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HolobiomicsLab

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1. ▌
   Probability Distribution Inverse Sampling · holobiomicslab

   Use when when you need to reduce a large compound set generated by reaction rule application while (1) retaining compounds ranked highest by Tanimoto similarity to target structures, (2) avoiding hard thresholds that may lose borderline-useful compounds, and (3) maintaining stochastic diversity to.
   0 installs
2. ▌
   Proteomics Normalization Method Selection · holobiomicslab

   Use when after loading peptide or protein-level quantification matrices with sample metadata into pmartR, and before downstream statistical analysis.
   0 installs
3. ▌
   Quality Control Metabolite Identification · holobiomicslab

   Use when you have loaded a metabolomics dataset with a metabolitedata dataframe containing annotation columns (e.
   0 installs
4. ▌
   Random Seed Reproducibility Documentation · holobiomicslab

   Use when you have generated multiple random partitions (e.g., 10-fold cross-validation splits) of a test set and need to deposit them in a shareable repository.
   0 installs
5. ▌
   Reaction Network Generation And Expansion · holobiomicslab

   Use when you have (1) a set of starting compounds as SMILES strings, (2) a collection of reaction rules in SMARTS format (e.g., from MetaCyc), and (3) a need to systematically predict all reachable products within a bounded number of generations.
   0 installs
6. ▌
   Regression Performance Metric Computation · holobiomicslab

   Use when after generating collision cross section predictions on a validation or test set using a trained graph neural network model, and you need to quantify prediction accuracy and compare against reported performance metrics in the literature or prior experimental runs.
   0 installs
7. ▌
   Signal Noise Ratio Improvement Validation · holobiomicslab

   Use when after executing multidimensional smoothing, spike removal, or saturation repair on raw TOF-MS or IM-MS data (.d format from Agilent MassHunter) to confirm that signal quality has improved.
   0 installs
8. ▌
   Spectral Clustering Membership Resolution · holobiomicslab

   Use when you have predicted BGC-spectrum link scores (e.g., IOKR or correlation values) for individual pairs and need to rank GCF-MF associations where each GCF contains multiple BGCs and each MF contains multiple spectra.
   0 installs
9. ▌
   Spectral Similarity Prediction Evaluation · holobiomicslab

   Use when use when the workflow requires spectral-similarity-prediction-evaluation.
   1 install
10. ▌
    Spectrum Fingerprint Contrastive Learning · holobiomicslab

    Use when when you have paired tandem MS spectra and corresponding molecular structures (SMILES or fingerprints), and you want to build a retrieval system for metabolite structure annotation that can rank candidate structures for novel spectra by embedding similarity rather than spectral matching.
    0 installs
11. ▌
    Structure Validation And Canonicalization · holobiomicslab

    Use when ingesting heterogeneous raw chemical structures from external datasets, publications, or user submissions into a retention time or molecular property prediction pipeline.
    0 installs
12. ▌
    Summarized Experiment Object Manipulation · holobiomicslab

    Use when when working with metabolomics, proteomics, or other high-throughput replicate experiments stored in Bioconductor SummarizedExperiment format (rows = features/metabolites, columns = samples/replicates), and you need to inspect raw feature dimensions, assess data completeness, or apply.
    1 install
13. ▌
    Unit Test Design For Analytical Chemistry · holobiomicslab

    Use when when implementing or modifying metabolomics feature detection pipelines (e.g., adduct detection, m/z matching, feature labeling) where correctness directly impacts downstream analysis.
    0 installs
14. ▌
    Version Specific Deployment Configuration · holobiomicslab

    Use when you have edited core R scripts (Modular.r, genEIC.r, MS1Spectragen.r, Stats.R) in the InnovativeOmics/Core-Match repository on GitHub and need to integrate those changes into a local LipidMatch-4.2 or FluoroMatch distribution.
    1 install
15. ▌
    Volcano Plot Construction From Omics Data · holobiomicslab

    Use when after statistical analysis (e.g., edgeR) has produced a results table containing lipid identities, fold-change values, and p-values for pairwise or multi-condition comparisons.
    2 installs
16. ▌
    Volcano Plot Interpretation Cancer Benign · holobiomicslab

    Use when when you have performed two-group differential expression analysis on preprocessed LipidomicsExperiment objects (with logged and normalized Area measurements) and need to identify and visualize lipid molecules with statistically significant differential regulation between cancer and benign.
    0 installs
17. ▌
    In Silico Biotransformation Prediction Workflow · holobiomicslab bundle

    Use when you have a parent structure (drug, natural product, xenobiotic) and untargeted LC-MS/MS data and want to find its biotransformation products — predict plausible metabolites in-silico by rule-based expansion (BioTransformer mammalian/gut-microbial/ environmental rules, EnviPath microbial degradation, or MINE/Pickaxe combinatorial reaction-network generation), filter candidates to those detectable in the experimental mass range, then screen and rank them against the observed LC-MS/MS features to annotate which predicted biotransformation products were actually seen.
    0 installs
18. ▌
    Design Matrix Construction Experiments · holobiomicslab

    Use when when you have microarray or RNA-seq expression data paired with phenotype/sample metadata describing experimental conditions, treatments, or group assignments, and you need to fit a linear model to test for differential expression across those conditions.
    0 installs
19. ▌
    Fold Change Interpretation And Ranking · holobiomicslab

    Use when after running DESeq() on a DESeqDataSet and extracting results with results(dds), you have a results table with log₂ fold changes, p-values, and adjusted p-values (padj). Use this skill when you need to (1) identify genes meeting a significance threshold (e.g., padj < 0.
    0 installs
20. ▌
    Oarfish Quantification Format Handling · holobiomicslab

    Use when you have long-read RNA-seq samples quantified by oarfish (output as quant.gz files) and need to extract transcript-level or gene-level abundance, count, and length matrices for downstream statistical analysis.
    0 installs
21. ▌
    Pathway Enrichment Statistical Ranking · holobiomicslab

    Use when you have a preranked gene list (e.g., genes sorted by log2 fold-change, t-statistic, or other continuous metric) and a collection of gene sets or biological pathways, and you need to determine which pathways are significantly over-represented among highly-ranked genes (positive enrichment).
    0 installs
22. ▌
    Psi Calculation From Isoform Abundance · holobiomicslab

    Use when you have transcript-level abundance estimates (from Salmon, kallisto, or similar) and a set of defined alternative splicing events (in ioe or ioi format), and you need to compute event-level or isoform-level inclusion ratios (PSI) to quantify splicing patterns across multiple samples or.
    0 installs
23. ▌
    Seed Representation Variant Comparison · holobiomicslab

    Use when you have observed mapping rate or quantification disagreement (e.g., >0.1% divergence in mapping rate or Pearson r < 0.
    0 installs
24. ▌
    Statistical Hypothesis Testing Rna Seq · holobiomicslab

    Use when you have RNA-seq count matrices (from alignment, transcript quantification, or HTSeq-count files) and need to test for differential expression between two or more conditions while controlling for batch effects or other covariates.
    0 installs
25. ▌
    Effective Mobility Calibration Single Marker · holobiomicslab

    Use when when you have CE-MS data with migration times that vary between runs due to electroosmotic flow drift, but you possess a reliable internal standard with a known effective mobility value.
    0 installs
26. ▌
    Floating Point Numerical Accuracy Assessment · holobiomicslab

    Use when when implementing or validating a lossy numeric codec for mass-spectrometry data (e.g., MSNumpressCoder in OpenMS). Specifically: after implementing both encoder and decoder, before shipping to production, or when comparing alternative compression schemes.
    2 installs
27. ▌
    Ms2 Spectral Library Matching Post Denoising · holobiomicslab

    Use when after frequency-based denoising of MS/MS spectra, when you need to validate that denoising improves metabolite identifications and quantify the trade-off between signal retention and annotation confidence. Specifically: (1) you have denoised MS/MS spectra from replicate measurements;
    0 installs
28. ▌
    Empirical Compound Construction And Grouping · holobiomicslab

    Use when after generating a feature table from mzML data (via Asari) and before performing MS1 or MS2 annotation.
    2 installs
29. ▌
    Gibbs Sampler Implementation And Convergence · holobiomicslab

    Use when your metabolomics dataset contains missing values below a known detection limit (left-censored MNAR data), and you need to recover these values while respecting the truncation constraint.
    0 installs
30. ▌
    Low Resolution Mass Spectra Library Matching · holobiomicslab

    Use when when processing low-resolution GC-MS data in NetCDF format where you have already performed retention-index calibration and peak deconvolution, and you need to assign compound identities by comparing experimental mass spectra to a curated reference library such as PNNLMetV20191015.MSL.
    0 installs
31. ▌
    Marker Feature Identification And Validation · holobiomicslab

    Use when when processing GC–MS or LC–MS data as m/z vs retention time chromatograms and you need to identify biomarker or chemical marker features without conventional peak picking, particularly when false positive detection rates from peak detection algorithms are problematic.
    0 installs
32. ▌
    Mass Calibration Against Reference Standards · holobiomicslab

    Use when when processing raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d) that requires assignment of molecular formulas to experimental m/z peaks. Calibration is necessary before SearchMolecularFormulas because uncalibrated mass error will cause false formula rejections or incorrect assignments.
    0 installs
33. ▌
    Molecular Fragment Prediction Interpretation · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision energy annotated) and a known molecular formula or candidate structure list, and you need to rank or discriminate between isomeric or isobaric candidates by comparing predicted fragment-level spectral patterns.
    0 installs
34. ▌
    Peak List Simulation With Controlled Effects · holobiomicslab

    Use when you need to validate batch correction or normalization algorithms, require ground-truth condition/batch effect annotations for method benchmarking, or want to systematically evaluate how different batch types (linear, random) and condition allocations affect feature recovery in metabolomic.
    0 installs
35. ▌
    Quality Control Metric Distribution Analysis · holobiomicslab

    Use when after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
    2 installs
36. ▌
    Two Dimensional Chromatography Data Handling · holobiomicslab

    Use when you have raw GCxGC-MS chromatogram data in NetCDF format from multiple samples (e.g., case and control groups) and need to prepare them for multivariate analysis such as multiway principal component analysis (MPCA).
    1 install
37. ▌
    Word Embedding Aggregation For Spectral Data · holobiomicslab

    Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular networking that correlate better with structural similarity than cosine-based methods.
    0 installs
38. ▌
    Word Embedding Based Spectrum Representation · holobiomicslab

    Use when when comparing large numbers of MS/MS spectra against spectral libraries or in molecular networking, particularly when molecules differ by multiple structural modifications and cosine-based scores produce excessive false positives.
    2 installs
39. ▌
    Adduct And Fragment Neutral Mass Calculation · holobiomicslab

    Use when you have an LC-MS peak-intensity matrix with observed m/z values (from negative or positive mode ionization) and need to map each peak to candidate neutral masses in KEGG. Use this skill when you have a curated Cpd.
    0 installs
40. ▌
    Background Distribution Threshold Derivation · holobiomicslab

    Use when when you have trained predictive models (e.g., neural networks) on paired microbiome-metabolome data and need to identify which metabolites are genuinely well-predicted above chance.
    0 installs
41. ▌
    Bag Of Fragments Representation Construction · holobiomicslab

    Use when after noise filtering and polarity selection of MS/MS spectra (from .mgf, .mzML, or .msp files), when you need to prepare spectra for unsupervised discovery of recurring fragmentation patterns without prior compound identification.
    2 installs
42. ▌
    Baseline Comparison Performance Benchmarking · holobiomicslab

    Use when when you have implemented a novel annotation algorithm or network and must verify it outperforms a simpler reference approach on held-out or independent spectral data. Specifically: (1) you have ground-truth annotations for a common test set;
    0 installs
43. ▌
    Bayesian Model Update With Experimental Data · holobiomicslab

    Use when you have completed one or more LC-MS gradient runs, extracted separation efficiency metrics from the resulting MS1 and MS2 spectra, and need to incorporate those real experimental observations into your Gaussian process model to improve the next gradient proposal.
    0 installs
44. ▌
    Class Imbalance Mitigation Via Normalization · holobiomicslab

    Use when preparing training batches for a neural network classifier on LCMS peak data where class counts are unequal (e.g., more high-quality peaks than low-quality peaks).
    0 installs
45. ▌
    Class Specific Modification Rule Application · holobiomicslab

    Use when after identifying putative BGC-encoded precursor peptides from a genome assembly via MetaMiner's BGC identifier, when preparing a RiPP structure database for downstream spectral matching via Dereplicator.
    0 installs
46. ▌
    Component Candidate Prioritization Filtering · holobiomicslab

    Use when after generateComponents has assigned candidate TP features to parent features and computed similarity metrics (spectrum similarity, fragment matches, neutral loss matches, retention time differences), use this skill to narrow the candidate pool to high-confidence parent–TP pairs that.
    2 installs
47. ▌
    Compound Internal Standard Ratio Calculation · holobiomicslab

    Use when immediately after loading metabolomics measurements into a SummarizedExperiment object, before any batch correction or quality filtering.
    0 installs
48. ▌
    Cross Dataset Feature Correspondence Mapping · holobiomicslab

    Use when you have two or more nontargeted LCMS feature tables from the same analytical method (same column, ionization mode, and acquisition parameters) and need to identify which features in one dataset correspond to features in another.
    0 installs
49. ▌
    Deep Learning Model Training With Monitoring · holobiomicslab

    Use when you have a pre-trained deep learning encoder (e.g., TCN spectrum encoder trained on a large corpus) and want to adapt it to a new task (e.
    0 installs
50. ▌
    Electronic Noise Generation Uniform Sampling · holobiomicslab

    Use when when you need to create synthetic noisy MS/MS spectra for benchmarking or validating denoising algorithms.
    0 installs
51. ▌
    Exploitation Exploration Trade Off Balancing · holobiomicslab

    Use when you are in the Bayesian optimization loop after fitting a Gaussian Process model to observed LC gradient runs, and you need to propose the next gradient to evaluate.
    0 installs
52. ▌
    Extracted Ion Chromatogram Eic Visualization · holobiomicslab

    Use when after running MS1 extraction and prescreening on mzML files with assigned adducts and tags, when you need to inspect detected compounds visually to verify peak shape, confirm retention time consistency across samples (e.
    0 installs
53. ▌
    Feature Annotation With Chemical Descriptors · holobiomicslab

    Use when you have a feature list (m/z values, retention times, and optionally molecular formulas or neutral masses) from LC- or GC-HRMS data and need to rapidly identify features matching characteristic chemical signatures (e.
    2 installs
54. ▌
    Feature Detection In Chromatographic Ms Data · holobiomicslab

    Use when you have vendor-independent centroided DDA mzML files from LC- or GC-HRMS and need to delineate chromatographic peaks across the mass-to-charge and retention-time dimensions before applying mass defect analysis, diagnostic fragment matching, or other prioritization rules.
    0 installs
55. ▌
    Feature Table Generation From Chromatography · holobiomicslab

    Use when after retention-time correction and alignment of centroided mzML or mzXML LC-MS files across a sample cohort.
    0 installs
56. ▌
    Feature Vector Similarity Search Preparation · holobiomicslab

    Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format and need to identify similar spectra for clustering, but exhaustive pairwise cosine-similarity computation would be prohibitively slow.
    2 installs
57. ▌
    File Format Identification Mass Spectrometry · holobiomicslab

    Use when you have raw MS data files from one or more instrument vendors (Agilent, Bruker, Thermo Fisher, or mzML-formatted) and need to convert them to a vendor-agnostic HDF5-based storage format for downstream software development, machine learning, or cross-platform data access.
    1 install
58. ▌
    Formula Transformer Architecture Application · holobiomicslab

    Use when you have tandem mass spectra (MS/MS) with unknown precursor formulas and need to rank chemical formula candidates conditioned on observed fragment m/z values and precursor mass. Use this skill when fragmentation tree computation (e.
    0 installs
59. ▌
    Fragmentation Pattern Extraction And Ranking · holobiomicslab

    Use when you have a collection of MS/MS spectra (≥2 spectra) and wish to identify fragmentation signatures common to subsets of those spectra.
    0 installs
60. ▌
    Gnn Architecture Design For Molecular Graphs · holobiomicslab

    Use when when you have preprocessed molecular graph data (node and edge tensors representing atoms and bonds) and need to train a regression model to predict a continuous molecular property (e.g., LC retention time).
    0 installs
61. ▌
    Graph Based Metabolite Similarity Assessment · holobiomicslab

    Use when you have a collection of MS/MS spectra (stored as Spectrum2 objects in an ms2Lib class) and need to identify which spectra share identical fragmentation patterns—particularly when coupled to a GNPS molecular network to focus on explaining network components (connected components, cliques.
    2 installs
62. ▌
    Ion Mobility Saturation Detection And Repair · holobiomicslab

    Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which distorts peak shape and abundance estimates across the m/z and drift-time axes.
    0 installs
63. ▌
    Lcims Msms Data Preprocessing Peak Detection · holobiomicslab

    Use when you have loaded mzML.gz or HDF5-formatted raw LC-IMS-MS/MS data and need to identify discrete peaks before feature alignment. Use it if your goal is to reduce noise, increase signal-to-noise ratio, and prepare multi-dimensional data for cross-sample feature matching and CCS calibration.
    2 installs
64. ▌
    Linear Regression Fitting For Chromatography · holobiomicslab

    Use when you have extracted retention times at peak maxima (rtFittedAPEX) from extracted-ion chromatograms (XICs) of known internal RT calibrants (e.
    0 installs
65. ▌
    Log Transform Normalization For Metabolomics · holobiomicslab

    Use when after chromatographic peak detection, fill-in of missing peaks, and retention-time-based grouping in LC-MS metabolomics workflows, apply log2 transformation when refining feature groups using correlation of abundances across samples.
    1 install
66. ▌
    Mass Spectrometry Data Constraint Validation · holobiomicslab

    Use when implementing replacement methods ($<-, [<-, spectraData<-, mz<-, intensity<-, peaksData<-) for a writable MsBackend subclass, or when modifying peak data in an existing backend.
    0 installs
67. ▌
    Mass Spectrometry Feature Extraction Ms1 Ms2 · holobiomicslab

    Use when when you have raw mzML files from LC-MS/MS metabolomics experiments and need to convert them into a structured feature table with accurate mass, retention time, and MS2 spectral data linked to a reference compound list.
    0 installs
68. ▌
    Mass Spectrometry Feature Table Construction · holobiomicslab

    Use when you have vendor-independent centroided mzML files from LC- or GC-HRMS data acquired in data-dependent acquisition (ddMS2) mode and need to extract detected features with m/z, retention time, and intensity attributes as input for non-target screening or PFAS prioritization workflows.
    2 installs
69. ▌
    Mass Spectrometry Quality Metrics Extraction · holobiomicslab

    Use when you have centroided .mzML LC–MS data, a validated target compound list with adjusted expected retention times (e.g., after a screening mode run), and need to quantify peak quality and integration reliability across multiple sample runs to support metabolomics or lipidomics workflows.
    2 installs
70. ▌
    Mass Spectrometry Reference Standard Mapping · holobiomicslab

    Use when you have acquired tunemix data (positive or negative ion mode, in .h5 format) with known CCS reference values and need to construct a calibration function that will later predict CCS values for unknown analytes.
    0 installs
71. ▌
    Mass Spectrometry Spectrum Quality Filtering · holobiomicslab

    Use when compiling or harmonizing MS/MS spectral libraries from multiple source repositories and you need to identify and remove spectra that fail quality thresholds (low resolution, precursor-fragment mass inconsistency, duplicate fragment patterns, noise-dominated, or missing critical metadata.
    0 installs
72. ▌
    Mass Spectrometry Transition Data Formatting · holobiomicslab

    Use when when you have raw mass spectrometry transition data from a triple-quadrupole or other tandem MS instrument and need to prepare it for suspect chemical screening using EISA-EXPOSOME, or when merging custom compound libraries into the T3DB format.
    0 installs
73. ▌
    Mass2motif Probability Distribution Learning · holobiomicslab

    Use when when you have preprocessed MS/MS spectra converted to a bag-of-fragments format (fragments and neutral losses extracted, noise filtered) and you seek to discover recurring fragmentation patterns without prior compound identification.
    0 installs
74. ▌
    Metabolite Feature Association Across Labels · holobiomicslab

    Use when after PuInc_seeker has identified putative incorporations (m/z features showing significant fold-change and p-value signals between labeled and unlabeled sample groups) and you need to assign base peaks—the most intense isotopologue signals—and validate isotope-pair mass gaps match.
    0 installs
75. ▌
    Metabolite Feature Correspondence Validation · holobiomicslab

    Use when after m/z grouping and pairwise alignment detection when you have a metabCombiner object containing candidate feature pair alignments and need to select a subset of mutually abundant, high-confidence anchors to anchor a nonlinear retention time mapping spline.
    0 installs
76. ▌
    Metabolite Structural Annotation Integration · holobiomicslab

    Use when after statistical analysis (e.g., MB-PLS with permutation testing) has identified a subset of significant LC-MS features (p < 0.05 or similar threshold) that require structural interpretation.
    0 installs
77. ▌
    Metabolomic Molecular Family Networking Gnps · holobiomicslab

    Use when when you have untargeted LC-MS/MS spectral data from microbial or environmental samples and aim to group related metabolites into molecular families for natural product discovery, especially when integrating with genomic biosynthetic gene cluster (BGC) annotations to link chemistry to.
    0 installs
78. ▌
    Metabolomics Feature Intensity Normalization · holobiomicslab

    Use when after peak detection and feature table construction (rows = features, columns = samples with intensity values) and before applying intensity-based filters (e.g., fold-change, phenotype score) or when preparing data for dashboard visualization.
    2 installs
79. ▌
    Metabolomics Quantification Table Processing · holobiomicslab

    Use when you have a quantification table (rows = metabolite features, columns = samples with abundance values), corresponding metadata table (sample annotations, groupings), and spectral data files, and you need to produce a unified JSON dashboard artifact that can be loaded into an interactive.
    0 installs
80. ▌
    Microbe Metabolite Prediction Neural Network · holobiomicslab

    Use when you have paired microbiome (16S or metagenomic taxonomy/functions at genus or finer level) and metabolome (LC-MS or similar profiled metabolites) data from the same samples and want to: (1) predict unobserved metabolite abundances from microbiome composition;
    0 installs
81. ▌
    Missing Value Imputation For Column Metadata · holobiomicslab

    Use when when preparing raw HPLC column parameter arrays for featurization into feature vectors for retention time prediction models. Specifically apply this skill when column metadata contains empty strings (indicating missing diameter or pH values) or non-standard string encodings (e.g., '2.
    0 installs
82. ▌
    Missing Value Replacement By Feature Minimum · holobiomicslab

    Use when after loading a feature table into memory when the table contains zero or missing values that represent true signal loss (not genuine absence), and you need to impute them before normalization, batch correction, or statistical analysis.
    0 installs
83. ▌
    Molecular Formula Computation From Structure · holobiomicslab

    Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings. The computed formulas are required before combining libraries or writing them to msp format for MS-DIAL compatibility.
    0 installs
84. ▌
    Classification Performance Metric Evaluation · holobiomicslab

    Use when after training multiple classifiers (traditional ML and deep learning) on a preprocessed metabolomics feature matrix with labeled samples, and you need to quantify and compare their predictive performance to select the model or ensemble for downstream analysis.
    2 installs
85. ▌
    Cross Member Metabolic Dependency Resolution · holobiomicslab

    Use when when you have consensus metabolic reconstructions for multiple community members (e.
    0 installs
86. ▌
    Cross Platform Reproducibility Configuration · holobiomicslab

    Use when when you have documented pinned package versions for a Python-based scientific implementation (e.g., from a README or project documentation) and need to distribute a reproducible computational environment to other users or CI/CD systems.
    0 installs
87. ▌
    Cyp450 Metabolite Prediction API Integration · holobiomicslab

    Use when you need to embed CYP450 metabolite prediction directly into a larger Java software pipeline or require dynamic toggling of the CypReact filter module based on experimental parameters.
    2 installs
88. ▌
    Data Format Conversion To Application Schema · holobiomicslab

    Use when you have m/z peak lists (positive and negative mode) and sample metadata from peak-picking software (e.g., XCMS with MetaboAnalyst export, MSnbase, or MetaboLights format) and need to load them into MetaboShiny for compound identification, statistical analysis, or machine learning.
    0 installs
89. ▌
    Dependency Resolution For Build Environments · holobiomicslab

    Use when when preparing to build LipidSpace or similar desktop/CLI applications from source across multiple target platforms (Windows 10, Ubuntu 22.04, macOS 12+ ARM64), or when encountering build failures due to missing headers, libraries, or incompatible tool versions.
    2 installs
90. ▌
    Deployment Mode Detection And Fallback Logic · holobiomicslab

    Use when building a Streamlit application that must support both cloud deployments (with Redis task queuing) and local/offline execution (with multiprocessing), and you need to automatically select the execution path without requiring separate code paths or manual configuration switches at runtime.
    1 install
91. ▌
    Diagnostic Plot Generation For Batch Effects · holobiomicslab

    Use when after loading log-transformed metabolomics feature abundance tables (samples as rows, metabolic features as columns) with batch identifiers, and before committing to a single batch-correction model.
    2 installs
92. ▌
    Directional Effect Assignment Across Studies · holobiomicslab

    Use when you have harmonized metabolite results from multiple independent studies, each with fold-change or trend classification data but no variance/standard deviation, and you need to produce a qualitative consensus on directionality for each compound.
    0 installs
93. ▌
    Duplicate Record Detection And Deduplication · holobiomicslab

    Use when when merging metabolomic data from multiple studies, you have compound identifiers in heterogeneous formats (chemical names, InChI, InChIKey, SMILES) and need to detect whether the same compound appears under different representations.
    0 installs
94. ▌
    Feature Matrix Preparation Mass Spectrometry · holobiomicslab

    Use when when you have raw mass spectrometry spectral data (peak intensities across m/z values) and need to feed it into MLP or GNN models for metabolite annotation, or when you need to generate LDA topic labels as auxiliary multi-task learning targets.
    0 installs
95. ▌
    Feature Metadata Alignment Across Dimensions · holobiomicslab

    Use when you have loaded a feature-by-pixel intensity matrix from an MSI HDF5 container and need to perform dimension-preserving corrections (e.
    2 installs
96. ▌
    Ft Icr Ms Data Processing Pipeline Execution · holobiomicslab

    Use when you have FT-ICR MS peak abundance data in Formularity .
    0 installs
97. ▌
    Gap Filling And Reaction Conflict Resolution · holobiomicslab

    Use when when merging multiple draft metabolic models (in JSON, XML, or SBML format) from community members or assembly variants and you encounter conflicting reaction annotations, missing metabolic pathways, or incomplete gap-filling decisions that require arbitration across inputs.
    0 installs
98. ▌
    Gene Protein Reaction Association Evaluation · holobiomicslab

    Use when you have a constraint-based metabolic model with embedded GPR rules (AND/OR associations between genes and reactions), paired with quantified gene-expression data (RNA-seq FPKM or read counts per cell line).
    1 install
99. ▌
    Imaging Mass Spectrometry Ion Identification · holobiomicslab

    Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for downstream spatial analysis (e.g., tissue region annotation or biomarker discovery).
    0 installs
100. ▌
     In Source Fragment Adduct Candidate Flagging · holobiomicslab

     Use when you have aligned, imputed time-resolved mass spectrometric data from direct-injection plasma ionization (e.g., DBDI, DESI) without chromatographic separation, and you suspect multiple m/z features belong to the same neutral analyte as in-source fragments or oxygen-bound adducts.
     0 installs