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HolobiomicsLab

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1. ▌
   Mass Spectral Missing Word Fraction Computation 4 · holobiomicslab

   Use when when applying a pre-trained Spec2Vec Word2Vec model to new mass spectra (particularly those outside the model's training distribution), you need to assess whether peaks and neutral losses in query spectra have been seen during model training.
   0 installs
2. ▌
   Mass Spectrum Peak Annotation And Normalization 2 · holobiomicslab

   Use when you have raw MS/MS spectra in MSP format or as numpy arrays and need to standardize them for comparison or library matching. Specifically, use it before performing electronic or chemical denoising, or before computing entropy-similarity metrics between query and reference spectra.
   0 installs
3. ▌
   Metabolite Concentration Stoichiometric Mapping 2 · holobiomicslab

   Use when you have intracellular metabolomics abundance data (absolute or relative concentrations) for multiple cell lines or conditions, a constraint-based stoichiometric metabolic model with reaction-metabolite associations, and you need to disentangle how differences in substrate concentration.
   0 installs
4. ▌
   Metabolite Feature Clustering By Retention Time 3 · holobiomicslab

   Use when after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table with retention times and intensity profiles across multiple samples and need to collapse redundant features into.
   0 installs
5. ▌
   Metabolite Feature Quantification Table Parsing 2 · holobiomicslab

   Use when when you have completed feature detection in MZmine3 or similar tools and produced a feature quantification table (rows = features, columns = samples with intensity values), and you possess a separate sample metadata file (sample identifiers, treatment groups, batch information).
   0 installs
6. ▌
   Transformation Network Topology Analysis 2 · holobiomicslab

   Use when when you have pre-processed FT-ICR MS peak lists with assigned molecular formulas and wish to move beyond univariate chemical composition analysis to understand metabolic transformation pathways and hub metabolites.
   0 installs
7. ▌
   High Resolution Mass Spectral Data Processing 2 · holobiomicslab

   Use when you have high-resolution mass-spectrometry data (Orbitrap, GC-CI-MS) from stable-isotope labeling experiments and need to quantify isotopologue abundances for a defined list of target compounds.
   0 installs
8. ▌
   High Resolution Mass Spectrometry Interpretation 2 · holobiomicslab

   Use when you have centroided LC- or GC-HRMS data (in mzML format, ideally from data-dependent acquisition) and need to identify potential PFAS candidates from a large feature list.
   0 installs
9. ▌
   Neural Network Based Molecular Formula Inference 2 · holobiomicslab

   Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting where spectrum database matching is unavailable or undesirable.
   0 installs
10. ▌
    Mass Spectrometry Fragmentation Pattern Modeling 3 · holobiomicslab

    Use when when building a re-usable spectral reference library for lipidomics workflows where you need to match experimental MS/MS spectra against a comprehensive theoretical fragmentation model.
    0 installs
11. ▌
    Metabolite Feature Extraction And Quantification 2 · holobiomicslab

    Use when after retention-time correction and data alignment have been completed on centroided LC-MS data (mzML or mzXML format).
    0 installs
12. ▌
    Molecular Dataset Partitioning And Preprocessing 2 · holobiomicslab

    Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and you need to format them for GNN training and held-out test evaluation with consistent standardization.
    0 installs
13. ▌
    Mass Difference Transformation Pair Derivation 2 · holobiomicslab

    Use when you have a formula-assigned DOM dataset from FT-ICR MS (or other mass spectrometry with compound annotations) and need to characterize how molecular transformations occur across the sample—e.
    0 installs
14. ▌
    Mass Spectrometry Feature Detection Validation 2 · holobiomicslab

    Use when when you have processed LC-HRMS mzML files through a non-targeted preprocessing tool (e.g., XCMS, MZmine 2, MS-DIAL) and need to assess whether peak detection rates, isotopologue ratio fidelity, and alignment accuracy meet acceptable thresholds before downstream analysis.
    0 installs
15. ▌
    Metabolite Adduct Correlation Spatial Analysis 2 · holobiomicslab

    Use when you have annotated mass-difference peaks with known adduct identities (via mass-matching to reference adduct tables) and possess MSI intensity matrices where each peak's abundance is measured across multiple tissue pixels or voxels.
    0 installs
16. ▌
    Representation Vector Dimensionality Reduction 3 · holobiomicslab

    Use when after obtaining 512-dimensional representation vectors from the Encoder module, when you need to compress these vectors for visualization, clustering, or downstream classification tasks on mass spectrometry imaging data while maintaining interpretability of ion relationships.
    0 installs
17. ▌
    File Format Conversion Peak Picking To Lipidmatch 2 · holobiomicslab

    Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest it into LipidMatch for lipid identification.
    0 installs
18. ▌
    Hierarchical Clustering Dendrogram Interpretation 2 · holobiomicslab

    Use when you have a pre-computed hierarchical dendrogram from correlation-based clustering of LC-MS features (with fixed linkage criterion and distance metric) and need to decide whether a single constant-threshold cut or data-driven silhouette optimization better resolves the underlying cluster.
    0 installs
19. ▌
    Tandem Mass Spectrometry Fragmentation Simulation 2 · holobiomicslab

    Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to evaluate without access to real mass spectrometry hardware.
    0 installs
20. ▌
    Background Distribution Significance Thresholding 2 · holobiomicslab

    Use when use when the workflow requires background-distribution-significance-thresholding.
    0 installs
21. ▌
    Comparative Performance Evaluation Across Methods 2 · holobiomicslab

    Use when when you have developed a new spectral similarity scoring method and need to quantify its retrieval performance relative to established methods (e.g., modified cosine, Spec2Vec). Use this skill if you have: (1) a test set of spectra with ground-truth structural similarity labels (e.
    0 installs
22. ▌
    Drop Down Interface Population From Filtered Data 2 · holobiomicslab

    Use when you have search results from DIA mass spectrometry data containing feature Q-value scores and need to restrict the analyte choices available to users in a GUI to only those meeting a 1% feature Q-value threshold.
    0 installs
23. ▌
    Mass Spectrometry Fragmentation Pattern Discovery 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (in positive or negative ion mode) and seek to discover recurring fragmentation and neutral-loss patterns that characterize molecular substructures across a dataset.
    2 installs
24. ▌
    Neural Network Inference And Embedding Extraction 2 · holobiomicslab

    Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to generate low-dimensional embeddings for spectral visualization, clustering, or retrieval tasks.
    0 installs
25. ▌
    Permanova Statistical Testing Multivariate Groups 2 · holobiomicslab

    Use when you have normalized peak intensities or abundance matrices from mass spectrometry (e.
    0 installs
26. ▌
    Tandem Mass Spectrometry Metadata Standardization 2 · holobiomicslab

    Use when you have raw MS/MS spectra from public repositories (e.
    0 installs
27. ▌
    Uncertainty Quantification From Model Predictions 2 · holobiomicslab

    Use when when you have a trained neural network (e.g., a Siamese model predicting molecular structural similarity) and need to identify and filter unreliable predictions before using them in downstream analysis. Apply this skill when raw model performance is suboptimal (~0.
    0 installs
28. ▌
    Ion Mobility Spectrometry Data Interpretation 2 · holobiomicslab

    Use when you have raw ion mobility-mass spectrometry data (drift time and m/z measurements) from DTIMS-MS, TWIMS-MS, or SLIM-based IMS-MS instruments and need to derive collision cross section values for molecular ion characterization. Use it specifically when calibrant standards (e.
    0 installs
29. ▌
    Mass Spectrometry Peak Detection And Extraction 2 · holobiomicslab

    Use when you have raw high-resolution mass-spectrometry data in mzML or mzXML format from breath analysis and need to identify individual volatile organic compounds before sample-to-sample alignment or comparative analysis.
    0 installs
30. ▌
    Sciex Multiquant Data Export Format Recognition 2 · holobiomicslab

    Use when you have txt files exported from Sciex MultiQuant (>v3.0.3) containing QCpool samples measured at regular intervals during mass spectrometry sequences, and you need to validate whether the file structure is compatible with the QComics package before parsing and quality assessment.
    0 installs
31. ▌
    Cascade Search Strategy For Peptide Identification 2 · holobiomicslab

    Use when use this strategy when analyzing tandem mass spectrometry data where you expect both unmodified and modified peptide identifications and require high confidence assignments with controlled false discovery rates.
    0 installs
32. ▌
    Exact Mass Utilization For Compound Identification 3 · holobiomicslab

    Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query chemicals are present in your samples and retrieve their -match factors (scoring the confidence of the spectral match) and.
    0 installs
33. ▌
    Mass Spectrometry Visualization Backend Comparison 2 · holobiomicslab

    Use when you have a mass spectrometry visualization library that claims to support multiple plotting backends and need to verify that: (1) all backends produce functionally equivalent outputs, (2) execution times are consistent with reported benchmarks, and (3) the library scales appropriately.
    0 installs
34. ▌
    Metabolite Annotation Integration Across Databases 2 · holobiomicslab

    Use when you have MZmine-aligned features with m/z and retention time, and you have generated spectral annotations from two or more database sources (e.g., GNPS/ISDB spectral matching and SIRIUS in silico structure elucidation).
    0 installs
35. ▌
    Over Representation Analysis Pvalue Interpretation 2 · holobiomicslab

    Use when when you have run ORA on a metabolomics dataset and obtained p-values for pathway enrichment, but you need to assess whether observed significance is genuine or an artifact of incomplete metabolite coverage.
    0 installs
36. ▌
    Parameter Range Filtering For Chromatographic Data 3 · holobiomicslab

    Use when you have raw MS data in instrument-native or mzML format (Agilent .d, Thermo .raw, Bruker .d) and need to isolate specific analyte regions defined by precise m/z windows, RT windows (in seconds or minutes), and/or ion mobility arrival-time windows.
    0 installs
37. ▌
    Peak Boundary Identification In Extracted Ion Data 3 · holobiomicslab

    Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
    0 installs
38. ▌
    Retention Time Abundance Correlation Visualization 2 · holobiomicslab

    Use when after applying AbundanceSimilarityParam (with threshold ≥0.7 and log2 transform) to retention-time-based feature groups from SimilarRtimeParam, when you need to examine the internal correlation structure of specific feature sub-groups (e.g., FG.
    0 installs
39. ▌
    Spectral Similarity Scoring And Reference Matching 2 · holobiomicslab

    Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from Metlin or GNPS).
    0 installs
40. ▌
    Mass Spectrometry Plot Taxonomy Implementation 2 · holobiomicslab

    Use when you are building a visualization library that must support multiple plot kinds (chromatogram, spectrum, mobilogram, peakmap) across multiple rendering backends (matplotlib, bokeh, plotly) and want to avoid code duplication.
    0 installs
41. ▌
    Feature Intensity Preservation Across Correction 2 · holobiomicslab

    Use when when you have loaded a raw MS quantification table (feature-by-sample intensity matrix) into QuantyFey and are applying drift-correction strategies (Internal Standard correction, statistical drift correction, Custom Bracketing, or Weighted Bracketing) but need to maintain traceability.
    0 installs
42. ▌
    Feature Table Annotation And Provenance Tracking 2 · holobiomicslab

    Use when after generating a filtered feature table from raw mass spectrometry data in openNAU.
    0 installs
43. ▌
    Metabolite Prediction Comparison Baseline Models 2 · holobiomicslab

    Use when you have paired microbiome (genus-level 16S or functional profiles) and metabolome datasets (e.g., mass spectrometry or metabolomics panels) with 100+ samples, and you want to demonstrate that a new prediction method outperforms prior work.
    0 installs
44. ▌
    Benchmarking And Comparative Performance Evaluation 2 · holobiomicslab

    Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains over established baselines. Use it specifically when you have access to ground-truth annotations (e.
    0 installs
45. ▌
    Constraint Based Model Sampling And Flux Prediction 2 · holobiomicslab

    Use when you have constraint-based metabolic models with integrated multi-omics constraints (transcriptomics via Reaction Activity Scores, extracellular flux ratios via YSI bioanalyzer or LC-MS, nutrient availability bounds), and you need to determine whether differential enzyme expression.
    0 installs
46. ▌
    Post Translational Modification Pattern Recognition 2 · holobiomicslab

    Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and genomically-predicted precursor peptide sequences, and you need to identify which predicted RiPPs are actually expressed and modified in the sample.
    0 installs
47. ▌
    Drift Time Retention Time Distance Metric Selection 3 · holobiomicslab

    Use when after peak detection in GCIMS when you need to group detected peaks across multiple samples into reproducible clusters.
    0 installs
48. ▌
    Naturally Occurring Isotope Contribution Accounting 2 · holobiomicslab

    Use when you have raw fractional abundances of measured isotopologues (FAM) from LC-MS instruments in an isotope labeling experiment and need to correct them to obtain true mass distribution vectors (MDV) reflecting only the contribution from the isotopic tracer.
    4 installs
49. ▌
    Spectral Annotation Filtering By Similarity Metrics 2 · holobiomicslab

    Use when after running GNPS molecular networking, SIRIUS compound identification, or ISDB in silico annotation on LC-MS/MS data, when you have provisional annotations for features but need to filter them to retain only high-confidence matches before calculating novelty scores, detecting chemical.
    0 installs
50. ▌
    Mass Spectrometry Data Structure Interpretation 3 · holobiomicslab

    Use when you have converted multidimensional MS data (from Agilent .d, Bruker ion mobility .d, Thermo .
    0 installs
51. ▌
    Approximate Nearest Neighbor Indexing For Spectra 2 · holobiomicslab

    Use when when you have a large spectral library (hundreds of thousands or millions of spectra) and need to search unknown query spectra against it for both unmodified and post-translationally modified peptides.
    0 installs
52. ▌
    Data Dependent Acquisition Controller Implementation 2 · holobiomicslab

    Use when you have a conceptual MS/MS fragmentation strategy (e.
    0 installs
53. ▌
    Metabolite Abundance Normalization Across Conditions 2 · holobiomicslab

    Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or conditions, and you need to create a normalized, cell-line-level metabolite dataset before computing Reaction Propensity.
    0 installs
54. ▌
    Mass Spectrometry Peak Filtering And Noise Reduction 2 · holobiomicslab

    Use when you have raw MS/MS spectra in MGF, mzML, or msp format and need to prepare them for mass2motif discovery or topic modeling.
    0 installs
55. ▌
    Precision Recall Curve Generation And Interpretation 2 · holobiomicslab

    Use when you have computed spectral similarity scores from multiple methods (e.g., MS2DeepScore, Spec2Vec, modified cosine) on the same set of spectrum pairs, have assigned ground-truth structural similarity labels (e.
    0 installs
56. ▌
    Tandem Mass Spectra Structural Similarity Assessment 2 · holobiomicslab

    Use when you have pairs of cleaned tandem mass spectra with known chemical structure annotations (InChIKey, SMILES, or InChI), and you need to predict Tanimoto structural similarity scores directly from spectral data without pre-computing molecular fingerprints.
    0 installs
57. ▌
    In Silico Fragmentation Simulation Validation 2 · holobiomicslab

    Use when you have experimental peak lists (m/z, retention time, intensity) from UHPLC-HRMS/MS or direct infusion MS/MS data and need to assign lipid identities with confidence scores. Use it when your instrument produces high-resolution tandem mass spectra (e.
    0 installs
58. ▌
    Peak Parameter Optimization For Targeted Compounds 2 · holobiomicslab

    Use when you have centroided high-resolution Orbitrap or GC-CI-MS mzML files and a formulaTable of target compounds with known m/z, retention time, and molecular formula, and you need to extract isotopologue abundances and quantification metrics (area, maxo intensity, ppm error) for each labeled.
    0 installs
59. ▌
    Metabolomics Data Integration With Metabolic Networks 2 · 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.
    0 installs
60. ▌
    Python Package Installation And Dependency Management 2 · 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
61. ▌
    Ionization Mode Detection From Mass Spectrometry Data 3 · 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
62. ▌
    Metabolic Reaction Classification By Regulatory Layer 2 · 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.
    0 installs
63. ▌
    Multimodal Spectral Alignment By Molecular Identifier 2 · holobiomicslab

    Use when you have parsed spectral data from four distinct modalities (NMR, HSQC, COSY, IR) stored as separate numpy arrays or DataFrames with normalized chemical shifts and intensity ranges, and you need to create paired multimodal training records where each molecule's spectra across all.
    0 installs
64. ▌
    Microbial Metabolomics Phage Impact Assessment 2 · holobiomicslab

    Use when you have normalized peak intensities (with assigned molecular formulas) from FT-ICR MS analysis of treated and control bacterial samples (or environmental microbial communities), grouped by two or more treatment factors (e.g., phage type: HP1, HS2, control;
    0 installs
65. ▌
    Molecular Formula Representation And Manipulation 2 · holobiomicslab

    Use when you need to represent, validate, and manipulate molecular compositions in MS analysis—specifically when annotating precursor or product ions with elemental formulas, computing monoisotopic masses for formula-to-charge assignments, predicting isotope patterns ([M]+, [M+H]+, [M+Na]+, etc.).
    0 installs
66. ▌
    Unified API Design For Heterogeneous Data Sources 2 · holobiomicslab

    Use when your analysis pipeline must ingest mass-spectrometry data from mixed vendor sources (e.g., Thermo RAW, Agilent .d, Waters .raw, and open mzML) without writing separate parser logic for each format.
    0 installs
67. ▌
    Metabolite Composition Comparison Across Treatments 2 · holobiomicslab

    Use when you have normalized peak intensity tables from FT-ICR MS data (e.g., MetaboDirect .
    0 installs
68. ▌
    Maldi Imaging Mass Spectrometry Data Interpretation 2 · 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
69. ▌
    Input Output Kernel Regression For Metabolite Matching 2 · 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
70. ▌
    Metabolomics Functional Prediction Workflow Validation 3 · 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
71. ▌
    Mass2motif Annotation Guidance Via Spectral Embeddings 2 · 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.
    0 installs
72. ▌
    Ms2 Spectrum Peak Filtering By Training Set Membership 2 · 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
73. ▌
    Precursor Region Handling And M Z Tolerance Management 2 · 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
74. ▌
    Strain Identifier Mapping Across Genomics Metabolomics 2 · 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
75. ▌
    Word2vec Vocabulary Matching And Unknown Peak Handling 4 · 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
76. ▌
    Feature Table Construction For Multivariate Analysis 2 · holobiomicslab

    Use when when you have high-resolution mass-spectrometry (HRMS) breath data in mzML or mzXML format from multiple subjects or conditions and need to prepare a sample-by-feature intensity matrix for downstream statistical comparison, biomarker discovery, or classification tasks.
    2 installs
77. ▌
    Empirical Compound Construction From Feature Clustering 2 · holobiomicslab

    Use when after feature detection and quality control have produced a feature table in TSV format from Asari or equivalent preprocessing.
    0 installs
78. ▌
    Multi Regime Model Performance Comparison Visualization 2 · holobiomicslab

    Use when you have paired microbiome-metabolome (or similar multivariate) datasets and want to quantify whether training on a superset of features (e.g., both annotated and unannotated metabolites) improves prediction accuracy for a well-defined target subset (e.
    0 installs
79. ▌
    False Positive Negative Detection In Pattern Matching 2 · holobiomicslab

    Use when when reconstructing or validating the ColumnFinder component in mwtab, you need to assess whether the combined NameMatcher.dict_match and ValueMatcher.series_match operations are correctly populating database-ID columns. Apply this skill after defining NameMatcher patterns (e.
    0 installs
80. ▌
    Retention Time And Mass Sorting Of Chromatographic Peaks 2 · holobiomicslab

    Use when you have raw GC-MS output from Agilent Unknowns Analysis (a .CSV with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    0 installs
81. ▌
    Backend Compatibility Verification Visualization Library 2 · holobiomicslab

    Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce visualizations (spectra, chromatograms, or peak maps) using a specific plotting backend (matplotlib, Bokeh, or Plotly) on real.
    0 installs
82. ▌
    Feature Attribution Score Interpretation Neural Networks 2 · holobiomicslab

    Use when after training a neural network model (e.
    0 installs
83. ▌
    Microbe Metabolite Feature Selection By Annotation Statu 2 · holobiomicslab

    Use when when you have paired microbiome-metabolome datasets where only a subset of metabolites carry curated biochemical annotations (e.
    0 installs
84. ▌
    Search Result Integration With Raw Mass Spectrometry Dat 3 · holobiomicslab

    Use when when you have completed a DIA-MS proteomics search (e.
    0 installs
85. ▌
    Benchmark Dataset Generation From Reference Metabolites 2 · holobiomicslab

    Use when you have a set of centroided mzML files from LC-HRMS analysis, a list of target metabolites with known molecular formula and retention time windows, and you need to create a reference dataset to benchmark the reliability of NPP tools (XCMS, MZmine, MS-DIAL, etc.) on the same files.
    0 installs
86. ▌
    Computational Efficiency Single Pass Vs Repeated Detecti 3 · holobiomicslab

    Use when when processing aligned LC-MS data across multiple samples where the computational bottleneck is repeated peak-detection algorithm calls (one per sample per m/z value). Typical scenario: >10 samples with >1000 m/z values each, where N individual find_peaks invocations dominate runtime.
    0 installs
87. ▌
    Kernel Regression Learning From Spectral Fingerprint Pai 2 · holobiomicslab

    Use when when you have a training set of MS2 spectra with known chemical structures (e.
    0 installs
88. ▌
    Microbiome Metabolome Data Preprocessing Clr Transformat 2 · holobiomicslab

    Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream regression or neural network modeling of microbe-metabolite relationships.
    0 installs
89. ▌
    Ion Chromatogram Mobilogram Visualization And Interpreta 3 · holobiomicslab

    Use when after loading raw diaPASEF or DIA mass spectrometry data (mzML format) and search results (DIA-NN, OpenSwath, or equivalent) to visually inspect extracted ion chromatograms and mobilograms for selected peptide precursors.
    0 installs
90. ▌
    Microbial Phage Infection Experimental Design Interpreta 2 · holobiomicslab

    Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1, HS2, control) and sample replicates (n ≥ 6–8 per group), and you need to test whether phage-type factor explains.
    0 installs
91. ▌
    Spearman Correlation Coefficient Calculation Cross Valid 2 · holobiomicslab

    Use when you have trained predictive models (e.g., MiMeNet neural networks) on microbiome-metabolome paired data using k-fold cross-validation, held out test folds for each fold-iteration, and generated continuous abundance predictions for metabolites.
    0 installs
92. ▌
    Two Dimensional Correlation Optimized Warping Parameter 2 · holobiomicslab

    Use when when you have a preprocessed sample chromatogram (smoothed and baseline-corrected) and a preprocessed reference chromatogram, and need to align them using 2D COW.
    0 installs
93. ▌
    Computational Performance Benchmarking And Timing Measur 2 · holobiomicslab

    Use when when you need to validate that a newly published bioinformatics pipeline meets stated performance claims, or when you must characterize how execution time scales with dataset size (sample count, peak count, or formula complexity) and optional analysis features (e.
    0 installs
94. ▌
    Peptide Sequence Composition Parsing 2 · holobiomicslab

    Use when you have peptide or protein sequences (as FASTA strings or text identifiers) and need to compute their mass, isotopic envelope, charge state, isoelectric point, or chromatographic retention time for MS matching, peak annotation, or property prediction.
    0 installs
95. ▌
    Percentile Threshold Based Filtering 2 · holobiomicslab

    Use when you have paired genomic-metabolomic link scores (e.
    0 installs
96. ▌
    Probability Product Kernel Denoising 2 · holobiomicslab

    Use when you have raw MS2 spectra (m/z and intensity pairs) that you want to match against a large training dataset of annotated library spectra (e.g., GNPS), and you need to reduce noise and computational burden before applying kernel-based scoring methods such as IOKR.
    0 installs
97. ▌
    Proforma Notation Parsing Validation 2 · holobiomicslab

    Use when you have peptide sequences with chemical modifications encoded in ProForma notation (e.g., '[Phospho]-PEPTIDE[Carbamidomethyl]-C') and need to validate their syntax, extract modification positions, or prepare them for downstream physico-chemical property calculations (mass, charge, pI).
    0 installs
98. ▌
    Quality Control Threshold Validation 2 · holobiomicslab

    Use when after executing Formation formatting on processed feature tables (output from Blueshift or Gravity modules).
    0 installs
99. ▌
    R Package Installation And Execution 2 · holobiomicslab

    Use when when you have a new or updated R package available via a non-CRAN repository (such as r-universe) and need to verify it installs cleanly, passes R-CMD-check compliance, and is ready for downstream workflow execution.
    0 installs
100. ▌
     Spec2vec Model Loading And Inference 2 · holobiomicslab

     Use when you have discovered Mass2Motifs or other fragmentation pattern representations via LDA and need to generate vector embeddings to query a reference motif database (MotifDB) for structural annotation candidates.
     0 installs