibration Curve Fitting 2 · holobiomicslab

    Use when you have TWIM-MS experimental data with arrival times and m/z values, and access to calibrant reference standards with known CCS values (typically loaded from a calibration template).
    11 installs
22. ▌
    Python Package Dependency Installation 3 · holobiomicslab

    Use when you need to enable optional modules in Pyteomics that depend on external libraries not bundled with the core package—such as h5py and hdf5plugin for mzMLb format access, sqlalchemy for Unimod database queries, or psims for ProForma parsing.
    11 installs
23. ▌
    Benchmark Table Generation And Reporting 2 · holobiomicslab

    Use when when you need to quantify and document the computational cost of a multi-stage analysis pipeline (such as MetaboDirect) across varying input sizes (e.
    12 installs
24. ▌
    Peak Filtering And Preprocessing Lc Ms 4 · holobiomicslab

    Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform library matching, molecular networking, or spectral similarity comparison.
    12 installs
25. ▌
    Peptide Sequence Prediction Comparison 2 · holobiomicslab

    Use when when you have a pre-trained Casanovo model, annotated MS/MS spectra in MGF format, and want to benchmark whether beam search decoding improves peptide prediction quality over the default greedy decoding strategy.
    10 installs
26. ▌
    Retention Time Mass Proximity Matching 3 · holobiomicslab

    Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for features that are detected in some samples but fall below the detection threshold in others.
    12 installs
27. ▌
    Sample Type Stratified Feature Masking 3 · holobiomicslab

    Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that fail to show meaningful enrichment in actual study samples relative to blank contamination.
    13 installs
28. ▌
    Small Molecule Chromatography Modeling 2 · holobiomicslab

    Use when when you have a set of small molecule structures (as SMILES or molecular graphs) and need to predict their elution order in RPLC systems with eluent pH around 2.
    6 installs
29. ▌
    Spectral Fingerprint Web Service Query 3 · holobiomicslab

    Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural classification (compound class and subclass) with confidence estimates.
    8 installs
30. ▌
    Workflow Pipeline Execution Validation 3 · holobiomicslab

    Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically informed annotation pipeline, or after pipeline execution to verify all outputs were generated correctly.
    11 installs
31. ▌
    Inference Performance Benchmarking 3 · holobiomicslab

    Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and need to rigorously compare their held-out test performance to determine which architecture balances prediction accuracy.
    10 installs
32. ▌
    Mass Spectrometry Peak Pair Analysis 3 · holobiomicslab

    Use when you have preprocessed MSI data (as a CSV intensity matrix or Cardinal MSProcessedImagingExperiment object) and suspect that observed peaks include both parent ions and their adducts formed with matrix or salt species.
    13 installs
33. ▌
    Chromatographic Retention Time Matching 2 · holobiomicslab

    Use when you have GC-MS data with multiple replicate injections or samples, need to identify a predefined set of query chemicals by name, and want to consolidate all instances of those chemicals (which may appear with varying match factors or peak areas across different samples or injection.
    10 installs
34. ▌
    Mass Spectrometry Data Table Formatting 3 · holobiomicslab

    Use when when you have raw or processed TWIM-MS data (arrival time and m/z values) from a mass spectrometry instrument and need to organize it into a feature table before biomolecular class assignment or CCS calculations.
    14 installs
35. ▌
    Confidence Score Assignment And Filtering 2 · holobiomicslab

    Use when after matching MRM transitions against a lipid reference database, when you have candidate lipid identities for each transition and need to rank them by quality and select a single match per transition for export to the labelled lipid-identity table.
    8 installs
36. ▌
    Ionization Mode Peak Retention Comparison 3 · holobiomicslab

    Use when when you have loaded a raw mass spectrum (e.g. ESI_NEG_SRFA.
    12 installs
37. ▌
    Deep Learning Architecture Implementation 3 · holobiomicslab

    Use when you have two augmented versions of the same ion image (from mass spectrometry imaging data) and need to extract learnable 512-dimensional feature representations using a shared-weight encoder for contrastive loss optimization.
    11 installs
38. ▌
    Summary Visualization Artifact Generation 3 · holobiomicslab

    Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and visualize the aggregated match results in a format compatible with metadataMASST web interface or downstream analysis.
    15 installs
39. ▌
    Mass Spectrometry Feature Table Construction 2 · holobiomicslab

    Use when you have vendor-independent centroided mzML files from LC- or GC-HRMS data acquired in data-dependent acquisition (ddMS2) mode and need to extract detected features with m/z, retention time, and intensity attributes as input for non-target screening or PFAS prioritization workflows.
    12 installs
40. ▌
    Neutral Loss Feature Extraction From Spectra 2 · holobiomicslab

    Use when you have MS2 spectra data (MGF/mzML format) and aligned feature tables, and your analysis goal is to compare samples that may have poor MS1 feature overlap, strong retention-time shifts across runs, or were acquired on different LC-MS platforms.
    9 installs
41. ▌
    Background Distribution Threshold Derivation 2 · holobiomicslab

    Use when when you have trained predictive models (e.g., neural networks) on paired microbiome-metabolome data and need to identify which metabolites are genuinely well-predicted above chance.
    11 installs
42. ▌
    Effective Mobility Calibration Single Marker 2 · holobiomicslab

    Use when when you have CE-MS data with migration times that vary between runs due to electroosmotic flow drift, but you possess a reliable internal standard with a known effective mobility value.
    9 installs
43. ▌
    Extracted Ion Chromatogram Eic Visualization 2 · holobiomicslab

    Use when after running MS1 extraction and prescreening on mzML files with assigned adducts and tags, when you need to inspect detected compounds visually to verify peak shape, confirm retention time consistency across samples (e.
    11 installs
44. ▌
    File Format Identification Mass Spectrometry 3 · holobiomicslab

    Use when you have raw MS data files from one or more instrument vendors (Agilent, Bruker, Thermo Fisher, or mzML-formatted) and need to convert them to a vendor-agnostic HDF5-based storage format for downstream software development, machine learning, or cross-platform data access.
    10 installs
45. ▌
    Formula Transformer Architecture Application 3 · 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.
    10 installs
46. ▌
    Gnn Architecture Design For Molecular Graphs 2 · holobiomicslab

    Use when when you have preprocessed molecular graph data (node and edge tensors representing atoms and bonds) and need to train a regression model to predict a continuous molecular property (e.g., LC retention time).
    11 installs
47. ▌
    Mass Spectrometry Data Constraint Validation 2 · holobiomicslab

    Use when implementing replacement methods ($<-, [<-, spectraData<-, mz<-, intensity<-, peaksData<-) for a writable MsBackend subclass, or when modifying peak data in an existing backend.
    6 installs
48. ▌
    Mass Spectrometry Feature Extraction Ms1 Ms2 2 · holobiomicslab

    Use when when you have raw mzML files from LC-MS/MS metabolomics experiments and need to convert them into a structured feature table with accurate mass, retention time, and MS2 spectral data linked to a reference compound list.
    9 installs
49. ▌
    Mass Spectrometry Spectrum Quality Filtering 2 · holobiomicslab

    Use when compiling or harmonizing MS/MS spectral libraries from multiple source repositories and you need to identify and remove spectra that fail quality thresholds (low resolution, precursor-fragment mass inconsistency, duplicate fragment patterns, noise-dominated, or missing critical metadata.
    6 installs
50. ▌
    Metabolite Structural Annotation Integration 3 · 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.
    12 installs
51. ▌
    Ion Mobility Mobilogram Visualization 3 · holobiomicslab

    Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across the ion mobility axis.
    9 installs
52. ▌
    Elemental Ratio Histogram Visualization 2 · holobiomicslab

    Use when after loading a numeric elemental ratio column (H/C, O/C, N/C, etc.) from a CSV file into Punc'data, when you need to visualize the distribution of molecular formulas across a sample and want bin spacing to adapt automatically: narrow bins (0.1) for low-range data (span ≤ 3.
    11 installs
53. ▌
    Lexical Tokenization And Grammar Design 2 · holobiomicslab

    Use when you need to enable users to express complex domain-specific queries in a natural, succinct syntax—particularly when SQL patterns are familiar but must be augmented with domain assumptions (e.
    8 installs
54. ▌
    Structured Data Compilation From Readme 3 · holobiomicslab

    Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic coverage) in its README, and you need to create a machine-readable inventory for downstream indexing, validation, or reuse.
    8 installs
55. ▌
    Fragment Assembly Transformer Architecture 2 · holobiomicslab

    Use when when you have 1D NMR spectra (1H and/or 13C) of an unknown compound with up to ~19 heavy atoms and need to predict both molecular formula and connectivity without manual structure hypothesis generation.
    12 installs
56. ▌
    Metabolomics Noise Perturbation Simulation 3 · holobiomicslab

    Use when when benchmarking or validating a pathway analysis method (such as PALS, ORA, or GSEA) on metabolomics data, you need quantitative evidence that the method's pathway rankings remain stable despite noise and missing peaks—conditions prevalent in real LC-MS/MS datasets.
    6 installs
57. ▌
    Software Architecture Documentation Review 3 · holobiomicslab

    Use when you need to verify the scope and completeness of a software platform's analytical capabilities—particularly when the project claims to support multiple input modalities (e.
    11 installs
58. ▌
    Tandem Ms Feature Table Import And Parsing 2 · holobiomicslab

    Use when when you have raw feature tables exported from a tandem LC-MS/MS preprocessing tool (e.g., Progenesis QI, MS-DIAL, Bruker Metaboscape) and need to combine them with sample metadata (group assignments, replicate structure) before applying feature filtering or quality control workflows.
    12 installs
59. ▌
    Deep Learning Model Inference On Test Sets 3 · holobiomicslab

    Use when you have a pretrained deep learning model, a reserved test set with ground-truth annotations, and need to evaluate prediction quality or generate embeddings for downstream analysis. Typical triggers: benchmarking a new model against classical baselines (e.
    8 installs
60. ▌
    Ionization Mode Merging And Reconciliation 2 · holobiomicslab

    Use when you have acquired MS-DIAL peak lists in both positive and negative ionization modes on the same sample set and want to consolidate detected features across modes to avoid reporting duplicate annotations for the same molecule.
    13 installs
61. ▌
    Mass Spectrometry Precursor Identification 3 · holobiomicslab

    Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate LC-MS retention time linearity, assess method reproducibility, or establish retention time calibration curves.
    7 installs
62. ▌
    Mass To Charge Ratio Matching Against Kegg 2 · holobiomicslab

    Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z and intensity; columns = samples) and need to assign KEGG compound identifiers to observed peaks.
    9 installs
63. ▌
    Metabolite Structural Network Construction 2 · holobiomicslab

    Use when after MamsiStructSearch has completed structural clustering of statistically significant LC-MS features (p < 0.
    14 installs
64. ▌
    Missing Value Imputation By Data Recursion 3 · holobiomicslab

    Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to features falling below the detection limit in some samples but being present above-threshold in others.
    9 installs
65. ▌
    Ms Ms Spectral Preprocessing Normalization 2 · holobiomicslab

    Use when you have paired MS/MS spectra from unknown and known metabolites with raw intensity values and need to prepare them as input for a deep-learning model that will predict structural similarity.
    13 installs
66. ▌
    Multi Head Attention Mechanism Application 2 · holobiomicslab

    Use when you have embedded sequences of chemical formulae (tokenized and converted to dense vectors) from tandem MS/MS spectra and need to learn context-dependent representations that capture dependencies between formula tokens at multiple semantic levels.
    10 installs
67. ▌
    Adduct Fragment Formula Interpretation 3 · holobiomicslab

    Use when after temporal correlation has identified candidate feature pairs with matching intensity profiles across time-resolved DBDI-MS experiments.
    9 installs
68. ▌
    Adduct Ion Parent Ion Pairing Analysis 4 · holobiomicslab

    Use when when you have binned mass spectrometry imaging peaks and want to understand which detected mass-to-charge ratios represent the same metabolite in different ionization states (parent vs. adduct form).
    10 installs
69. ▌
    Analyte Metadata Hierarchical Indexing 2 · holobiomicslab

    Use when after applying a stringent Q-value quality filter (e.
    11 installs
70. ▌
    Automated Reaction Network Exploration 2 · holobiomicslab

    Use when when you have a molecular geometry (XYZ format) and need to predict electron ionization (EI) mass spectrum fragmentation patterns by exhaustively sampling conformational space and reaction intermediates.
    9 installs
71. ▌
    Constraint Based Flux Balance Analysis 3 · holobiomicslab

    Use when you have a generic genome-scale metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, extracellular flux measurements from bioanalyzer or similar) from multiple biological samples (cell lines, conditions).
    9 installs
72. ▌
    Container Image Selection And Mounting 3 · holobiomicslab

    Use when when deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may differ. Choose this skill specifically when you need to process LC-HRMS .mzML or .
    10 installs
73. ▌
    Cross Tool Result Concordance Analysis 3 · holobiomicslab

    Use when you have executed multiple NPDtools database search pipelines (Dereplicator, VarQuest, Dereplicator+, or MetaMiner in different modes) on identical test spectra or RiPP sequence inputs and need to understand their relative sensitivity, specificity, and complementarity.
    8 installs
74. ▌
    Jpa Module Execution And Configuration 2 · holobiomicslab

    Use when when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to extract metabolic features as the first major step of untargeted metabolomics analysis. Choose MS1 peak picking for DDA/full-scan data;
    10 installs
75. ▌
    Lc Ms Feature Grouping And Compounding 4 · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data, when you have hundreds or thousands of individual m/z × retention-time peaks and need to associate them into biologically meaningful feature groups.
    8 installs
76. ▌
    Mass Spectrometry File Format Handling 3 · holobiomicslab

    Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into R for downstream statistical analysis, benchmarking, or integration with Bioconductor workflows.
    11 installs
77. ▌
    Mass Spectrum Histogram Interpretation 2 · holobiomicslab

    Use when after computing all pairwise mass differences from a mass spectrometry imaging dataset, when you need to identify which mass differences correspond to real molecular adducts (e.g., metabolite–matrix or metabolite–salt ions) rather than noise.
    10 installs
78. ▌
    Metabolite Structure Format Conversion 2 · holobiomicslab

    Use when when importing candidate metabolite structures from public chemical databases (PubChem, ChEBI, etc.) for use in MAGMa-based annotation workflows, or when integrating external structure datasets that may use divergent molecular representation formats or contain non-standard chemical.
    16 installs
79. ▌
    Molecular Graph Representation Parsing 2 · holobiomicslab

    Use when you have molecular identifiers (SMILES strings or molecular structure files) that need to be converted into node-edge graph tensors for input to message passing neural network models like chemprop or chemprop-IR.
    10 installs
80. ▌
    Molecular Network Attribute Enrichment 3 · holobiomicslab

    Use when you have a GNPS mass spectral molecular network (in .graphml or Cytoscape format) and wish to annotate its nodes and edges with chemical class assignments from the GNPS library and/or MS2LDA motif probabilities from an independent LDA experiment.
    10 installs
81. ▌
    Multi Score Complementarity Evaluation 3 · holobiomicslab

    Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine whether they capture complementary information that justifies combining them.
    12 installs
82. ▌
    Metabolite Candidate Ranking Interpretation 2 · holobiomicslab

    Use when after running annotateRC() on LC-MS AIF features, when you need to validate whether a feature's rank-1 annotation is reliable or when you suspect that structurally similar metabolites (e.
    7 installs
83. ▌
    Search Result Aggregation And Normalization 2 · holobiomicslab

    Use when you have executed batch searches across two or more domain-specific MASST tools and obtained separate output files (_microbe.json, _plant.json, _tissue.
    5 installs
84. ▌
    Acquisition Mode Enumeration And Validation 2 · holobiomicslab

    Use when adopting a mass spectrometry-based analysis tool (e.
    11 installs
85. ▌
    CI CD Pipeline Reproducibility Verification 2 · holobiomicslab

    Use when when a repository displays a GitHub Actions workflow badge (e.
    8 installs
86. ▌
    Cross Database Structural Homology Matching 3 · holobiomicslab

    Use when when you have antiSMASH-predicted BGCs and wish to link them to metabolomic data via structure prediction, but only BGCs with sufficient structural homology to characterized reference clusters will yield reliable predictions.
    8 installs
87. ▌
    Interactive Network Visualization Rendering 3 · holobiomicslab

    Use when after structural clustering (isotopologue grouping, adduct detection, cross-assay linking) and correlation clustering of LC-MS features, when you need to inspect and communicate the topology of structural relationships—particularly when the number of features or link types is too dense for.
    13 installs
88. ▌
    Isotopic Signature Validation And Filtering 4 · holobiomicslab

    Use when after isotope detection has enumerated C13 isotopologue patterns across m/z, drift time, and retention time dimensions, and you need to reduce false positives by retaining only well-populated isotopic signature clusters before annotation or export.
    7 installs
89. ▌
    Metabolite Feature Matching Across Datasets 3 · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature tables (e.
    11 installs
90. ▌
    Molecular Formula Isotopic Profile Matching 2 · holobiomicslab

    Use when you have detected peaks from untargeted LC/HRMS analysis (via IDSL.IPA or equivalent peak picker) with m/z and retention time values, and you need to assign molecular formulas to those peaks.
    10 installs
91. ▌
    Motif Pseudo Spectra Optimization Filtering 2 · holobiomicslab

    Use when after LDA has converged and inferred Mass2Motifs from preprocessed mass spectrometry spectral data, when the raw motif-fragment distributions contain noise or low-confidence associations that obscure the dominant fragmentation patterns.
    10 installs
92. ▌
    Orbitrap Spectrum Extraction From Raw Files 3 · holobiomicslab

    Use when you have a Thermo Fisher Orbitrap .raw file and need to retrieve a specific scan's spectral data (m/z and intensity arrays), validate instrument parameters (resolving power, AGC injection time), or assess signal-to-noise characteristics of fragment ions for a known precursor peptide (e.
    10 installs
93. ▌
    R Dependency Package Compatibility Auditing 2 · holobiomicslab

    Use when a Shiny application or R-based tool is known to run on only one operating system (e.g., Windows-only), and you need to identify the root causes preventing execution on Linux or macOS before undertaking cross-platform porting.
    11 installs
94. ▌
    Repository Cloning And Structure Navigation 3 · holobiomicslab

    Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.
    10 installs
95. ▌
    Spectral Overview Representation Generation 4 · holobiomicslab

    Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D projection suitable for dashboard visualization or high-level pattern discovery without losing similarity structure.
    14 installs
96. ▌
    Workflow Configuration And Parameterization 3 · holobiomicslab

    Use when when preparing to execute the Nextflow4MS-DIAL workflow on raw LC-HRMS metabolomics data (.mzML or .
    9 installs
97. ▌
    Analytical Pipeline Feature Documentation 3 · holobiomicslab

    Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses it supports—particularly when the pipeline is positioned as an alternative to or improvement over established tools.
    11 installs
98. ▌
    Ionisation Method Hardware Correspondence 4 · holobiomicslab

    Use when when evaluating whether a mass spectrometry analysis platform (such as mzmine) has comprehensive module support across multiple ionisation and separation techniques (LC, GC, IMS, MALDI MS imaging), or when planning a multi-technique MS study and needing to confirm that all intended.
    9 installs
99. ▌
    JSON Payload Construction For Nmr Spectra 3 · holobiomicslab

    Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.
    11 installs
100. ▌
     Knowledge Graph Generation And Validation 3 · holobiomicslab

     Use when after completing all per-sample annotation steps (molecular networking, ISDB/spectral matching, SIRIUS/CSI:FingerID, and compounds metadata enhancement with Wikidata IDs and NPClassifier ontology).
     7 installs