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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Uncertainty Estimation Across Models · holobiomicslab

   Use when when you have multiple independently trained models (e.g., ROASMI_1 through ROASMI_5) making predictions on the same set of compounds or samples, and you need to assess confidence in individual predictions.
   0 installs
2. ▌
   Unit Test Design For Scoring Metrics · holobiomicslab

   Use when when implementing new scoring components (inchikey score, neighbourhood score, or similar structural/spectral similarity metrics) that are integrated into an MS/MS candidate re-ranking pipeline.
   0 installs
3. ▌
   Vendor Format To Standard Conversion · holobiomicslab

   Use when when ingesting raw LC-MS/MS output from a mass spectrometry instrument and you need to prepare it for metabolite identification, fragmentation tree computation, or molecular formula annotation.
   0 installs
4. ▌
   Web Application Documentation Mining · holobiomicslab

   Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you need to produce a machine-readable inventory of those applications with verified live URLs and associated publications for.
   0 installs
5. ▌
   XML Structured Metadata Construction · holobiomicslab

   Use when when you have synthesized or assembled mass spectrometry spectral data (m/z values, intensities, retention times) and need to encode it as a portable, standard mzML file format rather than a proprietary binary or text representation.
   0 installs
6. ▌
   Chemical Graph Connectivity Validation · holobiomicslab

   Use when after a machine learning model has generated predicted molecular structures (connectivity graphs and molecular formulas) from 1D NMR spectra. Use it to quantify accuracy on a held-out test set, measure degradation when applying the model beyond its training scope (e.
   0 installs
7. ▌
   Conditional Allocation Design Patterns · holobiomicslab

   Use when when designing a dataset storage layer that must handle variable dataset sizes, block layouts, and platform-specific constraints (e.g., Windows vs. non-Windows). Specifically: (1) you have parsed dataset metadata including cache-file flags, total point counts, and block configuration;
   0 installs
8. ▌
   Dataset Storage Interface Architecture · holobiomicslab

   Use when you have NMR dataset metadata (cache-file flag, total point count, block layout configuration) and need to select an appropriate storage backend that balances memory efficiency, access patterns, and platform-specific constraints.
   0 installs
9. ▌
   Fusion Pooling Strategy Implementation · holobiomicslab

   Use when you have extracted parallel feature streams from a CNN backbone (local spectral patterns) and a Transformer backbone (global dependencies) in 1H NMR spectra, and you need to fuse them into a single embedding for bi-encoder or cross-encoder processing before compound identification scoring.
   0 installs
10. ▌
    Metabolite Reference Library Filtering · holobiomicslab

    Use when you have defined one or more proton NMR spectral regions-of-interest (ROIs) with lower and upper chemical-shift bounds (in ppm) from an experimental NMR spectrum of a biological sample, and you need to identify which metabolites in a reference database (HMDB) have published 1H NMR shifts.
    0 installs
11. ▌
    Nmr Spectral Data Format Serialization · holobiomicslab

    Use when you have generated 1D FID time-domain data and Fourier-transformed frequency-domain 1H NMR spectra, or computed 2D COSY/HSQC correlation matrices, and need to write them to disk in a format that standard NMR software (e.
    0 installs
12. ▌
    Nmr Spectral Preprocessing And Phasing · holobiomicslab

    Use when when working with raw 1H NMR FID data acquired on instruments like Bruker Avance spectrometers that require baseline correction, phase adjustment, and signal alignment before metabolite identification or statistical association testing can proceed reliably.
    0 installs
13. ▌
    Galaxy W4m Lcms Processing Workflow · holobiomicslab bundle

    Use when running the Workflow4Metabolomics LC-MS pipeline end to end on a Galaxy instance — MSnbase import, xcms peak detection, correspondence, alignment and gap filling, CAMERA annotation, three-table conformance, batch correction, statistics — in the stage order the wrappers' datatypes enforce.
    0 installs
14. ▌
    Chromatin Domain Boundary Detection · holobiomicslab

    Use when you have generated a .hic contact map from Hi-C raw sequencing data and need to identify topologically associating domains (TADs) or other chromatin structural boundaries.
    0 installs
15. ▌
    Compartment Strength Quantification · holobiomicslab

    Use when when you have a binned Hi-C cooler file, an associated eigenvector track (from prior eigs_cis calculation), and need to measure how strongly the genome is partitioned into active (A) and inactive (B) compartments.
    0 installs
16. ▌
    Computational Complexity Validation · holobiomicslab

    Use when when an algorithm claims linear or sublinear time/space complexity (e.g., matrix-free spectral embedding) and you need to verify that claim holds for datasets at the scale intended (10 million+ cells).
    0 installs
17. ▌
    Hpc Cluster Scheduler Configuration · holobiomicslab

    Use when when installing HiC-Pro on a shared HPC cluster or multi-node computing environment where job submission must be routed through a scheduler rather than running locally.
    0 installs
18. ▌
    Illumina Array Data Processing Epic · holobiomicslab

    Use when you have raw Illumina EPIC or 450k methylation array data (.idat files or beta-valued matrices) and need to perform comprehensive quality assessment, probe correction, batch effect adjustment, and identification of differentially methylated regions or blocks across sample groups.
    0 installs
19. ▌
    Narrow Peak Calling Score Threshold · holobiomicslab

    Use when after generating a q-value bedgraph track from ChIP-Seq pileup versus local lambda comparison, and you need to identify statistically significant narrow peaks with defined boundaries.
    0 installs
20. ▌
    Python Package API Interface Design · holobiomicslab

    Use when you are building or refactoring a scientific Python library and need to decide how to organize and expose utility functions (e.g., adaptive coarse-graining, filtering, analysis routines) so that end users can import and call them reliably.
    0 installs
21. ▌
    R Package Installation Verification · holobiomicslab

    Use when after installing R or modifying an R environment via conda, package managers, or container images; before running any pipeline step that depends on R packages for statistical analysis, visualization, or data normalization.
    0 installs
22. ▌
    Single Cell Chromatin Data Handling · holobiomicslab

    Use when after calling peaks and annotating cells in an ArchR project, when you need to perform trajectory analysis using STREAM or other external tools that require a peak-by-cell matrix in a specific tabular format (CSV or TSV) rather than native ArchR objects.
    0 installs
23. ▌
    Transcription Factor Motif Matching · holobiomicslab

    Use when you have corrected ATAC-seq footprint scores (from ATACorrect and ScoreBigwig) at open chromatin regions and a motif database (e.g., JASPAR PWMs), and you need to determine which TF motif matches are actually occupied across one or more experimental conditions.
    0 installs
24. ▌
    Batch Script Performance Profiling · holobiomicslab

    Use when you have a collection of N scripts (e.g., 19 gallery examples) that must run on multiple backends or configurations, and you need to produce a reproducible benchmark table showing per-script execution times and aggregate totals.
    0 installs
25. ▌
    Binary Classifier Ablation Testing · holobiomicslab

    Use when you have a trained binary molecular classifier (like BitterPredict) and want to understand which groups of chemical descriptors drive its predictions.
    0 installs
26. ▌
    Cardinal Imaging Object Conversion · holobiomicslab

    Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
    0 installs
27. ▌
    Chemical Structure Standardization · holobiomicslab

    Use when when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
    0 installs
28. ▌
    Chemical Transformation Annotation · holobiomicslab

    Use when you have computed a histogram of pairwise mass differences from MS peaks and want to determine which observed mass differences correspond to known chemical species such as matrix adducts (e.g. [M+Na]+, [M+K]+), salt ions, or neutral losses.
    0 installs
29. ▌
    Container Networking Configuration · holobiomicslab

    Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate internally—specifically when you have identified service interdependencies (e.
    0 installs
30. ▌
    Converter Specification Validation · holobiomicslab

    Use when adding a new converter class to MSMetaEnhancer or when modifying an existing converter's __init__ method to add/remove conversions.
    0 installs
31. ▌
    Encoder Output Dimension Reduction · holobiomicslab

    Use when you have 512-dimensional representation vectors output from paired ResNet18 encoders processing augmented ion images, and you need to: (1) introduce an intermediate projection space to enable contrastive loss optimization without trivial/collapsed solutions, (2) further compress learned.
    0 installs
32. ▌
    File Format Detection By Extension · holobiomicslab

    Use when when building a file I/O abstraction layer that must support multiple serialization formats (e.g., uncompressed mzML, gzip-compressed mzML, indexed gzip mzML, or SQLite-backed mzML) and route each to its correct handler class without exposing format logic to downstream consumers.
    0 installs
33. ▌
    File Handler Interface Integration · holobiomicslab

    Use when you have mass spectrometry data stored in a non-standard format (SQLite database, custom indexed gzip files, or other database backends) and want to enable pymzML's Reader to access it with both random-access by spectrum ID and sequential iteration capabilities, avoiding the need to.
    0 installs
34. ▌
    Ft Icr Ms Analysis Tool Evaluation · holobiomicslab

    Use when you are evaluating or selecting FT-ICR MS software for a specific metabolomics workflow and need to assess which tools support your required analytical dimensions (e.g., Van Krevelen diagrams, PERMANOVA, thermodynamic indices, chemodiversity metrics, transformation networks).
    0 installs
35. ▌
    Github Release Metadata Comparison · holobiomicslab

    Use when you have reproduced a release artifact locally (e.g., via Semantic Release or a build tool) and need to verify it matches the official GitHub release record.
    0 installs
36. ▌
    Gnn Model Inference And Prediction · holobiomicslab

    Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify how well the model generalizes to held-out data.
    0 installs
37. ▌
    Inference Performance Benchmarking · holobiomicslab

    Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and need to rigorously compare their held-out test performance to determine which architecture balances prediction accuracy.
    0 installs
38. ▌
    Intensity Drift Artifact Detection · holobiomicslab

    Use when processing raw MS intensity tables from long measurement sequences where you observe systematic, time-dependent changes in signal magnitude (e.g., progressive increase or decrease in peak intensity across a run).
    0 installs
39. ▌
    Mass Spectrometry Benchmark Design · holobiomicslab

    Use when when claiming that one mass spectrometry processing library achieves higher throughput than competitors, or when evaluating whether a new or optimized implementation delivers the expected computational efficiency gains.
    0 installs
40. ▌
    Mass Spectrometry Data Integration · holobiomicslab

    Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to correct for systematic shifts in mass-to-charge, drift time, or retention time caused by instrumental drift, column aging.
    0 installs
41. ▌
    Molecular Cheminformatics Pipeline · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format and need to prepare molecular descriptors as input to a descriptor-based classifier (e.g., BitterPredict.m).
    2 installs
42. ▌
    Ms Quantitative Analysis Standards · holobiomicslab

    Use when you have raw MS intensity data paired with known-concentration calibration standard measurements, and you need to convert intensities to absolute or relative concentrations.
    0 installs
43. ▌
    Ms Vendor Documentation Extraction · holobiomicslab

    Use when you need to determine the complete set of validated instrument/vendor and acquisition mode combinations for a mass spectrometry analysis tool, when assessing whether your specific instrument platform (vendor, model, acquisition method) is supported before committing to a workflow, or when.
    0 installs
44. ▌
    Multi Library Comparative Analysis · holobiomicslab

    Use when you need to evaluate whether a newly released or candidate library (e.g., spectrum_utils v0.4.
    0 installs
45. ▌
    Multivariate Regression Comparison · holobiomicslab

    Use when you have paired microbiome and metabolomic (or similar compositional) data with a new regression model and want to rigorously demonstrate its predictive advantage over alternatives (Elastic Net, Random Forest, CCA).
    0 installs
46. ▌
    Network Module Interaction Scoring · holobiomicslab

    Use when after biclustering a normalized microbe-metabolite feature attribution score matrix into distinct functional modules, use this skill to summarize pairwise module interactions by aggregating scores between all microbe-metabolite pairs from different modules.
    0 installs
47. ▌
    Neural Network Layer Instantiation · holobiomicslab

    Use when when you have a neural network layer definition (parameters, weight initialization, embedding dimension) from a trained or pretrained model checkpoint and need to generate embeddings or activations for a new batch of chemical formulas or spectrum fragments.
    0 installs
48. ▌
    Parameter Sharing Mechanism Design · holobiomicslab

    Use when designing a contrastive learning pipeline for ion images or other data modalities where you need to process multiple augmented versions of the same input through an encoder and enforce similarity between the resulting representations.
    0 installs
49. ▌
    Parser Error Reporting Diagnostics · holobiomicslab

    Use when when implementing or extending a DSL parser (lexer + recursive descent or LALR parser) that accepts user-authored query strings.
    0 installs
50. ▌
    Plant Metabolic Network Validation · holobiomicslab

    Use when after community-dependent gap-filling has proposed reactions to fill metabolic gaps in individual consensus reconstructions.
    0 installs
51. ▌
    Platform Specific Code Refactoring · holobiomicslab

    Use when a Shiny application or R package currently runs only on Windows and you need to enable deployment on Linux or macOS.
    0 installs
52. ▌
    Quality Control Interval Detection · holobiomicslab

    Use when when you have Sciex Multiquant TXT export files containing injection sequences from metabolomics or lipidomics studies where pooled QC samples were deliberately injected at regular intervals to monitor analytical quality.
    0 installs
53. ▌
    Quantitative Ms Data Preprocessing · holobiomicslab

    Use when you have raw MS intensity tables showing systematic drift during a measurement sequence (e.g., declining or variable ion counts across a run), particularly in targeted quantification workflows where external calibration standards are available.
    0 installs
54. ▌
    Random Access Index Implementation · holobiomicslab

    Use when you have a large compressed scientific data file (e.g., indexed gzip mzML) where you need to retrieve specific spectra, chapters, or records by integer ID without loading the entire file into memory.
    0 installs
55. ▌
    Regression Error Metric Evaluation · holobiomicslab

    Use when when you have trained multiple regression models (e.g., using different feature sets: descriptors-only, fingerprints-only, or combined) on the same training data and need to objectively rank their generalization performance on unseen test data.
    0 installs
56. ▌
    Representation Collapse Prevention · holobiomicslab

    Use when training a contrastive learning model on ion image data (mass spectrometry imaging) where augmented pairs of the same ion image must maximize similarity while different images minimize similarity.
    0 installs
57. ▌
    Smiles Inchi Round Trip Validation · holobiomicslab

    Use when you have implemented a new RDKit-based ComputeConverter for SMILES↔InChI conversions and need to verify that the conversion methods preserve molecular structure integrity across round-trip transformations (SMILES → InChI → SMILES or vice versa) before registering it in the MSMetaEnhancer.
    0 installs
58. ▌
    Structured Data Quality Assessment · holobiomicslab

    Use when when you have deposited a collection of JSON project documents in a platform or repository and need to verify that all conform to a published JSON Schema specification before publication, distribution, or integration with downstream systems.
    0 installs
59. ▌
    Technical Specification Tabulation · holobiomicslab

    Use when when you need to verify whether a specific mass spectrometry instrument platform (vendor and model), acquisition mode (e.g., targeted, ddMS2-topN, AIF, direct infusion, imaging), or file format is compatible with a lipidomics or proteomics software tool;
    0 installs
60. ▌
    Validated Link Enrichment Analysis · holobiomicslab

    Use when when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated links for the same strain(s), and need to assess whether combining or filtering by percentile thresholds improves.
    0 installs
61. ▌
    Abstract Base Class Implementation · holobiomicslab

    Use when when building a visualization library that must support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and multiple data types (e.g., chromatograms, spectra, peak maps) without duplicating core logic or configuration handling across backend–plot-type combinations.
    0 installs
62. ▌
    Adduct Mass Adjustment Calculation · holobiomicslab

    Use when you have a set of in silico-predicted compounds (with SMILES structures) and an experimental metabolomics peak list (m/z values), and you need to filter predictions to only those that could plausibly be detected.
    0 installs
63. ▌
    Autoencoder Encoder Decoder Design · holobiomicslab

    Use when when working with imaging mass spectrometry (IMS) datasets where you need to extract latent low-dimensional peak features from high-dimensional peak intensity data while preserving spatial adjacency information.
    0 installs
64. ▌
    Batch Corrected Data Visualization · holobiomicslab

    Use when after doAnalysis() has been completed and batch correction applied (ratio_corrected assay populated), use this skill when you need to inspect the effect of batch correction on QC sample clustering, verify that study samples group appropriately by type or aliquot, or identify remaining.
    0 installs
65. ▌
    Batch Effect Correction Combat Sva · holobiomicslab

    Use when you have a normalized count matrix (from Salmon or similar quantification tool) with sample metadata that documents batch variables (e.g., sequencing run, processing date, lab site), and you observe or suspect that batch effects—not biological signal—are driving variance across samples.
    0 installs
66. ▌
    Betweenness Centrality Computation · holobiomicslab

    Use when when you have a pathway-metabolite bipartite network and a filtered set of input metabolites (e.g., from differential analysis or experimental selection), and you need to rank metabolites by their topological importance within the network structure—i.
    0 installs
67. ▌
    Bgc Tokenization With Pfam Domains · holobiomicslab

    Use when you have GenBank-format BGC sequences annotated with Pfam domain assignments and you need to prepare them for sub-cluster detection, redundancy filtering via similarity networks, or linking to natural product substructures.
    0 installs
68. ▌
    Binary Data Integrity Verification · holobiomicslab

    Use when after implementing a lossless compression–decompression cycle on mzML or mzXML mass spectrometry files, or when validating that a lossy compression pipeline meets acceptable error thresholds.
    0 installs
69. ▌
    Biotransformation Rule Application · holobiomicslab

    Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its fate in soil or aquatic environments through microbial degradation pathways.
    0 installs
70. ▌
    Bounding Box Regression Prediction · holobiomicslab

    Use when when you have a trained CNN binary classifier for peak detection on rt×mz LC-HRMS images and need to additionally output precise bounding-box coordinates (left, right, top, bottom) and peak-center pixel positions for each detected peak to enable accurate feature quantitation or visual.
    0 installs
71. ▌
    Classyfire Batch Database Querying · holobiomicslab

    Use when you have a GNPS DBResult file with InChIKey identifiers but lack corresponding ClassyFire superclass, class, and subclass taxonomy annotations—particularly when GNPS spectral library matches no longer include this ontology information by default.
    0 installs
72. ▌
    Collision Cross Section Prediction · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) and need to predict their collision cross sections for ion mobility mass spectrometry workflows, particularly when generating large-scale searchable CCS databases for compound identification and characterization.
    0 installs
73. ▌
    Compound Reliability Rsd Filtering · holobiomicslab

    Use when after batch correction and internal standard ratio calculation when you have pooled study quality control (SQC) or pooled quality control (QC) samples and need to determine which compounds are sufficiently reliable for downstream reporting.
    0 installs
74. ▌
    Concentration Based Signal Scaling · holobiomicslab

    Use when you have loaded m/z peak data with metadata that includes a concentration column representing sample loading mass or volume, and systematic intensity variation across samples is suspected to reflect preparation differences rather than true biological variation.
    0 installs
75. ▌
    Correlation Threshold Optimization · holobiomicslab

    Use when after computing pairwise correlations across all features in a dataset (especially those exceeding 10,000 features), before constructing the final network object.
    0 installs
76. ▌
    Cross Table Metadata Harmonization · holobiomicslab

    Use when when you have obtained raw metabolite abundance data in a format that separates the measurement matrix from sample-level metadata (e.g., run day, plate ID, cohort variables) and feature-level annotations (e.
    0 installs
77. ▌
    Cross Validation Model Aggregation · holobiomicslab

    Use when after training multiple neural network models via k-fold cross-validation (e.g., 10 iterations × 10-fold = 100 models), when you need to extract and aggregate learned feature interactions rather than relying on a single trained model.
    0 installs
78. ▌
    CSV File Parsing And Peak Indexing · holobiomicslab

    Use when you have a metabolomics dataset (CSV format) containing detected peaks with m/z values and optionally retention time windows, and you need to filter a Pickaxe-generated compound expansion to keep only compounds whose masses match these observed peaks within a specified mass tolerance.
    0 installs
79. ▌
    Data Object Loading And Inspection · holobiomicslab

    Use when you have identified example R or MATLAB scripts in a repository's Codes-Explained folder and need to execute them on a documented sub-sample scenario. The link-to-codes-and-data-objects file specifies which data object(s) to load, and the Read-Me.
    0 installs
80. ▌
    Data Quality Validation Lipidomics · holobiomicslab

    Use when after loading and parsing raw MRM export files (TSV, CSV, or vendor-specific formats) into a pandas DataFrame and decomposing lipid nomenclature, before performing lipid matching, statistical analysis, or visualization.
    0 installs
81. ▌
    Database Record Conditional Update · holobiomicslab

    Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field (e.g., ionmode: 'pos'/'neg') that can deterministically populate the missing field.
    0 installs
82. ▌
    Datatype Validation Helper Methods · holobiomicslab

    Use when when implementing a custom MsBackend subclass and need to verify that spectra variables (e.g., precursor m/z, retention time, MS level) conform to expected data types before exposing them to Spectra objects.
    0 installs
83. ▌
    Deep Neural Network Regularization · holobiomicslab

    Use when when training a DNN on molecular properties (e.g., retention time) using high-dimensional feature sets (>2000 fingerprints + descriptors) where test performance is critical and overfitting risk is high due to model capacity or limited validation data;
    0 installs
84. ▌
    Dot Product Similarity Computation · holobiomicslab

    Use when when performing open modification spectral library searching and you need to sensitively match query spectra that may carry unknown post-translational or chemical modifications to an unmodified spectral library.
    0 installs
85. ▌
    Dotnet Project Build Configuration · holobiomicslab

    Use when you are attempting to compile a WPF-based .NET desktop application from source code that targets multiple .NET Framework versions, have cloned a repository with an .sln solution file, and need to resolve framework-specific NuGet dependencies (e.
    0 installs
86. ▌
    External Calibration Model Fitting · holobiomicslab

    Use when you have acquired targeted mass spectrometry data with measured ion intensities for known standard compounds at multiple concentration levels, and you need to convert sample intensities into absolute or relative concentrations.
    0 installs
87. ▌
    Feature Branch Workflow Management · holobiomicslab

    Use when when implementing a new feature or bug fix in a shared repository (such as Maven GUI metabolomics analysis software) where multiple contributors work in parallel and code quality is enforced via CI/CD pipelines (Travis, Appveyor).
    0 installs
88. ▌
    Feature Correlation Sparsification · holobiomicslab

    Use when you have a feature matrix (rows=samples, columns=features) and want to infer the conditional independence structure among features.
    0 installs
89. ▌
    Feature Set Performance Evaluation · holobiomicslab

    Use when when deciding which molecular representation to use for retention time prediction or similar regression tasks on small molecules, and you have access to multiple feature generation options (e.g., alvaDesc can generate both molecular descriptors and multiple fingerprint types).
    0 installs
90. ▌
    Feature Transformation And Scaling · holobiomicslab

    Use when after imputation and QC sample correction when: (1) your peak intensity data show heteroscedastic variance (e.g., variance increases with mean intensity); (2) you aim to improve normality of feature distributions for parametric statistical tests;
    0 installs
91. ▌
    Fingerprint Generation From Smiles · holobiomicslab

    Use when you have molecule IDs from PubChem or HMDB that have been converted to RDKit molecule objects, and you need to create a standardized fingerprint modality to combine with graph-based and physicochemical descriptor features for multimodal deep learning on molecular property prediction.
    0 installs
92. ▌
    Formula Deduplication And Counting · holobiomicslab

    Use when when you have loaded a chemical database (e.g., HMDB pickle file) and need to understand how many distinct molecular formulas remain after filtering for a specific m/z range (e.g., 100–1000) and MS acquisition level (typically MS level 1).
    0 installs
93. ▌
    Gene Domain Co Occurrence Analysis · holobiomicslab

    Use when you have a collection of BGCs tokenised as Pfam domain / subPfam combinations, have filtered them for redundancy using domain-based similarity networks, and need to discover latent gene sub-clusters that group together genes with correlated domain compositions.
    0 installs
94. ▌
    Graph Neural Network Model Loading · holobiomicslab

    Use when when you need to evaluate GNN performance on collision cross section prediction using the enveda/ccs-prediction repository, either by loading an existing pre-trained model checkpoint or by retraining from scratch using deposited datasets and published hyperparameters.
    0 installs
95. ▌
    Graphical Interface Error Handling · holobiomicslab

    Use when when building a standalone desktop application with a graphical user interface that depends on external binary tools or libraries, and you need to prevent user confusion from cryptic runtime errors. Specifically: when your GUI framework (e.
    0 installs
96. ▌
    Group Specification And Subsetting · holobiomicslab

    Use when when implementing a fold-change filter or similar feature-level metric that requires comparison across sample groups, and the analysis goal requires including or excluding specific groups (e.g., comparing only treated vs. control samples, or excluding low-quality replicates).
    0 installs
97. ▌
    Harmonized Metadata Schema Mapping · holobiomicslab

    Use when you have imported mass spectrometry spectra from multiple file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to standardize their metadata fields before performing spectral comparisons, similarity scoring, or library construction.
    0 installs
98. ▌
    Histogram Peak Occurrence Analysis · holobiomicslab

    Use when after you have computed a histogram of pairwise mass differences from MSI peak data and want to identify which mass shifts occur most frequently and whether they correspond to known chemical adducts.
    0 installs
99. ▌
    Imaging Data Workspace Integration · holobiomicslab

    Use when you have paired cdf files (raw mass spectrometry imaging data) and Matlab workspace (.mat) files for the same root sample, and you need to reproduce published linear-axis imaging analysis results (e.g., per-root mass spectrometry imaging metrics along a developmental or spatial axis).
    0 installs
100. ▌
     Interactive Plot Axis Selection UI · holobiomicslab

     Use when when you have a high-resolution mass spectrometry dataset with m/z values and need to generate Kendrick mass plots where users should choose between plotting raw m/z or computed Normalized Kendrick Mass (NKM) on the x-axis.
     0 installs