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HolobiomicsLab

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1. ▌
   Multivariate Lipid Metabolite Analysis · holobiomicslab

   Use when you have integrated, normalized lipidomic and metabolomic feature tables from the Multi-ABLE method or similar concurrent multiomics workflows, with matched sample phenotypes (e.
   1 install
2. ▌
   Mzml File Random Access By Spectrum Id · holobiomicslab

   Use when you have a compressed mzML file (mzML.gz or indexed gzip format) and need to extract a single spectrum or a small subset of spectra by their known numeric identifiers, rather than iterating through the entire file sequentially.
   0 installs
3. ▌
   Node Coordinate Assignment Computation · holobiomicslab

   Use when you have constructed a network object (edges and nodes) in MetaNet and need to compute spatial coordinates for visualization. Use this skill when preparing networks for static plots (e.
   0 installs
4. ▌
   Notebook Execution And Reproducibility · holobiomicslab

   Use when when you have access to a peer-reviewed manuscript with an accompanying interactive notebook and public data repository, and you need to verify that the published figures can be regenerated from the original data through the documented processing pipeline, or when you want to reuse the.
   0 installs
5. ▌
   Object Oriented Class Hierarchy Design · holobiomicslab

   Use when when you need to create a plotting or visualization framework that must support multiple plot kinds (spectrum, chromatogram, mobilogram, peakmap) each backed by multiple rendering engines (matplotlib, bokeh, plotly), and you want to avoid combinatorial explosion of concrete classes while.
   0 installs
6. ▌
   Open Modification Mass Shift Detection · holobiomicslab

   Use when query mass spectra do not confidently match unmodified peptides in the spectral library, or when you suspect the sample contains unknown or unexpected post-translational modifications.
   0 installs
7. ▌
   Outlier Detection Removal Metabolomics · holobiomicslab

   Use when after kNN imputation of metabolite measurements but before variance-stabilizing normalization, when you have a MultiAssayExperiment object with potentially problematic samples.
   2 installs
8. ▌
   Outlier Sample Removal Quality Control · holobiomicslab

   Use when visual inspection (PCA plots, TIC plots, or boxplots) reveals samples with aberrant lipid abundance profiles, or when domain knowledge suggests specific samples are technical replicates, biological outliers, or failed QC metrics.
   2 installs
9. ▌
   Oxidized Lipid Nomenclature Conversion · holobiomicslab

   Use when you have lipid identifiers from multiple sources (e.
   0 installs
10. ▌
    Package Version Pinning And Lock Files · holobiomicslab

    Use when when a multi-language analysis pipeline (R + Python) has been validated and you need to document the exact dependency tree so that other researchers or systems can recreate the same computational environment.
    0 installs
11. ▌
    Pathway Metabolite Mapping Integration · holobiomicslab

    Use when when you have metabolite-level summary statistics (p-values, log2 fold changes) from differential analysis and need to test whether specific metabolic pathways are significantly enriched in your dataset.
    0 installs
12. ▌
    Percentile Threshold Determination Scc · holobiomicslab

    Use when when you have paired microbiome and metabolome data and need to identify which metabolites are significantly well-predicted by microbes, but the relationship between prediction accuracy and biological relevance is unknown or varies across datasets (e.g., IBD PRISM: 0.136;
    0 installs
13. ▌
    Pixel Binning And Spatial Registration · holobiomicslab

    Use when you have raw line-scan mass spectrometry imaging data from nano-DESI or other line-scan acquisition modes and need to produce a georeferenced 3D pixel array.
    1 install
14. ▌
    Pytorch Distributed Training Execution · holobiomicslab

    Use when when you have a pre-trained GNN model checkpoint and need to apply transfer learning to a new chromatography or molecular property prediction dataset (e.g., Eawag_XBridgeC18_364.xlsx) by fine-tuning the model weights on domain-specific examples without retraining from scratch.
    0 installs
15. ▌
    Pytorch Or Tensorflow Model Definition · holobiomicslab

    Use when when you have molecular structure inputs (SMILES strings, molecular graphs, or feature vectors) and need to predict a continuous molecular property (e.g., CCS values, retention time, ionization efficiency).
    0 installs
16. ▌
    Quality Control Threshold Optimization · holobiomicslab

    Use when when you have extracted a peak feature table (CSV or tabular format) with mass-to-charge ratios, retention times, and intensity values across multiple samples, and you need to distinguish genuine differential metabolic signals from instrumental noise or low-abundance background before.
    2 installs
17. ▌
    R Environment Dependency Specification · holobiomicslab

    Use when when developing or reproducing an R-based analysis that integrates Python dependencies (e.g., via reticulate), particularly in contexts where deep learning (keras) or complex machine-learning frameworks (caret) depend on specific numpy versions or Python minor releases.
    0 installs
18. ▌
    Reference Feature Combination Strategy · holobiomicslab

    Use when when you have isolated, high-confidence reference chromatographic peaks (ground-truth) from reference LC-HRMS chromatograms that have been matched across multiple samples, and you need to train a CNN model to detect peaks in new chromatograms but lack sufficient labelled instances.
    2 installs
19. ▌
    Round Trip Data Integrity Verification · holobiomicslab

    Use when you have implemented or are validating a reader/writer library for a mass spectrometry file format (such as mzPeak, mzML, or similar), and need to confirm that data parsed from disk can be written back without loss of information.
    0 installs
20. ▌
    Ruv Iii Implementation In Metabolomics · holobiomicslab

    Use when you have metabolomics data distributed across multiple experimental batches, each batch contains sample replicates (the same sample measured multiple times within and across batches), PCA or visual inspection reveals systematic batch effects, and you need to distinguish unwanted variation.
    0 installs
21. ▌
    Script Repository Workflow Integration · holobiomicslab

    Use when you have cloned or downloaded scripts from a development repository (e.g., github.com/InnovativeOmics/Core-Match) and need to incorporate edits into an installed distribution copy of LipidMatch-4.2 or FluoroMatch.
    0 installs
22. ▌
    Signal Processing Prominence Filtering · holobiomicslab

    Use when when you have a 1D intensity array from a mass spectrum (m/z or retention time dimension) and need to identify and rank local maxima that are biochemically meaningful rather than noise-driven.
    0 installs
23. ▌
    Spatial Coordinate Metadata Extraction · holobiomicslab

    Use when you have raw imzML files (paired with .ibd binary data) from imaging mass spectrometry experiments and need to construct an AnnData object for spatial metabolomics analysis.
    0 installs
24. ▌
    Spatial Data Integration Preprocessing · holobiomicslab

    Use when when you have paired spatial transcriptome and metabolome datasets (in .h5ad or matrix format) with spatial location information, and you need to establish correspondence between features across modalities before performing spatial morphological alignment.
    0 installs
25. ▌
    Spectral Data Preprocessing Lipidomics · holobiomicslab

    Use when you have raw lipidomic and metabolomic spectral data files from a Multi-ABLE barocycler-based concurrent multiomics experiment and need to normalize ion intensities, align retention times and m/z values across samples, and remove noise or low-signal features before statistical comparison.
    2 installs
26. ▌
    Spectral Peak Picking Derivative Based · holobiomicslab

    Use when you have preprocessed MSImagingArrays objects (normalized via normalize(), smoothed via smooth(), and baseline-reduced via reduceBaseline()) and need to identify discrete peaks across all spectra in a mass spectrometry imaging dataset.
    0 installs
27. ▌
    Spectral Search Performance Evaluation · holobiomicslab

    Use when when you have implemented or obtained a spectral library search tool (e.
    0 installs
28. ▌
    Spectral Similarity Metric Computation · holobiomicslab

    Use when after clustering peak networks from INADEQUATE spectra and before filtering matches to retain high-confidence metabolite assignments.
    0 installs
29. ▌
    Spectrum Object Instantiation From XML · holobiomicslab

    Use when when you have parsed XML elements from an mzML or mzML.gz file (via ElementTree or a similar XML parser) and need to convert those elements into pymzML Spectrum objects for spectrum-level operations such as random access, spectral comparison, or data extraction.
    0 installs
30. ▌
    Stable Isotope Labeling Quantification · holobiomicslab

    Use when you have centroided high-resolution Orbitrap mzML files from stable isotope labeling experiments and need to measure isotopologue abundances (M+0, M+1, M+2, etc.) for a defined list of target compounds with 13C or other isotopic labels.
    0 installs
31. ▌
    Statistical Hypothesis Testing Biology · holobiomicslab

    Use when you have a metabolite abundance table (rows=metabolites, columns=samples) from Metabolomics Workbench format and need to test whether specific metabolites or metabolite classes are significantly enriched in particular biological pathways or conditions, beyond what would be expected by.
    0 installs
32. ▌
    Statistical Model Selection Assessment · holobiomicslab

    Use when after loading preprocessed metabolomics data (log-transformed feature abundance matrices with samples as rows, features as columns, and batch annotations) but before applying batch-effect correction.
    0 installs
33. ▌
    Statistical Threshold Parameterization · holobiomicslab

    Use when when you have computed fold-change and p-value statistics from differential expression analysis and need to partition the results into significant and non-significant regions for visualization or downstream filtering.
    0 installs
34. ▌
    Steady State Solution Uniform Sampling · holobiomicslab

    Use when when you have a constraint-based metabolic model with cell-specific flux boundaries (e.
    0 installs
35. ▌
    Structural Distance Metric Computation · holobiomicslab

    Use when you have two or more lipid structures (in standardized lipid nomenclature or chemical format) and need to: (1) quantify structural dissimilarity for hierarchical clustering of lipidomes; (2) identify lipids responsible for shaping lipidome composition via distance-based feature selection;
    1 install
36. ▌
    Structure Database Candidate Retrieval · holobiomicslab

    Use when you have a mass spectrum of an unknown metabolite with a known or inferred precursor m/z, you have run a deep-learning semantic similarity model (e.
    0 installs
37. ▌
    Structure Matching Via Smarts Patterns · holobiomicslab

    Use when when you need to identify compounds matching specific structural motifs or apply reaction transformation rules to a set of molecules.
    0 installs
38. ▌
    Synthetic Training Instance Generation · holobiomicslab

    Use when when you have a small set of matched reference features (isolated, high-quality chromatographic peaks from reference chromatograms that have been aligned to a ground-truth reference list) and need to train a CNN model for peak detection in LC-HRMS profile mode data.
    0 installs
39. ▌
    Tic Peak Identification Sliding Window · holobiomicslab

    Use when you have loaded raw mass spectrometry data (mzML, mzXML, or CDF format) into AutoTuner and need to identify peak regions in the TIC trace prior to extracted ion chromatogram (EIC) analysis.
    0 installs
40. ▌
    Truncated Normal Distribution Sampling · holobiomicslab

    Use when imputing left-censored missing values in metabolomics data where missingness is caused by values falling below the limit of quantification (LOQ) or limit of detection (LOD). The input matrix should have missing values flagged as NA, with a defined upper bound (e.
    0 installs
41. ▌
    Unit Test Validation For Preprocessing · holobiomicslab

    Use when after implementing or modifying basic peak filtering operations (e.g., low-intensity peak removal, intensity normalization) on mass spectrometry spectral data in supported formats (mzML, mzXML, msp, MGF, JSON).
    0 installs
42. ▌
    Windows Desktop Application Deployment · holobiomicslab

    Use when when you have cloned a .NET Framework or .NET Core WPF project from a GitHub repository and need to compile it into an executable binary for Windows deployment. Specifically, when the project uses ReactiveExtensions/ReactiveProperty packages, declares a .NET Framework 4.7.2 or .
    0 installs
43. ▌
    Paired Omics Bgc Metabolite Linking Workflow · holobiomicslab bundle

    Use when you have paired genomic and metabolomic data from the same microbial strains and want to link biosynthetic gene clusters (BGCs) to the metabolite features they plausibly encode — mine BGCs from assembled genomes with antiSMASH, tokenize BGC domains with iPRESTO/Pfam and cluster them into gene cluster families (GCFs) with BiG-SCAPE, build an MS/MS molecular network from paired LC-MS/MS data with GNPS to obtain molecular families (MFs), then score GCF-MF co-occurrence across strains (NPLinker-style Metcalf/hypergeometric scoring) to produce a ranked table of candidate BGC-metabolite links for natural-product discovery.
    2 installs
44. ▌
    Sirius Denovo Structure Elucidation Workflow · holobiomicslab bundle

    Use when you have MS/MS for unknown features (a SIRIUS-flavour mgf / .ms) and want de novo annotation without a spectral match — molecular formula (SIRIUS+ZODIAC), structure (CSI:FingerID + COSMIC), compound class (CANOPUS), optionally against a custom database, filtered by confidence. Library-FREE by design.
    0 installs
45. ▌
    Anndata Object Structure Validation · holobiomicslab

    Use when after applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to a Dask-backed AnnData object, or when performing any operation that could alter matrix dimensions, data types, or backing storage (dense, sparse, or lazy).
    0 installs
46. ▌
    Empirical Bayes Variance Estimation · holobiomicslab

    Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute stable variance estimates and differential expression statistics despite having few biological replicates or small numbers of arrays.
    0 installs
47. ▌
    Gene Expression Ranking Preparation · holobiomicslab

    Use when you have a gene expression matrix (RNA-seq counts, microarray intensities, or normalized expression values) and need to perform gene set enrichment analysis on preranked gene lists. Use this skill when you want to rank genes by a univariate statistic (e.
    0 installs
48. ▌
    Gene Expression Statistical Testing · holobiomicslab

    Use when you have fit a linear model to normalized gene expression data (microarray intensities or RNA-seq counts) and need to test for differential expression across experimental conditions or contrasts.
    2 installs
49. ▌
    Genomic Database Identifier Mapping · holobiomicslab

    Use when your gene expression matrix or pathway collection uses identifier formats incompatible with your enrichment analysis tool (e.g., gene symbols vs. Entrez IDs), or you need to reconcile gene sets from multiple sources (Reactome, KEGG) that employ different naming conventions.
    2 installs
50. ▌
    Neighborhood Enrichment Computation · holobiomicslab

    Use when when you have spatial transcriptomics or imaging data (e.
    1 install
51. ▌
    Spatial Enrichment Score Validation · holobiomicslab

    Use when after executing a spatial statistics function (e.g., squidpy.gr.sepal) on a spatial transcriptomics dataset in AnnData format, and before using the computed rankings or enrichment scores in downstream analysis.
    0 installs
52. ▌
    Spatial Neighbor Graph Construction · holobiomicslab

    Use when when you have spatial molecular data (e.g., Visium, imaging-based cytometry) stored in an AnnData object with coordinate information in .
    0 installs
53. ▌
    Chemical Annotation Confidence Assessment · holobiomicslab

    Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical explorer visualization, sample filtering, or comparative metabolomics).
    0 installs
54. ▌
    Extracted Ion Electropherogram Generation · holobiomicslab

    Use when you have CE-MS raw data (mzML or netCDF format) containing a target compound of known m/z ratio and you need to resolve it as a distinct peak on the effective mobility scale rather than migration time scale.
    0 installs
55. ▌
    Metabolomics Peak Detection Configuration · holobiomicslab

    Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram alignment.
    0 installs
56. ▌
    Pca Dimensionality Reduction Unsupervised · holobiomicslab

    Use when you have a feature-by-sample matrix (rows = annotated chemical features such as m/z, retention time, GNPS spectral library matches;
    2 installs
57. ▌
    Vendor File Format Specification Handling · holobiomicslab

    Use when you have a raw MSI data file from an unknown or mixed set of vendors and need to apply format-specific data extraction, spectral parsing, or image reconstruction. The file extension alone must determine which parsing module (MSIGen.raw, MSIGen.D, MSIGen.baf, MSIGen.tdf, MSIGen.
    0 installs
58. ▌
    Chemical Structure Fingerprint Comparison · holobiomicslab

    Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method actually reflects true chemical structural similarity.
    2 installs
59. ▌
    Injection Order Assignment And Scheduling · holobiomicslab

    Use when designing multi-batch LC/GC-MS experiments where you need to control for batch effects (e.g., instrument drift, reagent lot variation) and have identified both a balance dimension (e.g., sample group, treatment condition) and a randomization dimension (e.
    0 installs
60. ▌
    Ion Mobility Spectrometry Peak Extraction · holobiomicslab

    Use when after peaks have been detected in aligned GCIMS samples using findPeaks with CWT parameters and peaks have been clustered across samples, and you need to integrate peak signals into a matrix format where each entry represents the intensity of a peak cluster in a specific sample for.
    0 installs
61. ▌
    Ionisation Method Hardware Correspondence · 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.
    0 installs
62. ▌
    Mass Spectrometry M Z Accuracy Assessment · holobiomicslab

    Use when when you have detected peaks in a direct injection FTICR-MS mzML file (or similar high-resolution MS format) and need to assess whether m/z measurements are accurate and consistent across the m/z range.
    1 install
63. ▌
    Microbiome Metabolome Prediction Modeling · holobiomicslab

    Use when you have paired microbiome (16S rRNA, metagenomic) and metabolomic (LC-MS, GC-MS) abundance tables from the same biosamples, and you want to predict which metabolites are recoverable from microbial composition alone and identify groups of microbes and metabolites with correlated.
    2 installs
64. ▌
    Molecular Structure Generation Evaluation · holobiomicslab

    Use when you have access to pre-trained MSGO model weights (PFAS or lipid variants) and a set of 300+ real mass spectra (LC–QTOF or similar), and need to verify whether the model can generate correct molecular structures for unknown chemicals.
    0 installs
65. ▌
    Parallel Computing Workflow Orchestration · holobiomicslab

    Use when when compiling EI or MS/MS spectral libraries from multiple gigabyte-scale sources (e.
    0 installs
66. ▌
    Retention Index Calibration And Alignment · holobiomicslab

    Use when processing raw GC-MS data in NetCDF format where peaks have been detected but lack standardized retention indices.
    1 install
67. ▌
    Software Feature Inventory And Comparison · holobiomicslab

    Use when you need to assess whether a newly developed FT-ICR MS pipeline (e.
    0 installs
68. ▌
    Attention Mechanism For Spectral Decoding · holobiomicslab

    Use when when you have pretrained encoder-produced embeddings from MS/MS spectra and need to decode them into canonical SMILES strings representing molecular structures.
    2 installs
69. ▌
    Automated Feature Extraction From Spectra · holobiomicslab

    Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication, sample scoring, or comparative profiling without manual inspection.
    0 installs
70. ▌
    Automated Metabolite Property Computation · holobiomicslab

    Use when you have ion mobility-mass spectrometry data (raw drift times, m/z values, and feature intensities) from DTIMS-MS or SLIM-based IMS-MS platforms and need to compute collision cross section values using a calibration standard (e.g., Agilent tune-mix).
    0 installs
71. ▌
    Batch Construction Parameter Optimization · holobiomicslab

    Use when preparing labeled LC-MS peak data for neural network training and you need to decide whether class imbalance in your dataset should be preserved or corrected in batch construction. Use it particularly when your annotated peak dataset has unequal class distributions (e.
    0 installs
72. ▌
    Batch Effect Detection And Quantification · holobiomicslab

    Use when after merging feature tables from multiple LC-MS/MS analytical runs or sample cohorts processed in separate batches, and before applying batch correction.
    0 installs
73. ▌
    Bayesian Annotation Probability Inference · holobiomicslab

    Use when you have LC/MS feature data (m/z, retention time, intensity) and need to assign metabolite annotations with confidence scores rather than binary peak-to-compound matches.
    0 installs
74. ▌
    Bgc Spectrum Ranking By Kernel Similarity · holobiomicslab

    Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or predicted structures (e.
    0 installs
75. ▌
    Candidate Structure Ranking From Spectrum · holobiomicslab

    Use when you have an experimental tandem mass spectrum (m/z and intensity pairs) and a known or suspected chemical formula, and you need to narrow down the identity of an unknown compound from a large candidate pool (e.g., all PubChem entries matching that formula).
    2 installs
76. ▌
    Charge State Determination And Assignment · holobiomicslab

    Use when when analyzing high-resolution mass spectrometry data from natural-abundance or labeled peptides where multiple charge states (+2, +3, +4, etc.) may be present within the same m/z isolation window (e.g., 880–890 m/z).
    0 installs
77. ▌
    Chemical Classification Scheme Validation · holobiomicslab

    Use when you have structural annotations from in silico tools (SIRIUS, CANOPUS) and spectral library matches from GNPS, but need to (1) reconcile conflicting or incomplete ClassyFire ontology assignments, or (2) substitute NPClassifier taxonomy when ClassyFire ontology data is unavailable from GNPS.
    0 installs
78. ▌
    Chemical Formula Extraction And Filtering · holobiomicslab

    Use when when you have a loaded metabolite database (e.g., hmdb_compounds.p pickle file) and need to constrain the chemical space to a specific instrumental m/z range (e.
    0 installs
79. ▌
    Chemical Structure Annotation Oracle Mode · holobiomicslab

    Use when you have a known compound structure with validated MS/MS spectrum and a structural analog (modified version) with its own MS/MS spectrum, and you need to assess whether a modification site prediction method correctly identifies which atoms were altered.
    0 installs
80. ▌
    Chemical Structure Annotation Preparation · holobiomicslab

    Use when you have acquired composite fragmentation spectra from DIA experiments (MS^E, AIF, or SWATH-MS) that have been deconvoluted by IDSL.CSA, and you need to export the resolved spectra in a format suitable for chemical structure identification against reference libraries or spectral databases.
    0 installs
81. ▌
    Chemical Structure Descriptor Computation · holobiomicslab

    Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or molecular geometry files, and you need to train or apply a machine-learning model to predict an instrument-dependent.
    0 installs
82. ▌
    Chimeric Spectrum Detection And Filtering · holobiomicslab

    Use when you have acquired LC-MS/MS data in Data-Dependent Acquisition (DDA) mode for untargeted metabolomics and suspect contamination from chimeric (co-fragmented) MS/MS spectra.
    0 installs
83. ▌
    Chromatogram Extraction And Visualization · holobiomicslab

    Use when you have sqMass files containing pre-extracted transition group chromatograms from DIA-MS experiments and need to interactively visualize individual peptide precursor chromatograms, inspect peak quality via Q-values (typically 1% FDR cutoff), and overlay peak boundaries or apply on-the-fly.
    0 installs
84. ▌
    Comparative Machine Learning Benchmarking · holobiomicslab

    Use when you have developed a new machine learning model for predicting metabolomic profiles from microbiome data and need to quantify its performance improvement over existing methods.
    0 installs
85. ▌
    Compound Annotation Confidence Assessment · holobiomicslab

    Use when you have MS/MS spectra matched to a reference library via both identity search (exact or high-similarity matches) and fuzzy/analog search (structurally related compounds with similar fragmentation), and you need to prioritize which annotations to trust for downstream reporting, validation.
    0 installs
86. ▌
    Data Visualization From Tabulated Results · holobiomicslab

    Use when after executing a MassQL query that returns a tabulated results DataFrame (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to produce visual summaries suitable for publication, presentation, or exploratory analysis.
    0 installs
87. ▌
    Decision Tree Training And Interpretation · holobiomicslab

    Use when you have tandem mass spectra data and need to predict a discrete molecular property (e.g., presence/absence of a sulfo group) while maintaining full interpretability of the decision logic.
    0 installs
88. ▌
    Extracellular Flux Constraint Integration · holobiomicslab

    Use when you have constraint-based metabolic models of multiple cell lines, experimental measurements of extracellular metabolite concentrations at two timepoints (e.
    2 installs
89. ▌
    Feature Intensity Recovery Across Samples · holobiomicslab

    Use when after sample alignment in untargeted LC-MS workflows, when the aligned feature table contains missing (NA or zero) intensity entries for features that are detected in some samples but fall below the instrument detection limit or are absent in others.
    0 installs
90. ▌
    Feature List Harmonization Across Methods · holobiomicslab

    Use when you have feature lists in CSV format originating from different acquisition methods (e.
    0 installs
91. ▌
    Feature To Metabolite Network Propagation · holobiomicslab

    Use when you have an untargeted metabolomics feature table (m/z, retention time, p-value from statistical test) but lack comprehensive metabolite identifications or MS/MS annotations.
    0 installs
92. ▌
    Fragment Frequency Threshold Optimization · holobiomicslab

    Use when you have replicate MS/MS spectra with labeled fragment recurrence frequencies and need to select an optimal frequency threshold (beyond the default 0.1) that maximizes spectral quality metrics while minimizing false positive noise.
    0 installs
93. ▌
    Fragment Ion Mass Matching With Tolerance · holobiomicslab

    Use when denoising MS/MS spectra and you have: (1) a precursor ion with measured m/z and known molecular formula (from SMILES or direct formula input), (2) an adduct type ([M+H]+, [M+Na]+, etc.), (3) a list of fragment ions with observed m/z values, and (4) a need to distinguish chemically valid.
    2 installs
94. ▌
    Fragment Neutral Loss Annotation Matching · holobiomicslab

    Use when after generateComponents with algorithm='tp' has tentatively paired parent features with TP candidates based on retention time and spectrum similarity, and when formula annotations are available for both parents and candidates.
    0 installs
95. ▌
    Fragment Recurrence Frequency Calculation · holobiomicslab

    Use when after extracting and grouping fragments from top x% TIC-filtered replicate spectra for a given feature, to quantify which fragments consistently appear across replicates. Use this when you have multiple MS/MS spectra for the same precursor (e.
    0 installs
96. ▌
    Functional Module Inference From Networks · holobiomicslab

    Use when you have an untargeted metabolomics feature table (m/z and retention time columns) and a statistical test result (p-value) per feature, but lack confident metabolite identifications.
    0 installs
97. ▌
    Gaussian Process Regression Model Fitting · holobiomicslab

    Use when after you have accumulated experimental MS data from ≥2 LC gradient trials, extracted separation efficiency metrics (retention time spacing) from each trial, and encoded each gradient as a feature vector.
    0 installs
98. ▌
    Genome Cluster Family Scoring Computation · holobiomicslab

    Use when you have pre-processed AntiSMASH BGC annotations (optionally clustered via BigScape into GCFs), GNPS molecular networking spectra and molecular families, and you seek to computationally link biosynthetic gene clusters to observed metabolites without manual curation.
    0 installs
99. ▌
    Hierarchical Spectrum Object Construction · holobiomicslab

    Use when immediately after parsing and validating raw LC-MS/MS data files (mzML, mzXML, or vendor formats) when you need to prepare spectral data for fragmentation tree computation, isotope pattern analysis, or molecular formula ranking within the SIRIUS framework.
    0 installs
100. ▌
     In Memory Optimization For Large Datasets · holobiomicslab

     Use when you are repeatedly querying or iterating over multidimensional MS data stored in MZA HDF5 format (retention time, drift time, m/z dimensions) and profiling shows that repeated disk I/O for the same metadata or scan ranges dominates runtime.
     0 installs