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HolobiomicsLab

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1. ▌
   Untargeted Metabolomics Dataset Integration · holobiomicslab

   Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) from independent untargeted metabolomic experiments or replicates and need to establish one-to-one feature correspondence across them to compare abundances, detect shared metabolites, or merge datasets.
   0 installs
2. ▌
   Workflow Configuration And Parameterization · holobiomicslab

   Use when when preparing to execute the Nextflow4MS-DIAL workflow on raw LC-HRMS metabolomics data (.mzML or .
   0 installs
3. ▌
   Y Ion Signal Detection And Noise Assessment · holobiomicslab

   Use when you have extracted a centroided MS/MS spectrum from a Thermo Orbitrap raw file (via rawrr::readSpectrum or equivalent) and need to verify that the observed y-ion fragments for a known peptide precursor exhibit signal-to-noise ratios consistent with high-quality fragmentation.
   2 installs
4. ▌
   Metadata Extraction From Fixed Offset Records · holobiomicslab

   Use when you have a binary file (e.g., NV format) with a known fixed-size header block (e.
   2 installs
5. ▌
   Multimodal Tensor Construction And Validation · holobiomicslab

   Use when when you have downloaded raw spectroscopic datasets from multiple sources (NMR, HSQC, COSY, IR files) and need to combine them into a single coherent training corpus where each molecule is represented by all four modalities.
   0 installs
6. ▌
   Peaklist Metabolite Assignment Prioritization · holobiomicslab

   Use when you have extracted m/z and retention time (m/z-RT) information for peaks from untargeted LC/HRMS data (using tools like IDSL.IPA) and need to assign molecular formula identities to those peaks.
   0 installs
7. ▌
   Pfas Characteristic Mass Difference Detection · holobiomicslab

   Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
   0 installs
8. ▌
   Spectral Data Format Parsing Nmr Hsqc Cosy Ir · holobiomicslab

   Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert them into aligned, standardized tensors for multimodal machine learning.
   0 installs
9. ▌
   Bioinformatics Tool Binary Path Resolution · holobiomicslab

   Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all required tools are installed, executable, meet version requirements (e.g., samtools ≥1.
   2 installs
10. ▌
    Duplicate Read Filtering And Normalization · holobiomicslab

    Use when you have raw ChIP-Seq and control BED files with potential PCR duplicates or unequal sequencing depths. Duplicate filtering is mandatory before estimating fragment length (predictd) or generating coverage pileups.
    1 install
11. ▌
    End To End Bioinformatics Pipeline Testing · holobiomicslab

    Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.
    0 installs
12. ▌
    Fragment Length Estimation From Read Pairs · holobiomicslab

    Use when you have paired-end ChIP-Seq data (BEDPE format) and need to determine the empirical fragment length (insertion length) before peak calling. This is mandatory for paired-end ChIP-Seq workflows to ensure MACS3 correctly extends coverage tracks and calculates local bias;
    0 installs
13. ▌
    Principal Component Analysis Visualization · holobiomicslab

    Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships based on overall methylation similarity across all covered bases, or when you want to determine which principal components.
    2 installs
14. ▌
    Simulation Dataset Validation Benchmarking · holobiomicslab

    Use when when you have installed or updated a DNA methylation analysis tool (e.g., ChAMP) and need to verify that it produces documented expected outputs on a reference simulation dataset before applying it to real experimental data.
    0 installs
15. ▌
    Analytical Pipeline Feature Documentation · holobiomicslab

    Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses it supports—particularly when the pipeline is positioned as an alternative to or improvement over established tools.
    0 installs
16. ▌
    Call Graph Construction And Visualization · holobiomicslab

    Use when when you need to understand the computational structure of a modular scientific application (especially one with multiple subprojects or plug-in architectures) and static code inspection alone does not reveal algorithm entry points, parameter propagation, or intermediate data.
    2 installs
17. ▌
    Chemo Informatics Workflow Reconstruction · holobiomicslab

    Use when when you have access to the source code of a chemo-informatics tool (e.
    0 installs
18. ▌
    Constraint Based Model Output Integration · holobiomicslab

    Use when when you have (1) transcriptomics data and a metabolic network model with GPR rules to compute RAS scores; (2) constraint-based model predictions (RPS from optGpSampler or similar) quantifying how gene expression differences translate to flux differences;
    1 install
19. ▌
    Contrastive Learning Encoder Construction · holobiomicslab

    Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or isotope discovery.
    0 installs
20. ▌
    Database Schema Design And Implementation · holobiomicslab

    Use when when you have an mzML file that you want to store persistently in a queryable format for repeated access, or when memory constraints prevent loading entire mzML files into memory;
    0 installs
21. ▌
    Deep Learning Architecture Implementation · holobiomicslab

    Use when you have two augmented versions of the same ion image (from mass spectrometry imaging data) and need to extract learnable 512-dimensional feature representations using a shared-weight encoder for contrastive loss optimization.
    0 installs
22. ▌
    Error State Tracking Across Microservices · holobiomicslab

    Use when building or maintaining a system that fetches metadata from multiple independent external web services and needs to diagnose why annotation runs fail or slow down. Use it specifically when you need to distinguish between service-level failures (e.
    0 installs
23. ▌
    Fold Change Sign Determination Statistics · holobiomicslab

    Use when you have paired measurements (e.g., gene expression counts, protein abundance, or sampled flux distributions) from two cell lines or conditions and need to assign a directional sign to each reaction or gene for downstream concordance analysis.
    2 installs
24. ▌
    Instrument Platform Compatibility Mapping · holobiomicslab

    Use when when adopting a mass spectrometry data processing tool (e.g., LipidMatch) and needing to verify whether your specific instrument platform (vendor + model) and acquisition mode combination (targeted, ddMS2-topN, AIF, direct infusion, imaging) have been formally validated.
    2 installs
25. ▌
    Interactive HTML Figure Generation Plotly · holobiomicslab

    Use when your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration, web-based presentation, or interactive supplementary material.
    0 installs
26. ▌
    Ionization Mode Peak Retention Comparison · holobiomicslab

    Use when when you have loaded a raw mass spectrum (e.g. ESI_NEG_SRFA.
    0 installs
27. ▌
    Matplotlib Bokeh Plotly Backend Switching · holobiomicslab

    Use when when you have mass spectrometry data (chromatograms, spectra, mobilograms, or peak maps) in a Pandas DataFrame and need to generate the same visualization in multiple formats—e.
    2 installs
28. ▌
    Microbial Genome Annotation Harmonization · holobiomicslab

    Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single consensus model per organism that reflects only metabolic capabilities agreed upon across the input reconstructions, or when.
    0 installs
29. ▌
    Molecular Structure Input Format Handling · holobiomicslab

    Use when you are receiving molecular structures from external sources (COCONUT database, ZINC database, user-provided chemical data) in varying formats (SMILES strings, InChI identifiers, SDF files), and you need to unify them into a single canonical representation before computing biosynfoni.
    2 installs
30. ▌
    Multivariate Ordination Analysis Nmds Pca · holobiomicslab

    Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in overall molecular composition across experimental conditions or sample groups.
    2 installs
31. ▌
    Nmds Ordination Distance Metric Selection · holobiomicslab

    Use when when you have normalized peak intensity matrices from FT-ICR MS data or other high-resolution metabolomics experiments and need to visualize sample relationships and assess whether categorical grouping factors (e.
    0 installs
32. ▌
    Optional Dependency Extra Specifier Usage · holobiomicslab

    Use when when a Python package provides optional support for specialized data formats or functionality (e.
    0 installs
33. ▌
    Record Field Transformation And Collation · holobiomicslab

    Use when you have extracted tabular data into an intermediate JSON form and need to restructure records by mapping input fields to output dictionary keys, collating multiple records under a single grouping field, filtering records by test conditions or exclusion rules, or applying custom.
    0 installs
34. ▌
    Regression Metric Computation Rmse Mae R2 · holobiomicslab

    Use when you have model predictions and ground-truth labels for a test set and need to assess how well the trained model generalizes to unseen data. Typical triggers: after executing inference on a held-out test partition, after cross-dataset evaluation (e.
    0 installs
35. ▌
    Smiles Structure Annotation From Molfiles · holobiomicslab

    Use when you have a mass spectral library in MSP format (e.g., from NIST, SWGDRUG, or other sources) exported alongside a folder of MOL files, and you need to populate the SMILES field in each library record to enable structure-based filtering, annotation, or downstream MS-DIAL analysis.
    0 installs
36. ▌
    Spearman Correlation Statistical Analysis · holobiomicslab

    Use when you have paired predicted and observed metabolite abundance vectors from a predictive model (e.
    0 installs
37. ▌
    Summary Visualization Artifact Generation · holobiomicslab

    Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and visualize the aggregated match results in a format compatible with metadataMASST web interface or downstream analysis.
    0 installs
38. ▌
    Test Output Parsing And Status Validation · holobiomicslab

    Use when you need to verify whether a GitHub Actions workflow badge (e.g., main.yml) accurately reports the CI pipeline's true pass/fail status.
    0 installs
39. ▌
    Transcriptomics Reaction Activity Scoring · holobiomicslab

    Use when you have RNA-seq read counts (FPKM or similar) for multiple cell lines or biological samples, a genome-scale metabolic model with GPR associations, and you need to constrain or weight metabolic reactions based on transcriptional regulation.
    0 installs
40. ▌
    Version Control Feature Branch Management · holobiomicslab

    Use when when you have modifications to propose for a shared codebase (e.g., bug fixes, new features, or documentation updates) and need to integrate them without disrupting the main development branch.
    0 installs
41. ▌
    Association Ranking Statistical Filtering · holobiomicslab

    Use when you have identified co-occurring metabolite–genomic variant associations from a network-driven over-representation analysis and need to rank them by confidence and control the family-wise error rate.
    2 installs
42. ▌
    Build System Configuration Identification · holobiomicslab

    Use when you have cloned a source repository and need to compile it on a supported operating system (Windows 10, Ubuntu 22.04, macOS 12+ ARM64) but do not know what build tools, dependencies, or compilation commands are required.
    0 installs
43. ▌
    Chemical Structure Integrity Verification · holobiomicslab

    Use when you have received or downloaded an SDF-formatted compound database file and need to confirm it is not corrupted, contains the expected number of molecular records, and that each record is structurally valid before using it in compound identification, library matching, or database.
    1 install
44. ▌
    Chromatogram Retention Time Visualization · holobiomicslab

    Use when you have mass spectrometry data loaded as a pandas DataFrame with at minimum two numeric columns representing retention time and intensity values, and you need to generate a chromatogram visualization for exploratory analysis, quality control, or publication.
    0 installs
45. ▌
    Chromatographic Peak Detection Validation · holobiomicslab

    Use when you have centroided mzML data and a curated set of target molecules with known retention time (RT) boundaries, and you need to establish ground-truth peak detection performance metrics (e.
    0 installs
46. ▌
    Cnn Architecture Design For Spectral Data · holobiomicslab

    Use when when you have mass-spectrometry data (m/z and intensity pairs or spectral matrices) paired with ground-truth molecular fingerprints or InChIKeys, and you need to learn a non-linear mapping from spectral patterns to structural fingerprints for downstream metabolite ranking or annotation.
    1 install
47. ▌
    Composite Map Data Structure Construction · holobiomicslab

    Use when after mass track extraction and alignment across samples, when you have a MassGrid structure (m/z-aligned mass tracks) and corresponding retention time calibration dictionaries for each sample, and need to prepare input for composite peak detection rather than per-sample peak detection.
    0 installs
48. ▌
    Concordance Score Calculation Cohen Kappa · holobiomicslab

    Use when you have paired quantitative variation patterns for the same set of reactions across multiple biological samples (cell lines) and need to discriminate whether flux variations correlate monotonically with substrate abundance changes (metabolic control) versus gene expression changes.
    0 installs
49. ▌
    Conditional Dispatch Logic Implementation · holobiomicslab

    Use when when accepting a file path as input in an MSI data processing pipeline and you need to determine which data reader module to instantiate before calling get_image_data() or load_pixels(). This arises when building a multi-vendor instrument workflow (e.
    1 install
50. ▌
    Confidence Score Assignment And Filtering · holobiomicslab

    Use when after matching MRM transitions against a lipid reference database, when you have candidate lipid identities for each transition and need to rank them by quality and select a single match per transition for export to the labelled lipid-identity table.
    0 installs
51. ▌
    Cosine Annealing Learning Rate Scheduling · holobiomicslab

    Use when when training a heavily regularized deep neural network on large molecular datasets (e.
    0 installs
52. ▌
    Dataframe Construction And Column Merging · holobiomicslab

    Use when when implementing a new MsBackend subclass and need to return complete spectra data as a single DataFrame object that combines required core variables with backend-specific metadata columns, while avoiding cyclic function calls between spectraData() and spectraVariables().
    0 installs
53. ▌
    Deep Learning Neural Network Optimization · holobiomicslab

    Use when you have a preprocessed metabolomics expression matrix with labeled samples and need to compare deep learning performance against traditional classifiers (SVM, RF, GBM, LDA, LOG, Rpart, PAM), or when you need to build a prognosis model that incorporates non-linear interactions between.
    0 installs
54. ▌
    Dependency Installation And Configuration · holobiomicslab

    Use when when setting up a fresh clone of the ENPKG workflow repository or when onboarding to a new machine. Use this skill before attempting to run any workflow stages (data organization, taxonomical enhancement, MN generation, SIRIUS annotation, or graph building).
    0 installs
55. ▌
    Differential Metabolite Abundance Testing · holobiomicslab

    Use when you have preprocessed and normalized metabolite measurements from two or more distinct biological groups (e.
    1 install
56. ▌
    Dockerfile Multi Stage Build Architecture · holobiomicslab

    Use when when you need to containerize a Windows-only .NET Framework GUI application (such as AirdPro V5/V6 written in C# for .NET Framework 4.8) for execution on macOS or Linux hosts, and you want to avoid shipping compile-time tooling (SDK) in the production image.
    2 installs
57. ▌
    Feature Matrix Aggregation Across Samples · holobiomicslab

    Use when after per-sample quantification is complete (e.g., salmon has produced quant.sf files for all samples in the cohort) and you need to prepare data for differential expression analysis, quality control comparisons, or multi-omics integration.
    2 installs
58. ▌
    Gene Level Volcano And Ma Plot Generation · holobiomicslab

    Use when after completing differential expression analysis (edgeR, DESeq2, or RankProduct) on count matrices to visualize fold-changes versus p-values and to assess the relationship between average expression levels and log2 fold-changes for gene-level omics data.
    1 install
59. ▌
    Gnuplot Library Availability Verification · holobiomicslab

    Use when when deploying a Perl-based GUI application (such as LipidOne) on Microsoft Windows that depends on Gnuplot for visualization, and you need to ensure the application will not crash during dataset loading or plotting operations due to missing or inaccessible Gnuplot binaries.
    2 installs
60. ▌
    Gpu Accelerated Nearest Neighbor Indexing · holobiomicslab

    Use when when searching unknown mass spectra against large high-resolution spectral libraries for open modification identification and you need to reduce search latency from seconds to milliseconds while maintaining sensitivity and specificity.
    0 installs
61. ▌
    Graph Database Indexing And Serialization · holobiomicslab

    Use when you have retrieved and deduplicated chemical formulae and metadata from multiple heterogeneous sources (HMDB, ChEMBL, PubChem) and extracted both structural relationships (DBEdges) and biological reactant pairs (BioEdges from KEGG), and now need to merge them into a single queryable.
    2 installs
62. ▌
    Graph Visualization Interactive Rendering · holobiomicslab

    Use when after constructing a NetworkX graph object from structural clusters (via MamsiStructSearch), when you need to interactively explore feature relationships or publish a static network diagram showing isotopologue links, adduct relationships, and cross-assay connections.
    2 installs
63. ▌
    Inchikey Extraction From Spectral Library · holobiomicslab

    Use when you have a GNPS DBResult file from spectral library matching that lacks ClassyFire superclass, class, and subclass columns, and you need to restore chemical ontology annotations by submitting compound identifiers to external batch classification services for re-annotation.
    2 installs
64. ▌
    Interactive Filter Definition Trelliscope · holobiomicslab

    Use when you have omics statistical results (p-values, effect sizes, fold-changes) mapped to individual trelliscope panel rows and need to allow end users to interactively explore subsets of features (proteins, metabolites, genes) by thresholds or annotations without re-running the visualization.
    0 installs
65. ▌
    Interactive Region Of Interest Refinement · holobiomicslab

    Use when after loading a LA-ICP-MS image into pew², you need to isolate tissue or sample regions from instrumental background or matrix before calculating elemental concentrations or ratios.
    0 installs
66. ▌
    Internal Standard Area Aberrancy Flagging · holobiomicslab

    Use when after building a SummarizedExperiment from metabolomics data but before quantitative analysis.
    0 installs
67. ▌
    Linear Regression Absolute Quantification · holobiomicslab

    Use when you have a set of calibration samples (spiked compounds) with known concentrations, measured compound and internal-standard peak areas, and you need to convert compound/internal-standard ratios from study samples into absolute concentrations.
    0 installs
68. ▌
    Lipidomics Experiment Object Construction · holobiomicslab

    Use when when you have lipidomics quantitation data (lipid abundances across samples) that you need to load into a unified, annotated R object for analysis—either from public Metabolomics Workbench studies via API, Skyline mass spectrometry software exports, or a custom numerical matrix with.
    0 installs
69. ▌
    Low Resolution Mass Spectrometry Analysis · holobiomicslab

    Use when you have low-resolution MS data (e.g., from quadrupole instruments) in vendor format, a list of target compounds with known monoisotopic m/z and retention times, and need to extract per-isotopologue area and intensity values.
    0 installs
70. ▌
    Mass Spectral Library Benchmark Execution · holobiomicslab

    Use when you have access to the Flash Entropy Search implementation and want to validate that real-time spectral library querying achieves the reported timing and throughput metrics under the same library sizes, query parameters, and measurement methodology documented in the paper.
    0 installs
71. ▌
    Mass Spectrometry Data Quality Assessment · holobiomicslab

    Use when when raw mass spectrometry spectral data has been imported into matchms from common file formats (mzML, mzXML, msp, MGF, JSON) and you need to assess whether metadata fields are correctly normalized, validated against schema requirements, and peaks are appropriately filtered before.
    0 installs
72. ▌
    Mass Spectrometry Data Structure Decoding · holobiomicslab

    Use when when you have a mzPeak file (uncompressed ZIP archive containing Parquet tables) and need to access decoded spectral data arrays (m/z, intensity), spectrum metadata (scan descriptors, precursors), or chromatogram data in a form suitable for Python/R analysis pipelines.
    2 installs
73. ▌
    Mass Spectrometry Dataset Post Processing · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify molecular chemodiversity, characterize elemental stoichiometry patterns, or explore transformation pathways across samples.
    0 installs
74. ▌
    Mass Spectrometry Imaging Data Processing · holobiomicslab

    Use when you have raw or processed MSI data (in imzML or rMSIproc formats) and need to identify and annotate matrix-related peaks before statistical analysis or metabolite identification. Use it specifically when your MSI experiment employed a chemical matrix (e.
    0 installs
75. ▌
    Mass Spectrometry Peak Intensity Encoding · holobiomicslab

    Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity dimensionality while preserving spatial relationships between measurement points, or (3) apply iterative peak picking.
    0 installs
76. ▌
    Mass Spectrometry Target List Preparation · holobiomicslab

    Use when you have a raw .xlsx or tabular file listing candidate compounds with theoretical or measured m/z values, expected retention times, and ionization polarities, and you need to feed this into TARDIS or another targeted LC–MS analysis pipeline.
    0 installs
77. ▌
    Mass Spectrometry Wrapper Function Design · holobiomicslab

    Use when when you have a Spectra-based MS analysis workflow in R but need access to specialized spectral similarity, filtering, or normalization algorithms available only in Python libraries.
    0 installs
78. ▌
    Metabolic Module Significance Calculation · holobiomicslab

    Use when after you have constructed metabolic correlation modules via WGCNA on normalized and imputed metabolomic data, and you want to test whether specific modules (e.g., Module 2: Creatine/Glutathione metabolism) associate significantly with a categorical sample trait.
    0 installs
79. ▌
    Metabolite Detection Frequency Estimation · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative ionization modes) into an AnnData object, and before filtering metabolites or performing cross-modal integration.
    2 installs
80. ▌
    Metabolite Level Expression Summarization · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative mode files) into an AnnData object and before filtering or integrating with spatial transcriptomics.
    0 installs
81. ▌
    Metabolomic Biomarker Pathway Association · holobiomicslab

    Use when after marker identification (via fold-change, PLS-DA, t-test, or other feature selection methods) has produced a ranked list of metabolic features.
    0 installs
82. ▌
    Metabolomic Meta Analysis Workflow Design · holobiomicslab

    Use when you have multiple metabolomic studies with aggregate summary statistics (p-values, fold-change estimates) and need to perform meta-analysis while harmonizing compound nomenclature across datasets. Use this skill when the underlying R package (e.
    0 installs
83. ▌
    Metabolomics Data Loading Into Containers · holobiomicslab

    Use when you have raw metabolomics data (e.g., in standard bioinformatics formats supported by maplet) and need to initialize an analytical pipeline that will integrate multiple processing and analysis steps.
    0 installs
84. ▌
    Metadata Column Profiling Across Datasets · holobiomicslab

    Use when you are curating metabolomics datasets with variable column naming conventions and need to detect, normalize, and populate standardized database-ID columns (HMDB_ID, PubChem_ID, KEGG_ID, etc.) across many mwTab files before deposition.
    0 installs
85. ▌
    Molecular Descriptor Graph Representation · holobiomicslab

    Use when when you need to train or evaluate a graph neural network for molecular property prediction (collision cross section, ion mobility, or related descriptors) and have access to SMILES strings and/or 3D conformer coordinates.
    0 installs
86. ▌
    Msi Imaging Experiment Class Manipulation · holobiomicslab

    Use when when loading mass spectrometry imaging data from imzML or Analyze 7.
    2 installs
87. ▌
    Msi Preprocessing Parameter Configuration · holobiomicslab

    Use when you have raw line-scan MSI data (from Bruker .d/.baf, converted to .mzML, or other supported formats) and need to configure MSIGen before calling msigen() to generate image arrays.
    0 installs
88. ▌
    Msms Spectrum Data Structure Manipulation · holobiomicslab

    Use when you have raw or downloaded MSMS spectra (from online resources via Universal Spectrum Identifier, or from local mzML/mzXML files) that require standardization, cleaning, and fragment assignment before visualization, statistical comparison, or machine-learning feature extraction.
    0 installs
89. ▌
    Multi Model Molecular Prediction Ensemble · holobiomicslab

    Use when you have a set of molecular structures (as .sdf or .csv with SMILES) and need to predict metabolic susceptibility across multiple CYP isoforms (e.g., 1A2, 2A6, 2B6) to prioritize drug candidates or screen for potential metabolic liabilities across the major human CYP enzyme portfolio.
    0 installs
90. ▌
    Multi Omics Output Directory Organization · holobiomicslab

    Use when after completing pathway enrichment analysis on differentially expressed features from genes, miRNA, proteins, or lipids using either clusterProfiler or biotranslator.
    2 installs
91. ▌
    Multivariate Batch Confounding Assessment · holobiomicslab

    Use when after data preprocessing and quality control, when your metabolomics feature matrix and sample metadata show evidence of batch structure (e.
    0 installs
92. ▌
    Natural Product Classification Prediction · holobiomicslab

    Use when you have molecular structures encoded as SMILES strings and need to classify them into natural-product chemical classes.
    0 installs
93. ▌
    Natural Product Representation Assessment · holobiomicslab

    Use when you have a natural product dataset with taxonomy labels (Class, Superclass, or Pathway), pre-trained molecular models (both natural-product-specialized and synthetic-molecule baselines), and a question about whether standard molecular representations are sufficient for natural product.
    0 installs
94. ▌
    Natural Product Structural Representation · holobiomicslab

    Use when when you need to represent natural product molecules as numerical feature vectors for downstream machine learning (e.g., biosynthetic class prediction), comparative analysis, or when standard chemical fingerprints (e.
    0 installs
95. ▌
    Neural Network Architecture Instantiation · holobiomicslab

    Use when when you have retrieved a model definition file (e.g., TransGNet.py) and need to verify it can be loaded, configured with correct hyperparameters, and executed on representative multimodal inputs (e.g., molecular graphs and SMILES embeddings) before training or inference.
    0 installs
96. ▌
    Neural Network Model Deployment In Python · holobiomicslab

    Use when you have a trained conformer-based peak-picking model (in ONNX format) and need to apply it to chromatographic or ion-mobility mass spectrometry data (TransitionGroup objects) to detect peak boundaries and apex positions, generating TransitionGroupFeature records for downstream analysis or.
    0 installs
97. ▌
    Neural Network Module Architecture Design · holobiomicslab

    Use when when building an end-to-end deep learning model that must predict multiple correlated peptide properties (charge, isotope count, retention time) simultaneously from mass spectrometry data, and you need a principled way to merge learned representations from separate task-specific branches.
    0 installs
98. ▌
    Overlapping Peak Detection Interpretation · holobiomicslab

    Use when annotating matrix-related signals in MSI datasets where chemical formulas or spatial distributions alone are ambiguous, or when multiple ions share nominal m/z values (isobaric peaks).
    0 installs
99. ▌
    Parameter Configuration Conditional Logic · holobiomicslab

    Use when setting up a LipidMatch analysis run and you need to select among three mutually-exclusive analysis modes (PFAS, Lipid, or Tween-positive detection). The trigger is application-level metadata or user specification that indicates which detection mode should execute.
    0 installs
100. ▌
     Prefix Stripping And Case Standardization · holobiomicslab

     Use when valueMatcher.series_match has detected database-ID values (HMDB IDs, PubChem CIDs, KEGG compound identifiers) in raw metabolite metadata columns and you need to normalize them into a canonical form for storage in standardized database-ID columns (e.g., HMDB_ID, PubChem_ID, KEGG_ID).
     2 installs