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HolobiomicsLab

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1. ▌
   Outlier Detection Qc Sample Ratio Analysis · holobiomicslab

   Use when after building a SummarizedExperiment object from metabolomics LC-MS data with QC and Study Sample types defined, when you need to identify QC samples with aberrant Compound/Internal Standard ratios (indicating instrument drift, matrix effects, or sample degradation) and Study Samples with.
   0 installs
2. ▌
   Parent Ion Fragment Hierarchy Organization · holobiomicslab

   Use when after ISF features have been identified and annotated in Part 4 of the ISFrag workflow, and you need to represent the structural relationships among ISF features and their parent ions hierarchically.
   0 installs
3. ▌
   Positional Encoding For Spectral Sequences · holobiomicslab

   Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
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4. ▌
   Pytorch Transformer Backbone Instantiation · holobiomicslab

   Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata (chromatographic column parameters).
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5. ▌
   Quality Control Sample Identification Lcms · holobiomicslab

   Use when when you have XCMS-preprocessed LC-MS metabolomics data with a peak table and an accompanying covariate/metadata file that contains a 'SampleType' column, and you plan to apply QC-based quality filters (such as RSD filtering) or train classifiers for peak quality assessment.
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6. ▌
   Reference Prediction Comparison Evaluation · holobiomicslab

   Use when you have executed a structure annotation pipeline (like BAM) on a validation dataset for which ground-truth molecular structure annotations exist, and you need to assess whether the pipeline's predictions match the reference annotations at the required sensitivity and specificity.
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7. ▌
   Residue Position Mapping To Spectrum Peaks · holobiomicslab

   Use when when you have an MS2 spectrum (FT2 scan or mzML) with observed peak data (m/z, intensity, charge states), a peptide sequence, and need to annotate which amino acid residues generated each matched fragment ion—particularly in stable isotope labeling experiments where isotopic mass shifts.
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8. ▌
   Retention Time Agnostic Spectral Alignment · holobiomicslab

   Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts between acquisitions, or use of different LC-MS platforms (e.g., Orbitrap vs. Q-ToF).
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9. ▌
   Retention Time Extraction From Raw Spectra · holobiomicslab

   Use when when you have Thermo Orbitrap .raw files containing known reference peptides (e.
   0 installs
10. ▌
    Root Mean Squared Error Computation By Bin · holobiomicslab

    Use when when evaluating a regression or similarity prediction model and you need to understand whether prediction error is uniform across the outcome space or concentrated in particular ranges (e.g., low structural similarity vs. high similarity scores).
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11. ▌
    Sample Vectorization Via Spectral Features · holobiomicslab

    Use when you have unaligned MS2 spectra from multiple metabolomics samples (in mzML, mzXML, or MGF format) and need to compare them without relying on retention time or aligned m/z features.
    0 installs
12. ▌
    Sensitivity Threshold Stability Assessment · holobiomicslab

    Use when you have labeled MS/MS spectra from replicate measurements and need to determine a frequency threshold for denoising that balances competing objectives: retaining true fragment signals while removing noise.
    0 installs
13. ▌
    Silhouette Analysis Threshold Optimization · holobiomicslab

    Use when when you have a pre-computed hierarchical dendrogram from structural clustering (e.g., of LC-MS features based on m/z and retention time) and want to compare or validate the cluster assignments produced by a fixed constant-threshold method.
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14. ▌
    Spectral Data Export And Format Conversion · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-processed metabolomics data, export spectral data when you need to share clustered spectra with external annotation software (MSFinder, Sirius), perform spectrum matching against reference databases, or prepare results for collaborative analysis.
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15. ▌
    Spectral Feature Clustering And Comparison · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.
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16. ▌
    Spectral Feature Extraction And Annotation · holobiomicslab

    Use when you have raw LC/MS data in mzML format and need to perform non-targeted screening to discover unknown chemical features without a predefined list of target compounds.
    0 installs
17. ▌
    Spectral Graph Construction From Fragments · holobiomicslab

    Use when after you have aligned fragment ion pairs between two MS/MS spectra using maximum weight matching and need to compute statistical significance scores for the matched pairs.
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18. ▌
    Spectral Result Visualization Verification · holobiomicslab

    Use when after running annotateRC to generate ranked candidate annotations for LC-MS AIF features, when you need to confirm that (1) the top-ranked candidate match is chemically plausible given the observed fragment ions, (2) alternative candidate annotations exist and are correctly ranked, and (3).
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19. ▌
    Spectral Similarity Measure Implementation · holobiomicslab

    Use when you have MSMS spectra from two or more compounds and need to identify which are structurally related. Use this skill when you want to rank spectrum pairs by similarity to discover novel analogs or validate structural assignments in untargeted metabolomics or natural products discovery.
    0 installs
20. ▌
    Spectral Structural Similarity Computation · holobiomicslab

    Use when when you have pre-trained embedding vectors (e.g., from MSBERT) for a collection of mass spectra and need to establish which spectra are chemically similar for validation, clustering, or library matching.
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21. ▌
    Spectrum Normalization And Standardization · holobiomicslab

    Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) from one or more metabolomics samples, and you need to prepare them for MS2 fingerprint generation, similarity scoring, or cross-sample comparison.
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22. ▌
    Spectrum Object Creation And Preprocessing · holobiomicslab

    Use when when you have raw tandem mass spectrometry peak data (m/z and intensity pairs), precursor m/z, charge state, and adduct annotation for one or more compounds, and need to construct normalized spectrum objects suitable for downstream spectral alignment, modification site prediction, or.
    0 installs
23. ▌
    Stable Isotope Labelling Feature Detection · holobiomicslab

    Use when you have XCMS-processed LC/MS peak tables from paired unlabeled (12C) and labeled (13C) metabolic samples with replicate measurements, and you want to systematically detect which features show significant enrichment in the labeled condition relative to the unlabeled control.
    0 installs
24. ▌
    Structural Cluster Annotation Metabolomics · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.g., via MB-VIP with p < 0.01 and permutation testing), when you need to consolidate multiple ionization and isotopic forms of the same metabolite into structural groups for annotation and pathway mapping.
    0 installs
25. ▌
    Retention Time Mass Correspondence Resolution · holobiomicslab

    Use when you have two LC-MS untargeted metabolomic feature tables (each containing m/z, retention time, and intensity columns) and need to establish which features in dataset A correspond to which features in dataset B, typically for comparative metabolomics, batch effect correction, or.
    0 installs
26. ▌
    Root Mean Squared Error Regression Evaluation · holobiomicslab

    Use when you have a trained regression model (e.g., a neural network or similar predictor) and a held-out test set with ground-truth continuous labels, and you need to measure whether the model's predictions match the true values.
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27. ▌
    Spectra Object Instantiation And Manipulation · holobiomicslab

    Use when you have mass spectrometry spectral data (m/z and intensity pairs, precursor m/z, MS level, and metadata) in R memory or in a file format (mzML, mzXML, CDF, MGF, MSP), and you need to organize it into a queryable, processable object before performing spectral similarity calculations.
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28. ▌
    Spectral Artifact Identification In Tandem Ms · holobiomicslab

    Use when you have a raw or preprocessed peak table from tandem MS/MS data (e.g., from Progenesis QI, MS-DIAL, or Bruker Metaboscape) and observe features that may represent detector artifacts, incorrectly merged/split isotopic patterns, or sample carryover contaminants (e.
    0 installs
29. ▌
    Spectral Noise Filtering And Artifact Removal · holobiomicslab

    Use when you have raw MS/MS spectra in supported formats (.mgf, .mzML, or .msp) containing both chemical signal and experimental noise, prior to structural motif discovery via topic modeling.
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30. ▌
    Spectral Noise Synthesis Poisson Distribution · holobiomicslab

    Use when when you have clean, baseline MS/MS spectra and need to create test datasets with known noise characteristics to benchmark denoising algorithms, compare denoising search performance, or validate that electronic and chemical noise removal functions correctly identify and remove injected.
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31. ▌
    Spectral Similarity Distance Metric Selection · holobiomicslab

    Use when when you have processed LC-MS/MS spectral data in .mgf format with feature identifiers and need to compute a pairwise similarity matrix to support interactive exploration.
    0 installs
32. ▌
    Spectrum Similarity Nearest Neighbor Indexing · holobiomicslab

    Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise distance computation is computationally prohibitive.
    0 installs
33. ▌
    Tabular Data Parsing And Structure Conversion · holobiomicslab

    Use when you have a txt or tabular export file from a liquid chromatography–mass spectrometry (LC-MS) instrument (e.g., Sciex MultiQuant > v3.0.
    0 installs
34. ▌
    Tanimoto Fingerprint Ground Truth Computation · holobiomicslab

    Use when when preparing paired MS/MS spectra for training or validation of a siamese neural network model, and you have chemical structure annotations (InChI, SMILES, or InChIKey) for each spectrum but lack pre-computed structural similarity labels.
    0 installs
35. ▌
    Targeted Dia Data Extraction From Raw Spectra · holobiomicslab

    Use when when you have raw diaPASEF mzML files, a transition list with target analytes (protein, peptide, charge state), and search results (DIA-NN, OpenSwath output) containing feature metadata (retention time, ion mobility, m/z coordinates), and you need to isolate and visualize signal for.
    0 installs
36. ▌
    Transformer Input Representation Construction · holobiomicslab

    Use when you have variable-length MS/MS peak lists (m/z arrays and intensity arrays) that must be fed into a transformer architecture for tasks like compound identification or spectral clustering.
    0 installs
37. ▌
    True Positive False Positive Rate Calculation · holobiomicslab

    Use when you have a trained NeatMS neural network model (.h5 format) and need to assess its classification performance at a specific decision threshold (e.g., 0.01) to determine what fraction of true peaks are retained (TPR) versus what fraction of incorrect peaks are incorrectly accepted (FPR).
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38. ▌
    Variance Estimation Within And Between Groups · holobiomicslab

    Use when you have a QC-annotated LC-MS feature intensity table (CSV or data frame) with replicate QC samples and biological samples from multiple batches or run orders, and you need to assess which features maintain consistent signal intensity across technical replicates (within-group) relative to.
    0 installs
39. ▌
    Vendor Mass Spectrometry File Format Handling · holobiomicslab

    Use when you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird format for batch processing, cloud deployment, or integration with downstream analysis tools.
    0 installs
40. ▌
    Warping Function Comparison Across Algorithms · holobiomicslab

    Use when after applying two or more LC-MS alignment algorithms (such as XCMS and ncGTW) to the same dataset, use this skill to determine which produces warping functions. Specifically, apply this when: (1) you have detected or suspect misaligned features in XCMS output (e.
    0 installs
41. ▌
    Zero Value Handling In Mass Spectrometry Data · holobiomicslab

    Use when after feature detection has produced a feature table with zero and missing values (sparse abundance matrix) but before multivariate statistical analysis or annotation.
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42. ▌
    Transformer Encoder Architecture Implementation · holobiomicslab

    Use when when processing sequential spectroscopic data (1H NMR spectra) where both local chemical shift patterns and global spectral dependencies are needed for compound classification.
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43. ▌
    Chromatin Accessibility Occupancy Prediction · holobiomicslab

    Use when after you have (1) corrected ATAC-seq BAM files for Tn5 insertion bias using ATACorrect, (2) computed per-base footprint scores using ScoreBigwig, (3) obtained a motif database (e.
    0 installs
44. ▌
    Configuration File Generation And Templating · holobiomicslab

    Use when when deploying a complex bioinformatics pipeline (like HiC-Pro) across heterogeneous computing environments where required tools (bowtie2, samtools, R, Python) may be installed in non-standard locations, differ in version, or require scheduler-specific configuration (TORQUE, SGE, SLURM.
    0 installs
45. ▌
    Fragment Length Estimation Cross Correlation · holobiomicslab

    Use when when beginning ChIP-Seq analysis with single-end BED/SAM input and no prior knowledge of the library's fragment length.
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46. ▌
    Saddle Matrix Computation From Binned Tracks · holobiomicslab

    Use when you have a cooler Hi-C contact matrix file and an associated eigenvector track (from prior eigs_cis calculation or similar), and you need to quantify the preferential interaction patterns between A and B chromatin compartments.
    0 installs
47. ▌
    Acquisition Mode Enumeration And Validation · holobiomicslab

    Use when adopting a mass spectrometry-based analysis tool (e.
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48. ▌
    Adduct Annotation Against Reference Library · holobiomicslab

    Use when after computing a histogram of all pairwise mass differences from an MSI dataset, use this skill when you have observed mass difference peaks that may correspond to known adducts (e.g., [M+H]+, [M+Na]+, [M−H2O]+).
    0 installs
49. ▌
    Binary Classification Output Interpretation · holobiomicslab

    Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a structured CSV output file that maps molecule identifiers to their predicted class labels (bitter or not-bitter).
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50. ▌
    Chemical Informatics Data Format Conversion · holobiomicslab

    Use when when you have raw SMILES strings collected from multiple external databases that require standardization and deduplication before integration into a unified chemical structure database. Specifically, apply this skill when you need to convert interim/tables/0_original/structure/smiles.tsv.
    0 installs
51. ▌
    CI CD Pipeline Reproducibility Verification · holobiomicslab

    Use when when a repository displays a GitHub Actions workflow badge (e.
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52. ▌
    Collision Cross Section Bias Quantification · holobiomicslab

    Use when you have ion mobility-mass spectrometry lipidomics data from samples spiked with U¹³C-labeled lipid internal standards (fully labeled yeast extract) and want to assess whether measured CCS values systematically deviate from a validated DT CCS N₂ reference library, indicating bias that may.
    0 installs
53. ▌
    Count Verification Against Published Values · holobiomicslab

    Use when when you have access to a curated dataset (such as LOTUS) with published headline statistics in a peer-reviewed article or enriched index, and you need to validate data integrity, trace reporting accuracy, or establish a reproducible baseline before downstream analysis.
    0 installs
54. ▌
    Cross Language Implementation Compatibility · holobiomicslab

    Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.
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55. ▌
    Database Schema Design For Sequential Media · holobiomicslab

    Use when when you have large sequential media files (mzML spectra, text chapters, or similar) and need to enable both random access by ID and sequential iteration without loading the entire file into memory.
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56. ▌
    Dataframe Construction From Backend Sources · holobiomicslab

    Use when when implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
    0 installs
57. ▌
    Deep Learning Model Architecture Validation · holobiomicslab

    Use when after converting or loading a Keras model to HDF5 TensorFlow 2.3.0 format, especially when the model will be served through a pipeline (e.g., NP Classifier) that expects specific input/output layer names.
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58. ▌
    Deep Neural Network Training Regularization · holobiomicslab

    Use when training a DNN on retention time prediction or similar continuous regression tasks where: (1) the feature space is very high-dimensional (thousands of molecular descriptors and fingerprints), (2) the training set is moderately sized (tens of thousands of molecules), (3) you observe or.
    0 installs
59. ▌
    Dotnet Framework Installation In Containers · holobiomicslab

    Use when you need to containerize a C# application (e.g., AirdPro) that targets .NET Framework 4.8 and must run on Linux hosts via Docker, but the application was originally built for Windows. Use this skill when you are building multi-stage Docker images from a Ubuntu 22.
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60. ▌
    Linear Regression Concentration Calibration · holobiomicslab

    Use when your metabolomics experiment includes calibration line samples with known concentrations for spiked compounds, and you have computed batch-corrected compound/internal-standard ratios (ratio_corrected assay) and wish to convert relative ratios into absolute quantitative values for pathway.
    0 installs
61. ▌
    Mass Spectrometry Data Visualization Pandas · holobiomicslab

    Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV) loaded into a Pandas DataFrame with columns for m/z, retention time, ion mobility, or intensity values, and you need to render spectrum plots, chromatograms, mobilograms, or 2D peak maps.
    0 installs
62. ▌
    Molecular Descriptor Fingerprint Generation · holobiomicslab

    Use when you have a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or molecular property estimation.
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63. ▌
    Molecular Formula Assignment And Validation · holobiomicslab

    Use when you have a calibrated FT-ICR transient (ESI_NEG or similar ionization mode) and need to annotate each detected m/z peak with its most likely elemental composition.
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64. ▌
    R Dependency Package Compatibility Auditing · holobiomicslab

    Use when a Shiny application or R-based tool is known to run on only one operating system (e.g., Windows-only), and you need to identify the root causes preventing execution on Linux or macOS before undertaking cross-platform porting.
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65. ▌
    Shiny Application Cross Platform Adaptation · holobiomicslab

    Use when when a Shiny application is documented or observed to run only on Windows, blocking deployment to Linux or macOS users. Typical triggers include hardcoded Windows path separators, unavailable packages on non-Windows systems, or system calls specific to the Windows API.
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66. ▌
    Sonarcloud Static Code Analysis Integration · holobiomicslab

    Use when when you have a GitHub-hosted Python project (or other supported language) with an existing test suite and want to gate code contributions on multiple quality dimensions beyond unit tests—specifically when you need automated reporting of code coverage, technical debt, security issues, and.
    0 installs
67. ▌
    Application Server Datasource Configuration · holobiomicslab

    Use when when deploying a Java web application (such as CEU Mass Mediator) that requires access to a database managed outside the application server, and you have obtained database credentials from the maintainers.
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68. ▌
    Chemical Identifier Mapping Across Services · holobiomicslab

    Use when when you have .msp files with sparse or incomplete chemical metadata (e.g., only compound names) and need to populate missing identifiers (SMILES, InChI, InChI keys, CAS numbers, IUPAC names, formulas) by querying multiple external chemical databases.
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69. ▌
    Class Imbalance Handling In Neural Networks · holobiomicslab

    Use when your PPI prediction dataset has a large mismatch between positive (true interactions) and negative (non-interactions) labels—typical in CF-MS interactome prediction where true interactions are rare. When training an end-to-end neural network (e.
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70. ▌
    Computational Reproducibility Documentation · holobiomicslab

    Use when when releasing or archiving a computational workflow (e.g., an R or Python-based normalization pipeline) and you need to ensure that future users or reviewers can re-run the analysis in an identical computational environment.
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71. ▌
    CSV Table Validation And Integrity Checking · holobiomicslab

    Use when you have received a raw peak table CSV (in either standardized format or output from metabolomic software tools like XCMS, MZmine, etc.) and a corresponding label file, and you need to confirm both files are well-formed and mutually consistent before passing them to NOREVA preprocessing.
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72. ▌
    Deep Learning Model Training And Validation · holobiomicslab

    Use when you have paired mass-spectrometry spectral data (m/z and intensity arrays) with known molecular fingerprints or InChIKeys, and need to train a supervised deep learning model to predict fingerprints for novel spectra.
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73. ▌
    Descriptive Statistics Aggregation By Group · holobiomicslab

    Use when after lipid matching is complete and you have a table of matched lipid abundances with sample annotations (e.g., experimental condition, disease state, or treatment group).
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74. ▌
    Discrepancy Detection Threshold Calibration · holobiomicslab

    Use when normalizing metabolomics data using both QC and biological samples together.
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75. ▌
    Distance Metric Computation Adjacency Index · holobiomicslab

    Use when you have a collection of tokenised BGCs (each gene represented as a combination of Pfam domains and subPfams) and need to identify redundant or highly similar clusters before downstream analysis.
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76. ▌
    Domain Ontology Mapping Tcm And Ethnobotany · holobiomicslab

    Use when when integrating structure-organism pairs from TCM databases, ethnobotanical collections, or alternative medicine sources that use domain-specific or transliterated terminology (e.
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77. ▌
    Enrichment Metric Scaling And Normalization · holobiomicslab

    Use when you have parsed GO enrichment results (CSV with GO term identifiers, p-values or adjusted p-values, gene ratios, and gene counts) and need to prepare these metrics for dotplot visualization.
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78. ▌
    Feature Hashing Representation Mass Spectra · holobiomicslab

    Use when when you have high-resolution mass spectra that must be rapidly searched against large spectral libraries with open modifications, and you need to reduce the dimensionality of spectral data without losing the ability to retrieve spectrally similar peptides.
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79. ▌
    Fiams Spectra Window Extraction And Merging · holobiomicslab

    Use when you have raw FIA-MS full-scan data in mzML format and need to prepare it for untargeted metabolite discovery. Apply this skill when your goal is to detect and annotate unknown metabolites across a wide m/z range (e.
    0 installs
80. ▌
    Flux Distribution Segregation Visualization · holobiomicslab

    Use when you have sampled feasible flux distributions from multiple constraint-based models (e.g., cell-line-specific variants of a metabolic model) and need to visually and quantitatively compare how well different constraint scenarios segregate biological samples.
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81. ▌
    Ggplot2 Customization For Statistical Plots · holobiomicslab

    Use when when a statistical analysis function (e.g., random_forest or PCA_plot from Omu) returns a ggplot2 object and you need to adjust visual presentation—such as removing gridlines, applying a clean background theme (e.
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82. ▌
    Ggplot2 Theme Customization For Publication · holobiomicslab

    Use when you have generated a ggplot2 object from a domain-specific function (e.g., omu's plot_volcano) and need to refine its appearance for publication.
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83. ▌
    HTML Report Generation From Processed Omics · holobiomicslab

    Use when after completing batch normalization and quality control filtering on a Metaboprep object, when you need to communicate QC decisions, visualize exclusion patterns, and export final processed data for downstream analysis or sharing with collaborators.
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84. ▌
    Ion Image Augmentation Contrastive Learning · holobiomicslab

    Use when when you have preprocessed mass spectrometry ion images (single-channel 2D arrays or multi-channel spectral images) and need to train a self-supervised encoder to learn low-dimensional representations for downstream tasks such as co-localized ion discovery (COL mode) or isotope ion.
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85. ▌
    Ion Mobility Filtering And Tolerance Tuning · holobiomicslab

    Use when your raw MSI dataset is acquired on an ion-mobility-enabled instrument (e.g., Bruker .baf, .tsf, or .tdf formats) and your analyte of interest has a known or experimentally determined ion mobility value (1/K0 or drift time μs).
    0 installs
86. ▌
    Laser Ablation Isotope Image Interpretation · holobiomicslab

    Use when you have imported a raw LA-ICP-MS raster image (line-by-line, spot-wise, or ablation-time-aligned format) and need to isolate tissue regions from instrumental background or air before quantifying regional elemental abundance.
    0 installs
87. ▌
    Mass Spectrometry Data Object Instantiation · holobiomicslab

    Use when when you have mass spectrometry data stored in non-standard formats (SQLite, HDF5, custom binary) that pymzML does not natively support, and you want to enable random-access and sequential parsing of spectra without converting to mzML first.
    0 installs
88. ▌
    Mass Spectrometry Data Structure Conversion · holobiomicslab

    Use when when you have received metabolomics mass-spectrometry data in vendor-native or open formats (.raw, .d, mzXML) and need to ingest it into SMART for preprocessing, peak detection, or statistical analysis.
    0 installs
89. ▌
    Mass Spectrometry Quantification Extraction · holobiomicslab

    Use when you have raw LipidSearch or LIQUID output files (CSV or TSV format) containing lipid identifiers and per-sample quantification measurements, and you need to convert them into a machine-readable data matrix for downstream statistical analysis, normalization, or differential abundance.
    0 installs
90. ▌
    Mass Spectrum Scan Extraction And Windowing · holobiomicslab

    Use when when you have a full mass spectrum scan (e.g., FT1 or FT2 scan from an Orbitrap or IonTrap instrument) and need to isolate a narrow m/z window containing a known or predicted precursor ion before matching it to theoretical isotopic envelopes.
    0 installs
91. ▌
    Metabolite Column Filtering By Missing Rate · holobiomicslab

    Use when apply this filter when raw metabolomics data contains metabolite columns with varying amounts of missing values and you aim to conduct statistical analysis or imputation. The trigger is the presence of column-wise NA prevalence >10% in metabolite features;
    0 installs
92. ▌
    Metabolite Correlation Network Construction · holobiomicslab

    Use when after variance-stabilizing normalization and imputation of metabolomic data when you have a MultiAssayExperiment object containing normalized metabolite abundances and wish to identify groups of co-abundant metabolites that may share biochemical pathways or regulatory mechanisms.
    0 installs
93. ▌
    Metabolomic Data Preprocessing Optimization · holobiomicslab

    Use when you have multi-class or time-course metabolomic peak tables (with or without quality control samples and/or internal standards) and need to select the preprocessing workflow from hundreds of candidate combinations.
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94. ▌
    Metabolomics Software Build Reproducibility · holobiomicslab

    Use when when developing or maintaining a multi-platform metabolomics GUI tool (such as Maven GUI) that must produce binary executables for end users, and you need to ensure that builds are reproducible across different OS platforms, dependency versions are pinned and tracked, and release artifacts.
    0 installs
95. ▌
    Model Validation And Performance Evaluation · holobiomicslab

    Use when after training a MEISTER deep learning reconstruction model on mass spectrometry data, you must validate performance on independent test sets before applying the model to new experimental or clinical samples.
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96. ▌
    Molecular Formula Heteroatom Classification · holobiomicslab

    Use when after molecular formula assignment has been completed on detected peaks in a processed mass spectrum object.
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97. ▌
    Molecular Structure Representation Learning · holobiomicslab

    Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical structures.
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98. ▌
    Msi Data Visualization And Spatial Analysis · holobiomicslab

    Use when when you have imzML-format MSI data and need to identify biochemical species in specific tissue regions or anatomical structures.
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99. ▌
    Multi Channel Image Registration Validation · holobiomicslab

    Use when after importing and manually aligning two element channels in LA-ICP-MS images, use this skill to confirm registration quality before computing spatial relationships.
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100. ▌
     Multi Generation Transformation Hierarchies · holobiomicslab

     Use when the analytical goal requires detection of downstream transformation products that are not direct metabolites of the parent but rather products of further metabolism or degradation (e.g., secondary metabolites, conjugates of phase I products).
     0 installs