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HolobiomicsLab

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1. ▌
   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
2. ▌
   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
3. ▌
   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
4. ▌
   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
5. ▌
   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
6. ▌
   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
7. ▌
   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.
   1 install
8. ▌
   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.
   2 installs
9. ▌
   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).
   3 installs
10. ▌
    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
11. ▌
    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
12. ▌
    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
13. ▌
    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
14. ▌
    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
15. ▌
    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
16. ▌
    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
17. ▌
    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.
    2 installs
18. ▌
    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
19. ▌
    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
20. ▌
    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
21. ▌
    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
22. ▌
    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
23. ▌
    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
24. ▌
    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
25. ▌
    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
26. ▌
    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
27. ▌
    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
28. ▌
    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
29. ▌
    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.
    2 installs
30. ▌
    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
31. ▌
    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
32. ▌
    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
33. ▌
    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
34. ▌
    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
35. ▌
    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
36. ▌
    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
37. ▌
    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.
    2 installs
38. ▌
    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.
    2 installs
39. ▌
    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
40. ▌
    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.
    2 installs
41. ▌
    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
42. ▌
    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.
    1 install
43. ▌
    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
44. ▌
    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
45. ▌
    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
46. ▌
    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
47. ▌
    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
48. ▌
    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
49. ▌
    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
50. ▌
    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
51. ▌
    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
52. ▌
    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
53. ▌
    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.
    2 installs
54. ▌
    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.
    2 installs
55. ▌
    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.
    2 installs
56. ▌
    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
57. ▌
    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
58. ▌
    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
59. ▌
    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
60. ▌
    Metabolomics Data Format Validation · holobiomicslab

    Use when you have a tab-delimited metabolomics data file (raw measurement output from xcms, Sciex OS, or similar acquisition pipelines) and need to load it into mzQuality before building a SummarizedExperiment.
    0 installs
61. ▌
    Metabolomics Data Output Formatting · holobiomicslab

    Use when after completing feature annotation with the annotateRC function on LC–MS All-ion fragmentation (AIF) datasets, when you need to persist ranked metabolite candidates, matched ion spectra, and global summary tables to disk for archival, manual review, or integration into downstream.
    2 installs
62. ▌
    Mgf Metadata Completion From Smiles · holobiomicslab

    Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL import or polarity-based separation workflows.
    0 installs
63. ▌
    Mispicked Ion Detection And Merging · holobiomicslab

    Use when immediately after importing raw LC-MS peak tables (e.g., Progenesis format) and before applying group or replicability filters.
    0 installs
64. ▌
    Model Validation Regression Metrics · holobiomicslab

    Use when after training a deep-learning model on paired MS/MS spectra with annotated structural similarity labels, use this skill to assess whether predicted similarity scores correlate with ground-truth reference similarities on data the model has never seen.
    2 installs
65. ▌
    Molecular Family Graph Construction · holobiomicslab

    Use when you have downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING for GNPS1, or classical_networking_workflow/feature_based_molecular_networking_workflow for GNPS2) and need to construct a queryable molecular family graph.
    2 installs
66. ▌
    Molecular Property Data Structuring · holobiomicslab

    Use when you have a CSV file with rows of molecule definitions (chemical formulas, retention times, intensities, or other peak properties) and need to feed them into SMITER's simulation workflow.
    0 installs
67. ▌
    Ms2 Spectral Similarity Computation · holobiomicslab

    Use when you have two or more LC-MS/MS datasets (in mzML, mzXML, or MGF format) and need to quantify their overall spectral content similarity—typical scenarios include data quality control, species identification, molecular phylogenetics, or proteome comparison across samples, cell lines, or.
    0 installs
68. ▌
    Msms Spectrum Metadata Preservation · holobiomicslab

    Use when removing invalid or malformed entries (e.g., SMILES validation, format errors) from large spectral datasets (GNPS, MoNA, MTBLS1572, MassBank).
    2 installs
69. ▌
    Multi Criterion Scoring Integration · holobiomicslab

    Use when you have an LC-HRMS feature table (m/z, retention time, isotope ratios, fragmentation patterns) and a suspect compound database with reference properties (m/z, expected RT windows, theoretical isotope ratios, characteristic neutral losses), and you need to rank which features most likely.
    0 installs
70. ▌
    Multidimensional Feature Annotation · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic signatures to distinguish monoisotopic peaks from isotopologues, reduce feature redundancy, and support multi-dimensional.
    2 installs
71. ▌
    Multidimensional Ms Data Conversion · holobiomicslab

    Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments, and you need to: (1) store multidimensional spectra in a vendor-neutral, platform-agnostic format;
    0 installs
72. ▌
    Nearest Neighbor Index Construction · holobiomicslab

    Use when when you have millions of high-resolution MS/MS spectra converted to low-dimensional vectors (via feature hashing) and need to compute a sparse pairwise distance matrix for downstream density-based clustering.
    0 installs
73. ▌
    Network Based Functional Prediction · holobiomicslab

    Use when you have an untargeted metabolomics feature table with m/z values, retention times, intensity measurements, and p-values from statistical testing, but lack or wish to bypass metabolite identification.
    0 installs
74. ▌
    Nextflow Pipeline Configuration Hpc · holobiomicslab

    Use when your analysis target is an HPC environment (e.g., Slurm-managed cluster, university research computing center) where Singularity is available but Docker is restricted or unavailable; your workflow is already packaged in Docker but needs portability to HPC;
    0 installs
75. ▌
    Paired Omics Data Structure Mapping · holobiomicslab

    Use when when you have a paired omics project document (JSON format) that combines MS/MS mass spectrometry data with genome identifiers, biosynthetic gene cluster information, sample preparation, extraction method, and instrumentation metadata, and you need to verify it conforms to the platform's.
    0 installs
76. ▌
    Peak Area And Intensity Measurement · holobiomicslab

    Use when when you have vendor-format GC-CI-MS or LC-MS data from stable isotope labeling experiments, a target list of compounds with known monoisotopic m/z, retention time, and elemental formula, and you need per-isotopologue area and intensity values for quantification or downstream statistical.
    0 installs
77. ▌
    Per Sample Pass Fail Classification · holobiomicslab

    Use when after LC-MS data acquisition is complete (or during real-time monitoring) and you have loaded processed LC-MS data in mzML or vendor format and defined QC criteria (retention time windows, m/z tolerances, intensity thresholds) for your internal standards and target analytes.
    2 installs
78. ▌
    Permutation Test P Value Estimation · holobiomicslab

    Use when after computing Multi-Block Variable Importance in Projection (MB-VIP) scores on a fitted MB-PLS discriminant model, when you need to distinguish signal features from noise by establishing empirical significance thresholds rather than relying on parametric assumptions.
    2 installs
79. ▌
    Publication Image Asset Preparation · holobiomicslab

    Use when you have resolved a USI string pointing to a spectrum in a supported repository (GNPS, MassBank, MassIVE, MetaboLights, Metabolomics Workbench, ProteoXchange, or MS2LDA) and need to embed a publication-ready visualization or machine-readable reference that preserves the spectrum's.
    0 installs
80. ▌
    Retention Time Alignment Clustering · holobiomicslab

    Use when you have two or more nontargeted LCMS feature tables from the same analytical method and need to establish matched feature correspondences across datasets, then consolidate redundant features.
    2 installs
81. ▌
    Retention Time Alignment Correction · holobiomicslab

    Use when when processing a batch of centroided mzML or mzXML LC-MS raw data files where chromatographic retention times drift between sample acquisitions (common in large-scale metabolomics studies).
    0 installs
82. ▌
    Retention Time Alignment Validation · holobiomicslab

    Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
    0 installs
83. ▌
    Retention Time And Mz Weight Tuning · holobiomicslab

    Use when after anchor selection and RT mapping spline construction, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to tune the scoring metric that combines retention time, m/z, and cosine similarity components.
    0 installs
84. ▌
    Retention Time Clustering Alignment · holobiomicslab

    Use when you have extracted feature tables (via MS1 peak picking, MS2 recognition, or targeted list extraction) from two or more individual LC-MS samples and need to identify which features represent the same metabolite across samples before generating a unified, sample-aligned feature table for.
    0 installs
85. ▌
    Retention Time Co Elution Detection · holobiomicslab

    Use when after matching mass-to-charge ratios to a compound database (e.g., KEGG) and assigning adduct/fragment types, when you have an annotated feature table with retention times, m/z values, and intensity profiles across samples.
    2 installs
86. ▌
    Retention Time Intensity Tabulation · holobiomicslab

    Use when when you have a resolved mzML or mzXML spectrum file and need to visualize or analyze the temporal intensity profile of a specific analyte (defined by its m/z value).
    0 installs
87. ▌
    Retention Time Mz Intensity Mapping · holobiomicslab

    Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to rapidly detect instrumental drift, retention time shifts, or.
    2 installs
88. ▌
    Root Mean Squared Error Calculation · holobiomicslab

    Use when when you have paired predictions and ground-truth structural similarity labels (e.g., predicted Tanimoto scores from a neural network and reference Tanimoto scores from RDKit Daylight fingerprints) and need to report a single scalar metric of model prediction error across all pairs.
    2 installs
89. ▌
    S4 Class Definition And Inheritance · holobiomicslab

    Use when you are designing a new backend or data container that must integrate seamlessly with an existing Spectra-based workflow. You have identified a virtual parent class (e.
    1 install
90. ▌
    Sample Metadata Annotation For Lcms · holobiomicslab

    Use when when you have loaded centroided .mzML files into a Spectra object and plan to use TARDIS (tardisPeaks) with an MsExperiment object rather than file paths, and you need TARDIS to distinguish QC runs from sample runs for separate quality metric calculation, polarity filtering, and.
    0 installs
91. ▌
    Set Activity Prioritization Ranking · holobiomicslab

    Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
    2 installs
92. ▌
    Similarity Threshold Interpretation · holobiomicslab

    Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide which matches are sufficiently confident to include in per-motif annotation output.
    0 installs
93. ▌
    Singly Charged Ion Mass Calculation · holobiomicslab

    Use when you have detected monoisotopic features (m/z, drift_time, retention_time, intensity) from LC-IMS-MS/MS data and need to identify and cluster their C13 isotopologues for charge state z=+1.
    0 installs
94. ▌
    Singularity Container Backend Setup · holobiomicslab

    Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers Singularity for security and portability. You have .mzML or .
    0 installs
95. ▌
    Skyline Import Format Specification · holobiomicslab

    Use when you have computationally generated precursor m/z values, fragment m/z values, collision energies, and retention time predictions for a set of lipid targets (e.
    2 installs
96. ▌
    Sparse Distance Matrix Construction · holobiomicslab

    Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on low-dimensional spectrum vectors (via feature hashing), and you need to compute only the relevant pairwise distances between.
    0 installs
97. ▌
    Spectral Entropy Quality Assessment · holobiomicslab

    Use when after feature detection and alignment in untargeted MS data processing, when you need to filter or rank candidate metabolite annotations by spectral quality before committing to xenobiotic metabolite assignments. Use when combining fragmentation similarity scores (e.
    0 installs
98. ▌
    Spectral Feature Vector Aggregation · holobiomicslab

    Use when you have generated per-sample MS2 fingerprints (as spec2vec document representations counting MS2 peaks and neutral losses to precursor in each sample) and need to align them into a single matrix for downstream cross-sample comparison, filtering, or visualization (e.
    0 installs
99. ▌
    Spectral Library Record Structuring · holobiomicslab

    Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, molecular weight, annotation fields) that you need to bind together into a queryable spectral library record for local compound.
    2 installs
100. ▌
     Spectral Match Result Consolidation · holobiomicslab

     Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single coherent view.
     2 installs