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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Cross Dataset Entry Filtering · holobiomicslab

   Use when you have received MSBERT-preprocessed spectral data from GNPS, MoNA, or MTBLS1572 and need to ensure data integrity before training a spectral embedding model.
   0 installs
2. ▌
   Cross Omics Feature Alignment · holobiomicslab

   Use when you have preprocessed multiomics datasets from distinct biomolecular classes (e.
   0 installs
3. ▌
   Database Repository Retrieval · holobiomicslab

   Use when when you need to obtain a specific curated database (e.g., DNA adduct compounds) that is published in a GitLab or GitHub repository and available in structured formats (SDF, Excel, Word).
   0 installs
4. ▌
   Development Mode Installation · holobiomicslab

   Use when you need to run a local test suite, contribute code changes to a repository, or iterate rapidly on package modifications.
   0 installs
5. ▌
   Directed Edge Weight Encoding · holobiomicslab

   Use when after computing a Jacobian matrix from covariance data and extracting directed edges representing metabolite interactions, use this skill when you need to communicate the magnitude and direction of metabolite-to-metabolite influences in a single integrated visualization.
   0 installs
6. ▌
   Elemental Composition Parsing · holobiomicslab

   Use when when you have FT-ICR MS peak data with assigned molecular formulas (e.g., from CoreMS, Formularity, or similar formula assignment tools) and need to compute thermodynamic indices (DBE, GFE, AImod, NOSC) or classify peaks by elemental composition.
   0 installs
7. ▌
   Embedding Similarity Matching · holobiomicslab

   Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, and you need to identify the most likely candidate molecules from a reference database.
   0 installs
8. ▌
   Entry Point Script Validation · holobiomicslab

   Use when after installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows.
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9. ▌
   Fingerprint Generation Morgan · holobiomicslab

   Use when you have parsed molecular structures from the SMRT dataset or similar small molecule collections and need to create a vectorized molecular representation suitable for neural network input alongside molecular graph representations.
   0 installs
10. ▌
    Fisher Exact Test Application · holobiomicslab

    Use when you have a list of metabolites or lipids with associated p-values (e.
    0 installs
11. ▌
    Fisher Exact Test Computation · holobiomicslab

    Use when you have partitioned genomic-metabolomic links into discrete categories (e.
    0 installs
12. ▌
    Git Feature Branch Management · holobiomicslab

    Use when when contributing a new feature, bug fix, or documentation update to a shared repository (like iomega/ms2query), and you need to isolate your changes from the main development branch to allow for testing, review, and conditional integration without disrupting the primary codebase.
    0 installs
13. ▌
    Gpu Environment Configuration · holobiomicslab

    Use when you need to run a PyTorch model that was trained on GPU (e.g., JESTR with released NPLIB1 weights) and require verified GPU availability (torch.cuda.is_available() returns True). Apply this skill when you have a requirements.
    0 installs
14. ▌
    Hdf5 File Structure Traversal · holobiomicslab

    Use when when you have converted multidimensional mass spectrometry data (or other complex data) into MZA HDF5 format and need to understand the file hierarchy, validate the conversion output, extract metadata tables and array structure, or access spectra across different programming environments.
    0 installs
15. ▌
    Hmm Profile Database Querying · holobiomicslab

    Use when when you have BGC sequences (FASTA or GenBank format) or protein sequences and need to annotate them with biosynthetic or functional domains from a curated pHMM database (e.g., PFAM 35.0).
    0 installs
16. ▌
    Imputation Quality Validation · holobiomicslab

    Use when after applying BPCA imputation to a filtered metabolite matrix (with metabolites having >80% missingness already removed) and before proceeding to median normalization.
    0 installs
17. ▌
    Imzml File Loading And Import · holobiomicslab

    Use when when you have one or more imzML files containing mass spectrometry imaging data and need to import them into LipidQMap for ion image extraction, isotopic correction, and quantitative analysis.
    0 installs
18. ▌
    Ionomics Data Format Handling · holobiomicslab

    Use when you have raw ICP-MS ion concentration measurements (e.g., Ca44, Cd111, Fe56, Zn66 in ppm) organized as a data frame with multiple replicates per sample and batch identifiers, and you need to prepare this for ionomics analysis in Galaxy or the IonFlow R package.
    0 installs
19. ▌
    Irreversible Model Conversion · holobiomicslab

    Use when you have a constraint-based metabolic model in SBML or similar format with reversible reactions and need to sample the feasible steady-state flux region using optGpSampler or other samplers that require an irreversible stoichiometric matrix.
    0 installs
20. ▌
    Isotopic Envelope Calculation · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution for comparison against experimental MS peaks, validation of mass calibration, or simulation of expected peptide signals in a mass spectrometry assay.
    0 installs
21. ▌
    Iterative Fitting Convergence · holobiomicslab

    Use when you have 1D mass spectrometry signal data (e.
    0 installs
22. ▌
    Java Static Method Invocation · holobiomicslab

    Use when you have a Java application or standalone tool that needs to predict CYP450-catalyzed metabolites for one or more molecules and you require the option to compare predictions with and without CypReact filtering applied.
    0 installs
23. ▌
    Joint Embedding Space Scoring · holobiomicslab

    Use when you have a mass spectrum from an untargeted metabolomics experiment and a set of candidate molecules (e.g., downloaded from PubChem) that may explain that spectrum. You want to rank these candidates by likelihood of correctness to prioritize manual annotation or further validation.
    0 installs
24. ▌
    JSON Spectral Data Processing · holobiomicslab

    Use when you have raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize field names, validate chemical identifiers (SMILES, InChI, InChIKey), remove duplicates, filter by quality criteria.
    0 installs
25. ▌
    Archive Extraction And File Mapping · holobiomicslab

    Use when when you have downloaded a GNPS molecular networking job archive (from GNPS1 or GNPS2 workflows: METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING, classical_networking_workflow, or feature_based_molecular_networking_workflow) and need to extract and standardize.
    0 installs
26. ▌
    Batch Aware Normalization Workflows · holobiomicslab

    Use when your LC-MS feature table exhibits intensity variations across samples that correlate with technical batches (e.
    0 installs
27. ▌
    Batch Correction Quality Assessment · holobiomicslab

    Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have been attenuated without loss of data dimensionality or sample information.
    0 installs
28. ▌
    Bgc Spectrum Iokr Score Computation · holobiomicslab

    Use when when you have a collection of microbial genomes with predicted BGCs (via antiSMASH), a set of MS/MS spectra (e.g. from GNPS), and you want to score potential BGC-spectrum associations based on the presence of conserved molecular substructures inferred from the BGC's closest MIBiG homolog.
    0 installs
29. ▌
    Binary And XML Data Deserialization · holobiomicslab

    Use when you have raw LC-MS data in .mzML (XML-based) or Thermo .raw (proprietary binary) format and need to load it into memory for visualization, querying, or downstream analysis.
    0 installs
30. ▌
    Charge State Specific Peak Matching · holobiomicslab

    Use when you have peak-picked features with m/z, drift_time, retention_time, and intensity columns, and you need to identify monoisotopic peaks and their charge-state-specific isotopologue members (e.g., singly charged C13-substituted species).
    0 installs
31. ▌
    Chemical Class Metadata Integration · holobiomicslab

    Use when you have generated a GNPS molecular network (classical or feature-based workflow) and possess chemical class annotations (from GNPS library matching, ClassyFire, or other structural classifiers) that you wish to propagate onto network nodes and edges to enable chemical family-level.
    0 installs
32. ▌
    Chemical Formula Ranking Evaluation · holobiomicslab

    Use when after running formula inference on a benchmark dataset with known formula and adduct ground truth (e.g., NPLIB1, NIST20, or CASMI 2022). Apply this skill when you need to quantify ranking performance, isolate the contribution of specific model features (e.
    0 installs
33. ▌
    Chromatographic Coelution Detection · holobiomicslab

    Use when after feature detection when you have a feature table with m/z, retention time, and intensity columns, and you need to group features into empirical compounds (putative metabolites) that account for isotopologue patterns and multiple adduct forms arising from a single underlying analyte.
    0 installs
34. ▌
    Classification Metric Visualization · holobiomicslab

    Use when after training or evaluating a classification model (e.g., a Siamese neural network for spectrum similarity prediction) and obtaining a prediction array and corresponding ground-truth label array.
    0 installs
35. ▌
    Coefficient Of Variation Comparison · holobiomicslab

    Use when after normalization of a metabolomic feature matrix but before statistical testing, when you have both QC (technical replicate) and non-QC (study) samples and need to remove features with unstable or poorly reproducible signal patterns.
    0 installs
36. ▌
    Cohen Kappa Inter Rater Reliability · holobiomicslab

    Use when when you have two independent predictions of categorical outcomes (up/down/no-change variation signs) across multiple sample pairs and need to measure agreement beyond what would be expected by chance.
    0 installs
37. ▌
    Collision Cross Section Calibration · holobiomicslab

    Use when you have LC-IMS-MS/MS data with drift_time measurements and need to convert raw drift times into calibrated CCS values for structural annotation.
    0 installs
38. ▌
    Collision Cross Section Computation · holobiomicslab

    Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
    0 installs
39. ▌
    Comparative Omics Report Generation · holobiomicslab

    Use when when you have feature lists (in CSV format) from two or more different MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), different processing software (e.
    0 installs
40. ▌
    Container Image Building Conversion · holobiomicslab

    Use when your Nextflow metabolomics workflow has been validated with Docker locally, but you need to deploy it on an HPC cluster that mandates Singularity containerization (e.g., Red Hat Enterprise Linux 8.
    0 installs
41. ▌
    Cross Domain Metadata Harmonization · holobiomicslab

    Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate cross-domain summary statistics.
    0 installs
42. ▌
    Cross Validation Workflow Execution · holobiomicslab

    Use when you have paired microbiome (16S rRNA/metagenomic) and metabolome (LC-MS/MS or similar) count data and need to evaluate how well a predictive model (e.g., neural network, Elastic Net) generalizes across samples.
    0 installs
43. ▌
    CSV Format Specification Compliance · holobiomicslab

    Use when after feature extraction or feature alignment when you have FeatureSet or Sample objects that must be exported as CSV files for sharing, archival, or downstream analysis. Specifically: (1) when exporting single-sample feature tables from find_feature() output;
    0 installs
44. ▌
    Dataset Preprocessing And Filtering · holobiomicslab

    Use when when you have a raw GNPS or other spectral library dataset with inconsistent or incomplete instrument annotations, and you need to verify or reproduce reported dataset split counts (e.g., training/test compound ratios). Apply this skill when an instrument allowlist fix (e.
    0 installs
45. ▌
    Dataset Train Test Split Validation · holobiomicslab

    Use when when preparing MS/MS spectra for deep learning model training on a specific instrument type (e.g., Orbitrap, Q-TOF), and you need to verify that configuration-driven filtering (e.g., adding 'ftms' to an instrument allowlist) produces training and test sets of the expected size (e.
    0 installs
46. ▌
    Dda Precursor Fragment Ion Grouping · holobiomicslab

    Use when when you have raw DDA mass spectrometry data (mzML, mzXML, or netCDF format) where precursor ions have been fragmented and you need to associate each fragment ion back to its parent precursor ion to generate coherent, precursor-specific fragmentation spectra for chemical annotation.
    0 installs
47. ▌
    De Novo Structure Candidate Ranking · holobiomicslab

    Use when when you have high-resolution LC-MS/MS data for an unknown metabolite or small molecule, have computed or measured the molecular ion mass and fragmentation spectrum, and require de-novo structure generation because the compound is absent from spectral libraries or structure databases.
    0 installs
48. ▌
    Encoder Decoder End To End Training · holobiomicslab

    Use when you have a pretrained encoder that produces fixed-size embeddings from MS/MS spectra (or similar spectral data), a tokenized target dataset of canonical SMILES strings representing molecular structures, and you need to learn a decoder that reliably reconstructs the molecular structure from.
    0 installs
49. ▌
    Enrichment Statistical Thresholding · holobiomicslab

    Use when after running Enrichment() on a configured EnrichParam object (via KEGG_Enrich_PlotPanel or similar), when you have a full enrichment result table and need to reduce it to pathway hits meeting a specific significance threshold before visualization or export.
    0 installs
50. ▌
    Excel File Parsing For Metabolomics · holobiomicslab

    Use when you have a preprocessed LC-MS peak table exported from peak-picking software (e.g., MS-DIAL) in Excel format with three logical compartments: sample annotation (rows), feature annotation (columns), and abundance matrix (numeric values).
    0 installs
51. ▌
    False Discovery Rate Interpretation · holobiomicslab

    Use when when you have executed database search pipelines (Dereplicator, VarQuest, or Dereplicator+) on centroided LC-MS/MS spectra in MGF format and obtained match results with associated p-values and false discovery rates.
    0 installs
52. ▌
    False Positive Annotation Filtering · holobiomicslab

    Use when after high-scoring spectral library matching (e.g., EQ module output) of LC-MS/MS data yields candidate lipid annotations; when spectral similarity alone produces false positives and you have computed relative retention time intervals across species cohorts;
    0 installs
53. ▌
    Feature Intensity Ratio Calculation · holobiomicslab

    Use when after generating a feature table from LC-MS/MS data when your experiment includes blank control samples and you need to remove features driven by background ions or instrumental contamination.
    0 installs
54. ▌
    Feature Table Export And Formatting · holobiomicslab

    Use when after completing feature detection, alignment, and optional filtering (blank subtraction, QC reproducibility, feature occurrence thresholds) in MZmine2 or Optimus, and you need to prepare the feature table and MS/MS spectra for GNPS-based molecular networking, bioassay integration, or.
    0 installs
55. ▌
    Fixed Architecture Layer Validation · holobiomicslab

    Use when after loading a specXplore session data object file from the hard drive and instantiating a dashboard session layer with it, validate that the architecture layer has initialized without errors and that the interactive dashboard is responsive to user input.
    0 installs
56. ▌
    Flux Propensity Dataset Integration · holobiomicslab

    Use when when you have (1) LC-MS normalized intracellular metabolite abundance data across multiple cell lines or samples, (2) a constraint-based metabolic model with stoichiometric coefficients, and (3) a need to quantify metabolic control through substrate availability independently of enzymatic.
    0 installs
57. ▌
    Format Conversion Conditional Logic · holobiomicslab

    Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow.
    0 installs
58. ▌
    Formula Ranking Accuracy Evaluation · holobiomicslab

    Use when use this skill after training or fine-tuning a chemical formula transformer model on annotated tandem MS/MS spectra, when you need to measure whether the model's ranked formula candidates match ground truth.
    0 installs
59. ▌
    Fractional Abundance Transformation · holobiomicslab

    Use when you have raw LC-MS fractional abundances of isotopologues (FAM) from a stable isotope labeling experiment (e.
    0 installs
60. ▌
    Fragment Mass Tolerance Calibration · holobiomicslab

    Use when when implementing fragment ion annotation in proteomics workflows and needing to determine whether neutral loss annotation (e.g., H2O: -18.010565, NH3: -17.026549) should be enabled to maximize peak interpretation.
    0 installs
61. ▌
    Genome Annotation Format Comparison · holobiomicslab

    Use when when running metabologenomic RiPP detection pipelines (MetaMiner) on the same genomic dataset but with different input sequence formats (e.g., contigs.fasta vs. antiSMASH .final.gbk output), or when unexpected null results occur and input format choice is a plausible cause.
    0 installs
62. ▌
    Gpu Accelerated Spectrum Clustering · holobiomicslab

    Use when you have a large collection of tandem mass spectra (≥100k spectra) in MGF format and need to group spectra by similarity (precursor m/z, charge, and fragment ion patterns) for spectral library construction, peptide identification, or quality control.
    0 installs
63. ▌
    Gpu Acceleration Cuda Configuration · holobiomicslab

    Use when when clustering or encoding large MS/MS spectra datasets (>1 million spectra) where CPU-only runtime exceeds practical thresholds (hours to days).
    0 installs
64. ▌
    Graph Neural Network Encoder Design · holobiomicslab

    Use when when you need to compare spectrum prediction models fairly across different encoder architectures (GNN vs. FFN vs. Transformer), and you require equivalent settings (same covariates, identical hyperparameter sweeps) to isolate the effect of the encoder design.
    0 installs
65. ▌
    Hdf5 Output Validation Verification · holobiomicslab

    Use when after invoking the DEIMoS CLI with a configuration file and allowing the Snakemake workflow to execute, use this skill to confirm successful completion of all workflow rules.
    0 installs
66. ▌
    High Resolution Ms2 Peak Assignment · holobiomicslab

    Use when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their fragmentation patterns at scale.
    0 installs
67. ▌
    Hmdb Compound Database Manipulation · holobiomicslab

    Use when when you need to establish a reproducible inventory of compounds for LC-MS/MS simulation studies, particularly to determine how many unique molecular formulas fall within a target m/z window (e.g., 100–1000 Da) and MS1 detection level.
    0 installs
68. ▌
    Hplc Column Parameter Normalization · holobiomicslab

    Use when when you have raw HPLC column specifications from RepoRT or similar metadata repositories and need to prepare them as input features for machine learning models. Apply this skill before featurizing molecular structures or training graph transformers for retention time prediction.
    0 installs
69. ▌
    Hrms Feature Annotation Integration · holobiomicslab

    Use when you have LC- or GC-HRMS data in mzML format and a feature list (CSV/TSL/Excel) from external feature detection software (e.
    0 installs
70. ▌
    Identity Search Spectrum Annotation · holobiomicslab

    Use when you have experimental MS/MS spectra and need to assign definitive molecular identities by matching against a curated spectral library.
    0 installs
71. ▌
    In Silico Spectrum Generation Cfmid · holobiomicslab

    Use when when you have a list of SMILES strings representing chemical structures and need to create paired SMILES-spectrum training data for a generative model (like MSGO) without requiring experimental mass spectra.
    0 installs
72. ▌
    Installation Requirement Validation · holobiomicslab

    Use when before attempting to run QCxMS2 for the first time, after updating any external dependencies (xtb, CREST, molbar, orca, geodesic_interpolate), or when troubleshooting unexplained calculation failures.
    0 installs
73. ▌
    Intensity Normalization And Scaling · holobiomicslab

    Use when when working with raw or filtered MsmsSpectrum objects where peak intensities span a wide dynamic range and need to be normalized for downstream spectrum comparison, database matching, or publication-quality visualization.
    0 installs
74. ▌
    Intensity Threshold Noise Filtering · holobiomicslab

    Use when you have loaded a raw or partially processed MsmsSpectrum object and need to reduce spectral noise before annotation, matching, or visualization. Use it especially when spectra contain many weak peaks (e.
    0 installs
75. ▌
    Intensity Vector Manipulation Numpy · holobiomicslab

    Use when you have extracted mass tracks (EICs) from multiple LC-MS samples aligned into a MassGrid structure, and you need to combine their intensity vectors into a single composite intensity vector for peak detection on the aggregate signal rather than per-sample.
    0 installs
76. ▌
    Interference Profile Identification · holobiomicslab

    Use when after running saturation repair or multidimensional smoothing on IM-MS data when you need to validate whether corrected peaks are reliable or whether overlapping coeluting/comobiling ions may have caused incorrect signal reconstruction.
    0 installs
77. ▌
    Ion Adduct Isotope Pattern Matching · holobiomicslab

    Use when you have a preprocessed feature table (m/z, retention time, intensities) from LC-MS and need to group features into empirical compounds.
    0 installs
78. ▌
    Ion Mobility Calibration Validation · holobiomicslab

    Use when when you have positive- or negative-mode ion mobility spectrometry data with tunemix reference standards (known m/z, drift times, and CCS values) and need to verify that the calibration model accurately captures the relationship between drift time, reference m/z, and collision cross.
    0 installs
79. ▌
    Ion Species Confirmation Validation · holobiomicslab

    Use when after you have identified candidate ion-species pairs through pointwise correlation analysis of XIC temporal profiles and exact mass difference refinement, and you have MS2 fragment spectra available for those candidates.
    0 installs
80. ▌
    Irt Peptide Calibration And Scoring · holobiomicslab

    Use when when you need to assess whether retention times measured on a given LC-MS run follow the expected linear relationship defined by iRT peptide standards (e.g., Pierce or Biognosys iRT peptides).
    0 installs
81. ▌
    Isotopologue Mass Delta Calculation · holobiomicslab

    Use when when constructing a reference mass-matching framework for untargeted metabolomics or isotope-tracing LC-MS data, before pattern-matching observed features to isotopic and adduct variants.
    0 installs
82. ▌
    Isotopologue Pattern Detection Lcms · holobiomicslab

    Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you wish to group features that represent the same metabolite at different isotopologue states.
    0 installs
83. ▌
    Lc Hrms Data Preprocessing Pipeline · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform peak detection, feature alignment, and metabolite annotation in a reproducible, containerized environment.
    0 installs
84. ▌
    Lc Ms Roi Annotation Interpretation · holobiomicslab

    Use when when you have extracted LC-MS ROI windows (m/z × retention time snippets) from raw mzML data and need to distinguish genuine metabolite peaks from noise or artifacts.
    0 installs
85. ▌
    Lipid Chain Composition Enumeration · holobiomicslab

    Use when constructing a de novo or expanded lipid spectral library that must cover all theoretically possible chain compositions and double-bond positional isomers for one or more lipid classes.
    0 installs
86. ▌
    Lipid Species Annotation Assessment · holobiomicslab

    Use when after running MetaboAnnotatoR's annotateRC function when you need to (1) verify that the top-ranked annotation for a feature is correct, (2) understand what alternative lipid structures (e.
    0 installs
87. ▌
    Mass Accuracy Tolerance Calibration · holobiomicslab

    Use when you have experimental fragment m/z values from HRMS/MS instruments (Q-Exactive orbitrap, Q-TOF) in CSV or mzML-derived peaklist format, and need to match them against a library of 500,000+ in-silico fragmented lipid species.
    2 installs
88. ▌
    Mass Spectral Relationship Matching · holobiomicslab

    Use when after peak detection and feature table generation when you have a collection of m/z, retention time, and intensity values and need to identify which features are related variants (isotopes, adducts, or fragments) of the same parent compound.
    0 installs
89. ▌
    Mass Spectrometry Cluster Detection · holobiomicslab

    Use when you have 32-dimensional GLEAMS embeddings (output from the `gleams embed` step) and need to group spectra by their underlying peptide identity.
    0 installs
90. ▌
    Mass Spectrometry Data File Parsing · holobiomicslab

    Use when you receive raw MS data files from LC-MS, LC-IMS-MS, direct infusion, or DDA/DIA experiments and need to extract ion chromatograms, mobility heatmaps, quality metrics, or perform spectral matching.
    0 installs
91. ▌
    Mass Spectrometry Fragment Matching · holobiomicslab

    Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table formats) and need to assign lipid identities using untargeted or targeted tandem MS data.
    0 installs
92. ▌
    Mass Spectrometry Outlier Detection · holobiomicslab

    Use when you have multi-sample MS1 data (LC-MS, LC-IMS-MS, or direct infusion across any omics domain) and need to detect samples with abnormal global ion intensity patterns or unusual per-ion metric behavior (intensity distribution, signal-to-noise, retention time stability) that may indicate.
    0 installs
93. ▌
    Mass Spectrometry Query Formulation · holobiomicslab

    Use when you have a high-resolution LC-MS/MS experiment with a measured [M+H]+ or [M-H]− ion mass and optionally a parent ion fragmentation spectrum (peak list with m/z and intensity pairs), and you seek to generate candidate molecular structures for an unknown metabolite that may not be in.
    0 installs
94. ▌
    Mass Spectrometry Result Tabulation · holobiomicslab

    Use when after executing a MassQL query against mzML mass spectrometry data files and obtaining tabulated results (DataFrame or equivalent in-memory table), apply this skill to persist those results in both human-readable CSV format and visual image form for archival, sharing, and downstream.
    0 installs
95. ▌
    Metabolic Pathway Database Querying · holobiomicslab

    Use when you have a ranked list of metabolite identifiers (PubChemCIDs, KEGG IDs, or chemical names) from differential abundance or ANOVA testing and need to determine which metabolic pathways are overrepresented or enriched among the most significant features.
    0 installs
96. ▌
    Metabolite Annotation Result Export · holobiomicslab

    Use when after running the annotateRC function on LC-MS All-ion fragmentation (AIF) features and obtaining a populated annotations object with ranked candidate matches, use this skill when you need to persist results to disk for archival, sharing, or downstream interpretation (e.
    0 installs
97. ▌
    Metabolite Database File Formatting · holobiomicslab

    Use when after generating or filtering transformation products using generateTPs() or filter(), when you need to annotate MS/MS spectra using MetFrag and require a database of candidate structures (parent compounds and/or their TPs) in a format MetFrag can read.
    0 installs
98. ▌
    Metabolite Filter Status Extraction · holobiomicslab

    Use when after chaining one or more mpactr filter operations (mispicked, group, cv, insource) on an imported peak table and before generating quality-control reports or interactive visualizations.
    0 installs
99. ▌
    Metabolite Lipid Annotation Ranking · holobiomicslab

    Use when you have LC–MS All-ion fragmentation chromatograms processed through xcms and RamClustR, a feature table with unknown identities, and you want to recover lipid annotations by matching observed spectra against lipid fragment libraries (e.g., LipidPos).
    0 installs
100. ▌
     Metabolite Taxonomy Database Lookup · holobiomicslab

     Use when when you have MS/MS-annotated features from a natural extract (via SIRIUS, CANOPUS, or ISDB) and need to compute the Literature Component or Class Component of a priority rank—i.
     0 installs