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HolobiomicsLab

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1. ▌
   Cosine Distance Clustering Of Genomic Clusters · holobiomicslab

   Use when you have pre-computed BGC feature vectors (e.g., from HMM domain hits extracted via antiSMASH or BiG-SLiCE) and need to group similar BGCs into families for comparative genomics, functional prediction, or novelty assessment.
   0 installs
2. ▌
   Docker Container Orchestration For Ml Services · holobiomicslab

   Use when you have trained or pre-trained ML models (Keras, TensorFlow) that need to be exposed as HTTP endpoints for programmatic classification or inference, require reproducible deployment across environments, or need to coordinate multiple services (e.
   0 installs
3. ▌
   Eigenmetabolite Direction Of Effect Validation · holobiomicslab

   Use when after computing module significance (MS) statistics for metabolic modules against a sample grouping factor (e.g., tumor vs. normal), and detecting a statistically significant module association (p < 0.05).
   2 installs
4. ▌
   Environmental Microbial Degradation Prediction · holobiomicslab

   Use when you have a small-molecule structure (in SMILES, MOL, or SDF format) and need to predict how soil or aquatic microbiota will degrade or biotransform it, particularly for environmental risk assessment, metabolite identification in biodegradation studies, or tracing microbial transformation.
   0 installs
5. ▌
   Experiment Design Specification For Clustering · holobiomicslab

   Use when you have a CSV feature table from XCMS or other MS feature detection tools and are about to run RAMClustR clustering, but need to encode which samples are QC replicates, which batch they belong to, and their run order.
   0 installs
6. ▌
   Feature Property Refinement From Training Data · holobiomicslab

   Use when you have a set of training LC-HRMS chromatograms (retention time × m/z matrix format) and a manually curated reference list of isolated single chromatographic peaks, and you need to update the reference peak properties (retention time, m/z, peak shape) to match the actual peak signatures.
   2 installs
7. ▌
   Feature Redundancy Reduction With Ion Identity · holobiomicslab

   Use when when processing MZmine2/MZmine3 peak tables from LC–MS metabolomics data where you observe inflated feature counts due to multiple ionization states, isotopic satellites, and neutral losses of the same parent compound, particularly before computing extract-level metrics (e.
   2 installs
8. ▌
   Isotopologue Quantification Data Normalization · holobiomicslab

   Use when after autoQ has extracted and integrated peak areas for all isotopologues of your targeted compounds.
   2 installs
9. ▌
   Log Fold Change Computation And Interpretation · holobiomicslab

   Use when when you have completed differential expression analysis (via edgeR, DESeq2, or RankProduct) on preprocessed count matrices or abundance tables and need to quantify and interpret the magnitude of expression changes between conditions.
   0 installs
10. ▌
    Marker Feature Visualization Retention Time Mz · holobiomicslab

    Use when after NPFimg's automated detection algorithm has identified marker features from a two-dimensional MS map (m/z vs retention time), especially when you need to validate feature positions, inspect co-localization patterns, or communicate results to stakeholders.
    0 installs
11. ▌
    Mass Difference Transformation Pair Derivation · holobiomicslab

    Use when you have a formula-assigned DOM dataset from FT-ICR MS (or other mass spectrometry with compound annotations) and need to characterize how molecular transformations occur across the sample—e.
    0 installs
12. ▌
    Mass Spectrometry Feature Detection Validation · holobiomicslab

    Use when when you have processed LC-HRMS mzML files through a non-targeted preprocessing tool (e.g., XCMS, MZmine 2, MS-DIAL) and need to assess whether peak detection rates, isotopologue ratio fidelity, and alignment accuracy meet acceptable thresholds before downstream analysis.
    0 installs
13. ▌
    Mass Spectrometry Peak Detection And Alignment · holobiomicslab

    Use when after normalization, smoothing, and baseline reduction have been performed on raw MSImagingArrays data.
    0 installs
14. ▌
    Mass Spectrometry Plot Taxonomy Implementation · holobiomicslab

    Use when you are building a visualization library that must support multiple plot kinds (chromatogram, spectrum, mobilogram, peakmap) across multiple rendering backends (matplotlib, bokeh, plotly) and want to avoid code duplication.
    0 installs
15. ▌
    Metabolite Adduct Correlation Spatial Analysis · holobiomicslab

    Use when you have annotated mass-difference peaks with known adduct identities (via mass-matching to reference adduct tables) and possess MSI intensity matrices where each peak's abundance is measured across multiple tissue pixels or voxels.
    0 installs
16. ▌
    Metabolite Significance Filtering Volcano Plot · holobiomicslab

    Use when you have meta-analyzed metabolomic results from multiple studies with p-values and fold-change estimates (e.g., from amanida quantitative meta-analysis), and you need to identify compounds that meet both statistical rigor (p ≤ 0.05) and biological magnitude (|fold-change| ≥ 3.
    0 installs
17. ▌
    Microbial Metabolomics Phage Impact Assessment · holobiomicslab

    Use when you have normalized peak intensities (with assigned molecular formulas) from FT-ICR MS analysis of treated and control bacterial samples (or environmental microbial communities), grouped by two or more treatment factors (e.g., phage type: HP1, HS2, control;
    2 installs
18. ▌
    Model Training And Hyperparameter Optimization · holobiomicslab

    Use when you have raw co-elution profiles (27 fractions × 2+ proteins per pair) and a gold-standard PPI reference set, want to avoid manual feature engineering, and need to handle severe class imbalance (negative PPIs >> positive PPIs).
    0 installs
19. ▌
    Molecular Graph Construction Pytorch Geometric · holobiomicslab

    Use when when you have parsed molecular structures (SMILES or SDF) and need to represent them as attributed graphs for neural network models that accept graph-based inputs. Specifically applicable when your architecture requires dual representations (e.
    0 installs
20. ▌
    Msi Metadata Harmonization Across Image Stacks · holobiomicslab

    Use when you have processed and quantified MSI data from one or more imzML files in LipidQMap and need to export them as a unified, standards-compliant HDF5 container that preserves feature-by-pixel intensity matrices, per-feature lipid annotations (m/z, lipid class, adduct, neutral ID), per-pixel.
    0 installs
21. ▌
    Multi Backend Plot Generation And Benchmarking · holobiomicslab

    Use when when you have a suite of Sphinx gallery example scripts targeting multiple plotting library backends and need to verify that all examples execute successfully within expected time constraints and produce output across matplotlib (static), bokeh (interactive), and plotly (interactive).
    0 installs
22. ▌
    Multiple Hypothesis Correction In Metabolomics · holobiomicslab

    Use when after computing raw p-values from differential metabolomics analysis or Fisher's exact test enrichment, and before reporting significant pathways or metabolites. Essential when testing multiple metabolites against multiple pathway hypotheses (e.
    0 installs
23. ▌
    Mzml Spectrum Chromatogram Object Construction · holobiomicslab

    Use when you have an indexed gzip–compressed mzML file (mzML.gz with internal index structure) and need to retrieve and work with individual spectra or chromatograms by integer index without decompressing the entire file.
    0 installs
24. ▌
    P Value And Confidence Interval Interpretation · holobiomicslab

    Use when after running gentab_lm_long with mode='lm' to obtain a results table for multiple metabolomic features.
    0 installs
25. ▌
    Quality Control Metric Threshold Configuration · holobiomicslab

    Use when you have a SummarizedExperiment object from a metabolomics study with compound peak areas, internal standard assignments, and sample type annotations (QC, Study, Calibration, Blank), and you need to decide which samples and compounds are reportable.
    0 installs
26. ▌
    Redundant Node Removal And Edge Classification · holobiomicslab

    Use when after network partitioning, when you have identified connected subnetworks of features matched by isotope or adduct patterns and need to sanitize and categorize the relationships before tree construction. Use it when redundant features (e.
    2 installs
27. ▌
    Reproducibility Signal Detection Nonparametric · holobiomicslab

    Use when when you have high-dimensional replicate experimental data (e.g., metabolomics, proteomics, genomics assays) where technical or biological variability threatens reproducibility, and you need to distinguish genuine reproducible signals from noise without assuming normality.
    2 installs
28. ▌
    Sequential And Random Access Dual Mode Support · holobiomicslab

    Use when when parsing mzML or other blockwise-structured scientific data files where analysis requires both sequential scanning (e.g., iterating all spectra) and random direct access by identifier (e.
    0 installs
29. ▌
    Spectrum Metadata Normalization Across Formats · holobiomicslab

    Use when you have mass-spectrometry data files in mixed formats (e.
    2 installs
30. ▌
    Statistical Result Interpretation And Plotting · holobiomicslab

    Use when after statistical analysis has produced a results table with lipid identities, quantitative expression values, p-values, fold-changes, and experimental condition labels.
    0 installs
31. ▌
    Statistical Significance Threshold Application · holobiomicslab

    Use when you have generated omu_summary or anova_function output (a dataframe with padj values for all tested metabolites) and need to subset compounds for class-specific frequency counting, fold-change analysis, or visualization.
    0 installs
32. ▌
    Statistical Threshold Application Metabolomics · holobiomicslab

    Use when when you have completed a weighted meta-analysis of metabolomic studies using amanida and need to isolate robust, reproducible metabolite signals from the combined results.
    2 installs
33. ▌
    Temporal Signal Drift Detection And Adjustment · holobiomicslab

    Use when raw MS quantification data (feature-by-sample intensity matrix) shows systematic variation in detector response across the run sequence—i.e., when the same analyte produces different intensities at different timepoints in the measurement despite constant sample concentration.
    2 installs
34. ▌
    Variable Importance Ranking And Interpretation · holobiomicslab

    Use when after fitting a random forest classifier to metabolomics count data with a binary or multiclass grouping variable (e.
    0 installs
35. ▌
    Gene Identifier Deduplication And Filtering · holobiomicslab

    Use when when loading gene expression data (e.g., from GEO via getGEO or microarray ExpressionSet objects) that contains duplicate rows mapped to the same Gene ID, missing gene identifiers, or identifiers encoded with placeholder strings ('///') that indicate failed or ambiguous annotation.
    0 installs
36. ▌
    Multi Conditional Data Coregulation Scoring · holobiomicslab

    Use when you have a normalized gene expression matrix (bulk RNA-seq or microarray) from a time-course or multi-condition experiment and need to quantify whether known gene sets (pathways, functional modules) show statistically significant coordinated expression changes.
    0 installs
37. ▌
    Single Cell Graph Construction Neighborhood · holobiomicslab

    Use when you have preprocessed single-cell RNA-seq data (normalized and dimensionality-reduced via PCA) and need to establish cell-to-cell connectivity for trajectory inference, clustering validation, or graph-based visualization.
    0 installs
38. ▌
    Spatial Coordinate Indexing Dense To Sparse · holobiomicslab

    Use when you have computed k-nearest neighbors for spatial coordinates (e.g., via pynndescent or another NN backend) and need to store the resulting adjacency and distance information in a memory-efficient format compatible with downstream graph algorithms.
    0 installs
39. ▌
    Statistical Comparison P Value Conservation · holobiomicslab

    Use when you have run the same pathway enrichment analysis (e.
    2 installs
40. ▌
    Test Failure Diagnosis And Logging Analysis · holobiomicslab

    Use when you have modified the Scanpy codebase (e.g., added a feature or bugfix) and need to confirm that all unit and integration tests pass before submitting a pull request, or when a CI workflow fails and you need to reproduce the failure locally to diagnose the root cause.
    2 installs
41. ▌
    Annotation Quality Filtering By Cosine Similarity · holobiomicslab

    Use when you have in silico annotations (e.g. from GNPS, timaR, or SIRIUS) paired with experimental MS/MS spectra and need to select only the highest-confidence structural matches.
    0 installs
42. ▌
    Mirror Plot Visualization For Spectrum Comparison · holobiomicslab

    Use when after computing compareSpectra similarity scores between an experimental consensus MS2 spectrum and candidate reference spectra (e.
    0 installs
43. ▌
    Least Squares Optimization Spectral Deconvolution · holobiomicslab

    Use when after GCMSFormer has predicted the pure mass spectral matrix S from overlapped GC-MS peaks.
    0 installs
44. ▌
    Missing Fraction Quality Filtering For Embeddings · holobiomicslab

    Use when after converting MS/MS spectra to fixed-length vector representations using a pre-trained Word2Vec model (as in Spec2Vec), filter spectra before computing similarity scores to flag those where a large fraction of the observed intensity comes from peaks or neutral losses not present in the.
    0 installs
45. ▌
    Parallel Computation For Large Library Processing · holobiomicslab

    Use when your input consists of multiple large MSP files (hundreds of megabytes) with associated structure folders containing hundreds of thousands of MOL or SDF files that require sequential processing steps (structure extraction, SMILES matching, RI assignment).
    0 installs
46. ▌
    Peak Intensity Normalization Weighted Aggregation · holobiomicslab

    Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments without allowing a single dominant peak to overwhelm the learned word associations.
    2 installs
47. ▌
    Adduct Signature Identification Mass Spectrometry · holobiomicslab

    Use when you have statistically significant LC-MS features (e.g., filtered by p-value < 0.01) from multi-assay metabolomics datasets and need to group features that represent the same metabolite ionized under different ESI conditions (e.g., [M+H]+, [M+Na]+, [M+NH4]+).
    0 installs
48. ▌
    Bayesian Meta Learning Chromatographic Projection · holobiomicslab

    Use when you have experimental retention times (RTs) for a small set of calibration molecules (≥10) measured on both a source chromatographic method and a target method, and you need to predict RTs for candidate metabolites on the target method to rank annotation candidates.
    1 install
49. ▌
    Comparative Performance Evaluation Across Methods · holobiomicslab

    Use when when you have developed a new spectral similarity scoring method and need to quantify its retrieval performance relative to established methods (e.g., modified cosine, Spec2Vec). Use this skill if you have: (1) a test set of spectra with ground-truth structural similarity labels (e.
    0 installs
50. ▌
    Computational Resource Profiling And Benchmarking · holobiomicslab

    Use when when evaluating a new or updated version of a data processing tool (especially asari or similar LC-MS workflows) before production deployment, or when verifying claims about scalability, memory efficiency, or throughput on specific hardware classes (e.g., ≤16 GB RAM single-core systems).
    0 installs
51. ▌
    Cross Language Function Invocation And Validation · holobiomicslab

    Use when your R-based Spectra analysis workflow requires a specific mass spectrometry algorithm (e.g., CosineGreedy similarity scoring, spectral normalization, or advanced filtering) that is available only in a Python MS package (matchms, spectrum_utils) and not yet in native R.
    0 installs
52. ▌
    Drop Down Interface Population From Filtered Data · holobiomicslab

    Use when you have search results from DIA mass spectrometry data containing feature Q-value scores and need to restrict the analyte choices available to users in a GUI to only those meeting a 1% feature Q-value threshold.
    0 installs
53. ▌
    Feature Table Moniker Registration And Versioning · holobiomicslab

    Use when after Asari completes feature detection and produces multiple feature table variants (full and quality-filtered preferred tables) from centroid mzML files within a PCPFM experiment.
    2 installs
54. ▌
    File Format Conversion Peak Picking To Lipidmatch · holobiomicslab

    Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest it into LipidMatch for lipid identification.
    0 installs
55. ▌
    Fragmentation Strategy Comparison Across Datasets · holobiomicslab

    Use when you have extracted a chemical mixture from a real mzML acquisition (e.g., Beer1pos), simulated the same chemicals through ViMMS using a chosen controller (e.
    2 installs
56. ▌
    Hierarchical Clustering Dendrogram Interpretation · holobiomicslab

    Use when you have a pre-computed hierarchical dendrogram from correlation-based clustering of LC-MS features (with fixed linkage criterion and distance metric) and need to decide whether a single constant-threshold cut or data-driven silhouette optimization better resolves the underlying cluster.
    0 installs
57. ▌
    Ion Mobility Mass Spectrometry Data Preprocessing · holobiomicslab

    Use when when you have raw IM-MS data from drift tube (DT) or SLIM instruments in Agilent MassHunter (.
    0 installs
58. ▌
    Mass Spectrometry Annotation Engine Customization · holobiomicslab

    Use when when you have baseline MS/MS peak annotations from a known compound but need to refine them using newly available structural information (e.
    2 installs
59. ▌
    Mass Spectrometry Fragmentation Pattern Discovery · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (in positive or negative ion mode) and seek to discover recurring fragmentation and neutral-loss patterns that characterize molecular substructures across a dataset.
    0 installs
60. ▌
    Metabolite Annotation By Chromatographic Behavior · holobiomicslab

    Use when when you have an untargeted metabolomics dataset from HPLC–MS (e.g., mzML, NetCDF) with detected peaks of unknown identity, and you need to disambiguate or validate tentative compound annotations by comparing observed retention time against machine-learning predicted retention time.
    0 installs
61. ▌
    Metabolomics Peak Data Normalization And Handling · holobiomicslab

    Use when when you have raw peak intensity matrices from metabolomics LC-MS/MS experiments with zero values (missing peaks or undetected compounds) and need to prepare data for pathway-level analysis using PLAGE, ORA, or GSEA.
    0 installs
62. ▌
    Missing Value Imputation In Quantification Tables · holobiomicslab

    Use when after feature alignment across multiple LC-MS/MS runs, when the unified feature list contains zeros or nulls for specific feature–sample pairs because peaks were not detected in those individual runs, but the feature was detected in other samples in the cohort.
    0 installs
63. ▌
    Nearest Neighbor Clustering For Mass Spectrometry · holobiomicslab

    Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
    0 installs
64. ▌
    Negative Adduct Tokenization In Mass Spectrometry · holobiomicslab

    Use when you have negative-mode MS/MS spectra with annotated molecular formulas and negative adducts (from repositories like MassIVE or MetaboLights), and your current formula inference model is restricted to positive mode only.
    0 installs
65. ▌
    Neural Network Inference And Embedding Extraction · holobiomicslab

    Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to generate low-dimensional embeddings for spectral visualization, clustering, or retrieval tasks.
    0 installs
66. ▌
    Outlier Detection And Downweighting In Regression · holobiomicslab

    Use when when fitting a nonlinear regression (GAM spline) through retention time anchor points derived from feature pair alignments in LC-MS metabolomics, and you suspect some anchor points are measurement errors or misaligned features that could bias the smooth curve.
    0 installs
67. ▌
    Receiver Operator Characteristic Curve Generation · holobiomicslab

    Use when when you have computed similarity scores (cosine, modified cosine, Spec2Vec, or other metrics) between a set of query spectra and a reference library with known structural annotations (InChIKey), and you need to evaluate how well each scoring method distinguishes true structural matches.
    0 installs
68. ▌
    Reference Based Vs Global Coordinate Registration · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples (each with mz, drift_time, retention_time, and intensity columns) and need to match corresponding features across datasets to enable cross-sample quantitation or cohort analysis.
    0 installs
69. ▌
    Smiles Identifier Assignment From Structure Files · holobiomicslab

    Use when when you have a mass spectral library (MSP format) that lacks SMILES annotations but is paired with a folder of MOL structure files (from Lib2NIST export or similar source).
    0 installs
70. ▌
    Spectral Data Object Construction And Integration · holobiomicslab

    Use when you have centroided mzML files from LC–MS experiments and need to perform targeted metabolomics or lipidomics analysis. Specifically, use it when you require polarity filtering, QC-sample stratification, or batch-aware peak detection—all of which depend on sampleData$type annotations (e.
    0 installs
71. ▌
    Tandem Mass Spectrometry Fragmentation Simulation · holobiomicslab

    Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to evaluate without access to real mass spectrometry hardware.
    0 installs
72. ▌
    Tandem Mass Spectrometry Metadata Standardization · holobiomicslab

    Use when you have raw MS/MS spectra from public repositories (e.
    2 installs
73. ▌
    Tandem Mass Spectrometry Mirror Plot Construction · holobiomicslab

    Use when when you have raw LC-MS or LC-IMS-MS data in instrument format (Agilent .d, Thermo .raw, Bruker .
    1 install
74. ▌
    Uncertainty Quantification From Model Predictions · holobiomicslab

    Use when when you have a trained neural network (e.g., a Siamese model predicting molecular structural similarity) and need to identify and filter unreliable predictions before using them in downstream analysis. Apply this skill when raw model performance is suboptimal (~0.
    0 installs
75. ▌
    Metabolite Identification From Transformation Rules · holobiomicslab

    Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological compartment (e.g., soil/aquatic microbiota, mammalian liver, or gut microbiota).
    0 installs
76. ▌
    Performance Degradation Quantification And Analysis · holobiomicslab

    Use when you have a pretrained model with documented performance on a bounded input domain (e.g., molecules ≤19 heavy atoms, sequences <1000 bp) and you need to establish whether and how much accuracy drops on held-out test cases outside that domain boundary.
    2 installs
77. ▌
    Sample Prioritization Through Structural Clustering · holobiomicslab

    Use when you have 2D NMR spectral data (HSQC, HMBC, COSY) from multiple samples in a natural products screening campaign and need to rank samples by structural novelty or identify which samples share common molecular scaffolds.
    2 installs
78. ▌
    Unknown Chemical Identification In Complex Mixtures · holobiomicslab

    Use when you have experimental LC–QTOF mass spectra from complex environmental samples (e.
    0 installs
79. ▌
    Cluster Umap Layout Reproducibility Benchmarking · holobiomicslab

    Use when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10k_multiome dataset (or a similar single-cell ATAC-seq dataset with a published reference) and need to validate that spectral embedding, Leiden clustering, and UMAP layout have converged to expected cluster identities and.
    0 installs
80. ▌
    Contact Frequency Aggregation By Genomic Feature · holobiomicslab

    Use when you have a cooler Hi-C contact matrix, a set of genomic features (e.g., CTCF peaks, enhancers, or TAD boundaries defined in BED format), and want to quantify average contact patterns around those features to detect local organization principles.
    2 installs
81. ▌
    Genome Alignment And Contact Matrix Construction · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a kilobase-resolution Hi-C experiment and need to produce a processed Hi-C contact map (.hic file) for visualization, loop calling, or chromatin structure analysis. This is the entry point for any Hi-C dataset that has not yet been aligned and normalized.
    0 installs
82. ▌
    Genome Sequence Matching For Nucleotide Patterns · holobiomicslab

    Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined motifs (e.
    0 installs
83. ▌
    Background Distribution Null Hypothesis Testing · holobiomicslab

    Use when when predicting one data modality (e.g., metabolite abundances) from another (e.g., microbiome composition) and you need to distinguish genuine microbe–metabolite associations from false positives driven by data compositionality, sample size artifacts, or confounding variation.
    0 installs
84. ▌
    Compound Reliability Filtering By Rsd Threshold · holobiomicslab

    Use when apply this filter after batch correction of compound/internal-standard ratios when you have pooled study quality control (SQC) samples and need to determine which compounds are sufficiently reproducible for downstream reporting. Use it specifically when the nonReportableRSD threshold (e.
    0 installs
85. ▌
    Containerized Application Deployment Validation · holobiomicslab

    Use when when deploying containerized versions of a multi-variant application (e.g., CLI, development, Linux, and Windows flavors) and you need to verify that each built image meets documented size constraints before registry push or production release.
    0 installs
86. ▌
    Derivatizing Matrix Ionization Rule Application · holobiomicslab

    Use when when working with mass spectrometry imaging data from metabolites treated with derivatizing matrices (e.
    2 installs
87. ▌
    Mass Difference Calculation From Spectral Peaks · holobiomicslab

    Use when you have a list of detected masses (m/z peaks) from MALDI-MS imaging data and want to systematically search for adduct relationships. Apply this skill when you suspect that observed peaks include not just parent metabolites but also their adducts with matrix ions (e.
    0 installs
88. ▌
    Mass Spectrometry Data Structure Interpretation · holobiomicslab

    Use when you have received an mzPeak archive (a ZIP file containing Parquet tables) and need to understand its internal structure, validate that spectrum metadata aligns with signal data, reconstruct m/z and intensity arrays (especially when null marking or zero-run stripping is present), or verify.
    0 installs
89. ▌
    Metabolite Candidate Ranking Likelihood Scoring · holobiomicslab

    Use when you have a query mass spectrum matched to multiple candidate metabolites (by accurate mass, database lookup, or spectral similarity), and you possess or can train a DNN model for retention time prediction on your target chromatographic method.
    0 installs
90. ▌
    Metabolite Concentration Stoichiometric Mapping · holobiomicslab

    Use when you have intracellular metabolomics abundance data (absolute or relative concentrations) for multiple cell lines or conditions, a constraint-based stoichiometric metabolic model with reaction-metabolite associations, and you need to disentangle how differences in substrate concentration.
    0 installs
91. ▌
    Molecular Duplicate Detection And Deduplication · holobiomicslab

    Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
    0 installs
92. ▌
    R Package Installation And Runtime Verification · holobiomicslab

    Use when before running any R function that wraps compiled C# methods or system executables (e.g., rawrr::readSpectrum), especially when the package depends on language runtimes (.NET, Mono) or proprietary third-party assemblies that must be downloaded and configured separately.
    0 installs
93. ▌
    Wine Windows Runtime Initialization Diagnostics · holobiomicslab

    Use when you are deploying a Windows .NET application (e.g., AirdPro CLI) inside a Docker container on a non-Windows host and need to understand whether Wine initialization completes, how long it takes (documented as >30 minutes), whether .
    0 installs
94. ▌
    Anndata Object Integration And Metadata Mapping · holobiomicslab

    Use when you have preprocessed and filtered ST and SM AnnData objects with spatial coordinates and features, and you need to establish spot-level correspondence between the two modalities to enable downstream joint analysis.
    0 installs
95. ▌
    Association Strength Normalization For Networks · holobiomicslab

    Use when after generating metabolite-disease correlations and protein association predictions from a deep learning module (e.g., DeepMSProfiler's feature extraction), before constructing a bipartite network graph for publication.
    2 installs
96. ▌
    Biotransformation Rule Extraction From Database · holobiomicslab

    Use when you need to populate or reconstruct a biotransformation prediction module and have access to a curated biotransformation database (such as EAWAG BBD) that documents empirically validated microbial degradation pathways, enzyme-substrate relationships, and reaction outcomes.
    2 installs
97. ▌
    Chemical Formula Deduplication Across Databases · holobiomicslab

    Use when you have retrieved chemical formulae and metadata from two or more of HMDB, ChEMBL, or PubChem and need to merge them into a single searchable database without formula duplication.
    0 installs
98. ▌
    Chemical Identifier Standardization And Mapping · holobiomicslab

    Use when you have structure-organism pairs originating from multiple open databases (e.g., ChEMBL, PubChem, Wikidata) with disparate identifier schemes, file formats (TSV, JSON, XML, proprietary schemas), and taxonomic rank naming conventions.
    0 installs
99. ▌
    Chromatographic Peak Detection Gradient Descent · holobiomicslab

    Use when you have LC-HRMS profile-mode data (retention time × m/z matrix format) and need to automatically identify chromatographic peak locations and boundaries prior to feature extraction, reference matching, or training a peak-classification CNN model.
    0 installs
100. ▌
     Controlled Vocabulary Lookup Table Construction · holobiomicslab

     Use when after ingesting and parsing multiple external databases with diverse identifier schemes and nomenclatures. Trigger conditions: (1) you have interim standardized tables with local identifiers (structure_id, organism_name, reference_doi) that lack semantic normalization;
     1 install