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HolobiomicsLab

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1. ▌
   Unified Mobility Scale Construction Across Polarities · holobiomicslab

   Use when you have CE-MS raw data in OnDiskMSnExp format with both positive and negative polarity acquisitions, migration times that vary due to electroosmotic flow drift, and access to two well-characterized mobility markers (e.g., Paracetamol and Procaine with known charges and migration times).
   0 installs
2. ▌
   Automated Peak Detection Without Conventional Picking · holobiomicslab

   Use when you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak picking algorithms. This is especially valuable when analyzing complex, low-abundance samples (e.
   0 installs
3. ▌
   Comparative Algorithm Benchmarking For Peak Detection · holobiomicslab

   Use when you have developed or adapted a peak detection method for chromatography–mass spectrometry and need to validate its reliability against an established baseline on the same raw GC–MS dataset. Specifically when: (1) the input is raw GC–MS data in m/z vs retention time format;
   0 installs
4. ▌
   Ionization Mode Detection From Mass Spectrometry Data · holobiomicslab

   Use when when you have raw LC-MS data in mzML format (converted from .raw or acquired directly in that format) and need to invoke Asari for feature extraction, but the ionization mode is not explicitly specified in your experimental metadata or pipeline configuration.
   0 installs
5. ▌
   Ppb Level Marker Detection And Sensitivity Assessment · holobiomicslab

   Use when you have raw GC–MS or LC–MS data in two-dimensional m/z vs retention time format and need to identify marker features at parts-per-billion sensitivity without relying on conventional peak picking.
   0 installs
6. ▌
   Spectrum Document Conversion Peak Loss Representation · holobiomicslab

   Use when when preparing MS/MS spectral data for training word-embedding models (Word2Vec, Skip-gram, CBOW) that will learn relationships between fragment ions and neutral losses.
   0 installs
7. ▌
   Deep Learning Model Inference And Ensemble Prediction · holobiomicslab

   Use when you have a trained deep learning model and want to quantify prediction uncertainty for each input pair or decision point. Use this when you need to identify low-confidence predictions (high IQR) and filter them out to reduce error in specific score ranges (e.
   0 installs
8. ▌
   Machine Learning Model Training With Cross Validation · holobiomicslab

   Use when when you have a labeled peak quality matrix (with known pass/fail labels), need to objectively compare performance across multiple classification algorithms (e.
   0 installs
9. ▌
   Mass Spectrometry Data Coordinate System Construction · holobiomicslab

   Use when when you have processed LC-MS/MS spectral data in .mgf format with precomputed ms2deepscore similarity matrices and need a 2-D overview representation that preserves local spectral relationships for interactive exploration and visualization.
   0 installs
10. ▌
    Mass Spectrometry Deconvolution Algorithm Application · holobiomicslab

    Use when you have raw DDA, DIA (MS^E, AIF, SWATH-MS), or MS1-only mass spectrometry data in mzML, mzXML, or netCDF format and need to deconvolute fragmentation spectra by linking precursor ions to their fragment ions based on retention time and m/z relationships.
    0 installs
11. ▌
    Metabolic Reaction Classification By Regulatory Layer · holobiomicslab

    Use when you have integrated transcriptomics, intracellular metabolomics, and extracellular flux ratio data from multiple cell lines or conditions, and need to determine whether observed differences in metabolic fluxes originate from gene expression changes, substrate availability changes, or both.
    2 installs
12. ▌
    Metabolomics Data Integration With Metabolic Networks · holobiomicslab

    Use when you have measured intracellular metabolite concentrations (e.g., via LC–MS/MS) across multiple cell lines or samples and want to predict which metabolic reactions are substrate-limited versus transcriptionally regulated.
    2 installs
13. ▌
    Metabolomics Feature Selection Significance Filtering · holobiomicslab

    Use when you have fitted an MB-PLS model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG), computed MB-VIP scores for all features, and need to identify which features are statistically significant for your phenotypic outcome.
    0 installs
14. ▌
    Python Package Installation And Dependency Management · holobiomicslab

    Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that depends on specific versions of auxiliary packages (like spectrum-utils==0.3.5).
    0 installs
15. ▌
    Relative Standard Deviation Calculation Qc Replicates · holobiomicslab

    Use when you have a peak table from XCMS preprocessing with intensity measurements for the same set of metabolites across multiple QC replicate injections (samples marked SampleType='LQC'), and you need to filter out EICs with poor reproducibility before evaluating peak quality or training a.
    1 install
16. ▌
    Spectral Dataset Partitioning And Train Test Curation · holobiomicslab

    Use when when you have a pre-cleaned spectral library (e.g., GNPS, MoNA, or MTBLS1572) with an existing training/test boundary established by prior work (e.g., MSBERT), and you need to report model performance with uncertainty quantification across multiple random partitions.
    2 installs
17. ▌
    Statistical Significance Estimation Mass Spectrometry · holobiomicslab

    Use when after aligning fragment ions between two tandem mass spectra (query and reference) using maximum weight matching and you need to assign confidence scores to the matched ion pairs.
    0 installs
18. ▌
    Tandem Mass Spectrum Deconvolution Isotope Annotation · holobiomicslab

    Use when you have aligned features characterized across multiple dimensions (m/z, drift time, retention time) and need to: (1) resolve MS/MS spectra that may contain fragments from multiple co-eluting or co-mobilizing precursors; (2) identify and validate isotopic signatures (e.
    0 installs
19. ▌
    Bioinformatics Tool Version Compatibility Assessment · holobiomicslab

    Use when before executing a complex bioinformatics pipeline (such as Hi-C data processing) that depends on multiple third-party tools with explicit version constraints.
    0 installs
20. ▌
    CI CD Workflow Adaptation To Organization Standards · holobiomicslab

    Use when when a Python package is being relocated to a new GitHub organization (e.
    0 installs
21. ▌
    Collision Cross Section Measurement Quality Control · holobiomicslab

    Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and you need to quantify whether measured CCS values deviate systematically from theoretical values, or when you want to correct CCS measurements before downstream lipid.
    2 installs
22. ▌
    Principal Component Extraction From Pathway Subsets · holobiomicslab

    Use when you have a log2-normalized, zero-mean and unit-variance standardized intensity matrix of metabolite features (rows=metabolites, columns=samples) and need to compute a single activity score per pathway that reflects the coordinated expression behavior of all metabolites assigned to that.
    0 installs
23. ▌
    Statistical Significance Testing Metabolic Networks · holobiomicslab

    Use when you have sampled flux distributions from two or more constraint-based metabolic models representing different biological conditions (e.
    0 installs
24. ▌
    Structural Similarity Calculation Fingerprint Based · holobiomicslab

    Use when you have a set of compounds (e.g., novel NPS analogues in an evaluation dataset) and need to classify them as structurally similar to or divergent from a reference set (e.g., training compounds).
    0 installs
25. ▌
    Antismash Bgc Directory Organization And Validation · holobiomicslab

    Use when when preparing genomic data for NPLinker analysis and you have AntiSMASH BGC predictions that need to be validated and organized into NPLinker's standardized directory layout.
    0 installs
26. ▌
    Batch Effect Preprocessing With Replicate Structure · holobiomicslab

    Use when you have metabolomics data from multiple experimental batches (≥2) with embedded replicate samples (identical samples run at different points within or across batches), log-transformed raw assays containing ≥50% missing values per batch, and a need to harmonise metabolite quantification.
    0 installs
27. ▌
    Bigscape Output Version Detection And Compatibility · holobiomicslab

    Use when when preparing NPLinker input data and the BigScape directory exists but its format is unknown or mixed (e.g., migrated workflows, third-party data, or legacy archives). Specifically: if local mode and BigScape directory is missing, generate it;
    2 installs
28. ▌
    Comparative Output Analysis Across Parameter States · holobiomicslab

    Use when when you need to validate that a boolean control parameter in BioTransformerAPI (useCypReact) properly gates a filtering module, or when you want to understand the qualitative and quantitative impact of CypReact filtering rules on predicted metabolite outputs for a given substrate and.
    1 install
29. ▌
    Corrected Uncorrected Data Comparison Visualization · holobiomicslab

    Use when after preprocessing and log-transformation of metabolomics feature abundance matrices (samples as rows, metabolic features as columns), when you have multiple candidate batch-correction models (e.
    0 installs
30. ▌
    Cross Batch Metabolite Quantification Harmonization · holobiomicslab

    Use when you have multiple SummarizedExperiment objects representing separate metabolomics assay batches with different metabolite coverage and missing-value patterns, and you need to identify a common metabolite set quantified across all batches before applying hierarchical batch normalization or.
    1 install
31. ▌
    Cross Validated Model Performance Evaluation 10fold · holobiomicslab

    Use when when you have trained a neural network or regression model to predict metabolite abundances from microbiome features and need to measure how well the model generalizes to unseen samples. Apply this skill when you want to compare multiple competing models (e.
    2 installs
32. ▌
    Custom File Handler Class Design For Indexed Access · holobiomicslab

    Use when your input is a large mzML or text file that would benefit from compression without sacrificing random-access performance, and you need to retrieve specific logical blocks (e.g., a chapter, spectrum, or database record) by key without decompressing the entire file.
    2 installs
33. ▌
    Deep Learning Architecture Design For Sequence Data · holobiomicslab

    Use when when you have raw co-fractionation/mass-spectrometry elution profiles (normalized intensity vectors across fractions) paired with labeled protein interaction ground truth, and you want to avoid hand-crafted features (e.
    0 installs
34. ▌
    Docker Container Environment Variable Configuration · holobiomicslab

    Use when when deploying a Java application in a Docker container and you need to adjust JVM heap memory settings (maximum and initial heap size) without modifying the container image.
    0 installs
35. ▌
    Feature Metadata Extraction From Clustering Objects · holobiomicslab

    Use when after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
    0 installs
36. ▌
    Grid Search Evaluation And Threshold Identification · holobiomicslab

    Use when you have a fitted alignment model (e.g., metabCombiner object with pre-aligned feature pair candidates and RT spline mapping) and known shared compound identities (ground truth) from reference datasets, and you need to determine which combination of three or more continuous parameters (e.
    2 installs
37. ▌
    Hierarchical Cluster Analysis Dendrogram Generation · holobiomicslab

    Use when you have a feature-by-sample matrix (finalData) of metabolomic intensities and sample group labels (finalLabel), and you want to visualize how samples cluster together based on their overall metabolomic similarity.
    0 installs
38. ▌
    Hypergeometric Distribution Probability Calculation · holobiomicslab

    Use when when you have raw strain correlation scores computed across GCF–MF pairs of varying sizes (different numbers of strains in each set) and need to make those scores comparable.
    0 installs
39. ▌
    In Memory Cache Implementation For Repeated Queries · holobiomicslab

    Use when when deploying a high-throughput molecular classification API (e.g., /classify endpoint) where the same SMILES strings are expected to be queried repeatedly across multiple users or time windows, and response latency is a performance constraint.
    0 installs
40. ▌
    Maldi Imaging Mass Spectrometry Data Interpretation · holobiomicslab

    Use when you have paired pre- and post-MALDI microscopy images with visible, non-overlapping ablation marks, MALDI raw data files (.RAW, .UDP, .imzML, .ibd) analyzed by METASPACE, and a segmented cell mask from CellProfiler.
    0 installs
41. ▌
    Metabolic Network Database Output And Serialization · holobiomicslab

    Use when after completing a Pickaxe reaction network expansion across N generations, when you need to store the predicted compounds and reactions in a format suitable for querying, sharing, or integration with other bioinformatic pipelines.
    0 installs
42. ▌
    Metabolite Composition Comparison Across Treatments · holobiomicslab

    Use when you have normalized peak intensity tables from FT-ICR MS data (e.g., MetaboDirect .
    0 installs
43. ▌
    Metabolomic Dataset Preprocessing And Normalization · holobiomicslab

    Use when you have raw or minimally processed FT-ICR MS peak tables in Formularity .
    0 installs
44. ▌
    Metabolomic Feature Filtering Threshold Application · holobiomicslab

    Use when after running the Marr() function on preprocessed metabolomic data (with missing value imputation and normalization already complete) when you need to distinguish reproducible from non-reproducible features and sample pairs.
    1 install
45. ▌
    Molecular Structure Canonicalization And Validation · holobiomicslab

    Use when immediately after generating candidate transformation products from biotransformation rules.
    0 installs
46. ▌
    Multi Mode Filter Application High Dimensional Data · holobiomicslab

    Use when you have high-dimensional biological data (e.
    0 installs
47. ▌
    Multiprocessing Process Spawning And Pid Management · holobiomicslab

    Use when when deploying a Streamlit workflow app in offline mode (online_deployment: false) or when Redis is unavailable in online mode, and you need to launch workflows as independent background processes while maintaining the ability to track, recover, or cancel them later by their PID.
    0 installs
48. ▌
    Omics Data Quality Assessment Normalization Context · holobiomicslab

    Use when after loading peptide or protein-level quantification matrices with sample metadata into pmartR, and before proceeding to statistical analysis (ANOVA, G-test).
    2 installs
49. ▌
    P Value Computation And Multiple Testing Correction · holobiomicslab

    Use when after matched lipid abundances have been grouped by experimental condition and descriptive statistics (mean, SD, median) calculated per group.
    0 installs
50. ▌
    Pc Selection Via Acceleration And Parallel Analysis · holobiomicslab

    Use when when preparing metabolomic or multivariate count data for outlier detection in PC space, or when you need to reduce dimensionality while retaining only statistically significant components.
    0 installs
51. ▌
    Principal Component Analysis Multivariate Reduction · holobiomicslab

    Use when after normalizing and log-transforming lipidomics abundance data (e.
    0 installs
52. ▌
    Pymzml Reader Initialization With Custom Parameters · holobiomicslab

    Use when you have an mzML file (e.g. Manuels_customs_ids.mzML) with non-standard custom index identifiers that cannot be parsed by pymzML's default index parser.
    0 installs
53. ▌
    Quality Control Sample Integration In Normalization · holobiomicslab

    Use when your multi-class metabolomic peak table includes quality control samples (technical replicates) but no internal standards, and you need to compare the performance of multiple preprocessing workflows (normalization, imputation, transformation methods) to select the optimal pipeline for.
    0 installs
54. ▌
    Semantic Role Assignment For Mass Spectrometry Data · holobiomicslab

    Use when you have uploaded a delimited data file (comma-, semicolon-, or tab-separated) with a header row into Punc'data and need to ensure that each column is correctly mapped to its semantic role (m/z, intensity, formula, or other mass spectrometry attributes) before proceeding to analysis.
    0 installs
55. ▌
    Summarized Experiment Initialization And Population · holobiomicslab

    Use when when beginning a metabolomics analysis workflow in maplet, you have raw or preprocessed metabolomics data (assay measurements) and associated sample metadata (colData) or feature annotations (rowData), and you need to create a single, unified container that will hold data, intermediate.
    0 installs
56. ▌
    Taxonomic Nomenclature Normalization And Validation · holobiomicslab

    Use when you have organism names originating from 31+ heterogeneous natural product databases that use different taxonomic authorities, nomenclature versions, or rank assignments, and you need to harmonize them into a single organism subgraph with validated ranks before linking to chemical.
    0 installs
57. ▌
    Microarray Expression Normalization Log Quantile · holobiomicslab

    Use when when you have raw or minimally processed microarray expression data (e.g., from GEO) with intensity values that exhibit sample-to-sample distributional differences and variance heterogeneity.
    0 installs
58. ▌
    Spatial Coordinate Integration With Imaging Data · holobiomicslab

    Use when you have a spatial omics dataset (AnnData object with coordinate columns like 'x', 'y', 'z') and an associated tissue image file (e.g., TIFF, PNG, or HE-stained histology), and you need to extract image-based morphological features (e.
    0 installs
59. ▌
    Consensus Spectrum Assembly From Fragmentation Spectra · holobiomicslab

    Use when you have detected a single chromatographic peak in DDA LC-MS/MS data that generated multiple MS2 fragmentation spectra (e.
    2 installs
60. ▌
    Peak Quality Assessment By Selectivity And Snr Metrics · holobiomicslab

    Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence thresholds, and before mapping detected features back to individual samples or performing pre-annotation.
    1 install
61. ▌
    Chromatographic Peak Detection With Prominence Control · holobiomicslab

    Use when after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature extraction in LC-MS or GC-MS metabolomics workflows.
    0 installs
62. ▌
    Ensemble Model Weight Learning For Spectral Prediction · holobiomicslab

    Use when you have pre-trained MLP and GNN models that generate different spectral predictions for the same metabolite candidates, and you want to combine them to improve ranking performance (average rank, Rank@K metrics) without retraining the base models.
    0 installs
63. ▌
    Multiway Principal Component Analysis Score Extraction · holobiomicslab

    Use when after preprocessing and aligning 2D chromatogram data (baseline correction, smoothing, peak alignment) and after running m_prcomp multiway PCA on the joined chromatogram matrix.
    0 installs
64. ▌
    Word2vec Vocabulary Matching And Unknown Peak Handling · holobiomicslab

    Use when converting MS/MS spectra into Spec2Vec embeddings using a pre-trained Word2Vec model that was trained on reference data (e.g., a subset of GNPS or MassBank).
    0 installs
65. ▌
    Candidate Neighbourhood Analysis For Spectral Matching · holobiomicslab

    Use when you have a query MS/MS spectrum matched against a library and need to re-rank the top 2000 candidate spectra by combining spectral similarity (MS2Deepscore) with structural neighbourhood information.
    0 installs
66. ▌
    Categorical Numerical Feature Concatenation For Graphs · holobiomicslab

    Use when when preparing heterogeneous column-metadata inputs for a graph transformer model that operates on molecular graphs. Specifically: (1) you have both categorical metadata (e.
    2 installs
67. ▌
    Connected Component Decomposition In Mass Spectrometry · holobiomicslab

    Use when you have a feature list from LC-MS preprocessing (e.g., asari output) and have already identified all pairwise feature matches to isotope and adduct patterns. Apply this skill when you need to separate feature matches into disjoint empirical compounds—i.
    1 install
68. ▌
    Diagnostic Quality Assessment Of Chromatographic Peaks · holobiomicslab

    Use when after running targeted peak detection in TARDIS (screening_mode = FALSE) on centroided .mzML LC–MS files, apply this skill to verify that integrated peaks for your target compounds exhibit acceptable quality.
    2 installs
69. ▌
    Generalized Additive Model Hyperparameter Optimization · holobiomicslab

    Use when when fitting a nonlinear retention time (RT) mapping spline to anchor feature pairs (m/z and RT values) from two LC-MS datasets acquired under different conditions, you need to determine both the optimal B-spline basis dimension and identify which anchor points are outliers.
    0 installs
70. ▌
    Input Output Kernel Regression For Metabolite Matching · holobiomicslab

    Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links using metabolite structure information rather than genomic or strain-based features alone.
    0 installs
71. ▌
    Mass2motif Annotation Guidance Via Spectral Embeddings · holobiomicslab

    Use when after discovering Mass2Motifs through LDA topic modeling of MS/MS fragmentation data, when you need to assign chemical meaning (substructure classes, candidate annotations) to motifs by leveraging pre-trained spectral embeddings and a reference motif database.
    2 installs
72. ▌
    Metabolomics Functional Prediction Workflow Validation · holobiomicslab

    Use when a Python-based metabolomics analysis package has been relocated to a new GitHub organization (e.g., metabolomics-cloud) and you need to confirm that the migration preserved package integrity, installation, and runtime correctness.
    0 installs
73. ▌
    Method Equivalence Verification Across API Invocations · holobiomicslab

    Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode diagnostic outputs (e.g., EIC plots, peak detection metrics) are identical regardless of which invocation pattern is used.
    0 installs
74. ▌
    Ms2 Spectrum Peak Filtering By Training Set Membership · holobiomicslab

    Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a training dataset of known spectra (e.g., GNPS library spectra with structural annotations).
    0 installs
75. ▌
    Neutral Loss Calculation From Precursor Fragment Pairs · holobiomicslab

    Use when during MS/MS spectral preprocessing when converting raw spectra from .mgf, .msp, or .mzML formats into a bag-of-fragments corpus for LDA modeling. Use it after fragment ion masses have been extracted and normalized within each spectrum, and before noise filtering and corpus generation.
    2 installs
76. ▌
    Precursor Region Handling And M Z Tolerance Management · holobiomicslab

    Use when when computing entropy_similarity() between experimental (noisy or denoised) MS/MS spectra and reference library spectra, if the precursor m/z value is known and available.
    0 installs
77. ▌
    Quality Metric Computation From Mass Spectrometry Data · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, or .wiff format) from timsTOF, TripleTOF, or Orbitrap instruments and need to assess their quality before downstream proteomics analysis.
    0 installs
78. ▌
    Receiver Operating Characteristic Curve Interpretation · holobiomicslab

    Use when you have a trained NeatMS neural network model and labelled peak validation data, and need to select an operational classification threshold or understand how TPR and FPR vary across probability thresholds (e.g., 0.00–0.99).
    0 installs
79. ▌
    Separation Efficiency Calculation From Retention Times · holobiomicslab

    Use when you have extracted retention times from MS1 spectra for top signals in a single LC-MS/MS run and need to evaluate whether that gradient's separation performance is sufficient, or when you are building the objective function for an iterative gradient optimization loop where each candidate.
    2 installs
80. ▌
    Strain Identifier Mapping Across Genomics Metabolomics · holobiomicslab

    Use when when preparing multiomics datasets for NPLinker that combine GNPS metabolomics, AntiSMASH genomics, and MIBiG reference data, and you need to establish which strain IDs or sample identifiers appear in both genomic and metabolomic experiments.
    0 installs
81. ▌
    Molecular Fragment Assembly From Transformer Predictions · holobiomicslab

    Use when when you have encoded spectral features (from a CNN featurizer applied to 1D 1H and/or 13C NMR spectra) and a set of candidate molecular fragments predicted for a molecule with ≤19 heavy atoms, and you need to determine the correct connectivity and assembly order to recover the.
    0 installs
82. ▌
    Chromatin Accessibility Binding Status Classification · holobiomicslab

    Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually occupied by proteins in your cell type or condition.
    0 installs
83. ▌
    Transcription Factor Binding Depletion Quantification · holobiomicslab

    Use when after bias-correcting ATAC-seq cutsite signal (using ATACorrect or equivalent) when you have a set of genomic regions of interest (e.
    2 installs
84. ▌
    Python Workflow Execution And Orchestration · holobiomicslab

    Use when you have raw LC/MS data in mzML format and need to execute a complete non-targeted screening workflow to extract and annotate chemical features.
    0 installs
85. ▌
    Replicate Spectrum Aggregation Sample Level · holobiomicslab

    Use when after frequency-based denoising has been applied to individual replicate spectra within each feature (via generate_denoised_spectra), you have a collection of denoised fragment ion lists per feature per scan.
    2 installs
86. ▌
    Repository Cloning And Structure Navigation · holobiomicslab

    Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.
    0 installs
87. ▌
    Retention Time Indexed Spectral Aggregation · holobiomicslab

    Use when you have Thermo Fisher Scientific .raw files from an LC-MS experiment and need to extract spectral features (base-peak m/z, intensity, scan-level properties) indexed by retention time for downstream statistical analysis, method optimization, or diagnostic visualization.
    0 installs
88. ▌
    Ripp Peptide Sequence Database Construction · holobiomicslab

    Use when when you have genomic sequences (assembled contigs or antiSMASH/BOA mining results) and want to match experimental tandem mass spectra against predicted RiPP structures.
    0 installs
89. ▌
    Scan Number Mapping Dictionary Construction · holobiomicslab

    Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable, memory-efficient lookup table that can be applied during feature alignment without recomputing the regression for every sample.
    2 installs
90. ▌
    Score Standardisation Z Score Normalization · holobiomicslab

    Use when when comparing raw link scores (strain correlation or IOKR) across different GCF-MF or BGC-spectrum pairs and you need to distinguish true positive links from background noise. Raw scores depend on overlap size and are incomparable across links with different cluster sizes;
    0 installs
91. ▌
    Search Result Aggregation And Normalization · holobiomicslab

    Use when you have executed batch searches across two or more domain-specific MASST tools and obtained separate output files (_microbe.json, _plant.json, _tissue.
    2 installs
92. ▌
    Similarity Ranking And Retrieval Evaluation · holobiomicslab

    Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
    0 installs
93. ▌
    Spectral Embedding Rationality Verification · holobiomicslab

    Use when after training a transformer-encoder-based mass spectrometry embedding model (e.
    0 installs
94. ▌
    Spectral Preprocessing For Machine Learning · holobiomicslab

    Use when when preparing raw MS2 spectra (m/z and intensity pairs) for kernel-based scoring methods such as IOKR, especially when the training dataset is large and represents diverse ion types.
    0 installs
95. ▌
    Spectrum Alignment Performance Benchmarking · holobiomicslab

    Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a spectral library search.
    2 installs
96. ▌
    Spectrum Visualization And Figure Rendering · holobiomicslab

    Use when when you have a processed or annotated MsmsSpectrum object (from USI loading or direct instantiation) and need to generate a figure showing observed peaks, their intensities, and assigned fragment ions (e.g., b/y ions) for publication or presentation.
    0 installs
97. ▌
    Structure Annotation Via Similarity Ranking · holobiomicslab

    Use when you have an unknown tandem MS spectrum and seek to assign a chemical structure by matching against a curated reference database (e.g., NIST, GNPS, or custom metabolite libraries) without requiring an exact spectral match.
    0 installs
98. ▌
    Structured Molecule Relationship Evaluation · holobiomicslab

    Use when when you have tandem mass spectra (MSMS) from related or candidate molecules and need to determine which similarity metric—cosine, modified cosine, or neutral loss— ranks structurally similar compounds in your dataset. Particularly useful when structural relationships are known a priori (e.
    0 installs
99. ▌
    Subformula Enumeration And Mass Calculation · holobiomicslab

    Use when when performing chemical denoising of MS/MS spectra: after modifying a master formula based on SMILES and adduct information, enumerate all possible subformulas to establish the set of chemically valid neutral losses.
    0 installs
100. ▌
     Thread Utilization Profiling And Validation · holobiomicslab

     Use when when deploying Mass2SMILES inference on CPU-only hardware (e.g., when GPU/CUDA support is unavailable), you need to verify that the InferenceModel cpu_threads parameter (e.g., cpu_threads=128) actually controls thread allocation during execution.
     0 installs