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HolobiomicsLab

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1. ▌
   Lcms Feature Detection And Quantification 3 · holobiomicslab

   Use when you have raw LC-MS data (mzML or equivalent format) from a metabolomics experiment and need to extract a reproducible, quantified feature table with intensity measurements before conducting metabolite identification or statistical analysis.
   9 installs
2. ▌
   Mass Spec Tolerance Parameter Application 2 · holobiomicslab

   Use when when you have a feature table from Orbitrap LC-MS containing m/z, retention time, and intensity columns, and you need to group individual mass features into putative metabolites that represent the same chemical entity across different ionization states and isotopic compositions.
   13 installs
3. ▌
   Mass Spectrometry Chromatogram Generation 2 · holobiomicslab

   Use when after MS2 annotation and sample alignment have been completed in JPA, when you need to visualize ion chromatograms for quality control, validate feature identities, or export chromatographic evidence for specific metabolic features across multiple samples.
   11 installs
4. ▌
   Metabolite Feature Annotation Aggregation 3 · holobiomicslab

   Use when after selecting statistically significant features from multi-assay LC-MS metabolomics datasets (e.g., via MB-VIP and permutation testing with p < 0.01).
   13 installs
5. ▌
   Metabolomics Peak Detection Configuration 4 · holobiomicslab

   Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram alignment.
   7 installs
6. ▌
   Microbiome Metabolome Prediction Modeling 4 · holobiomicslab

   Use when you have paired microbiome (16S rRNA, metagenomic) and metabolomic (LC-MS, GC-MS) abundance tables from the same biosamples, and you want to predict which metabolites are recoverable from microbial composition alone and identify groups of microbes and metabolites with correlated.
   9 installs
7. ▌
   Molecular Graph Neural Network Adaptation 2 · holobiomicslab

   Use when you have an in-house collection of liquid chromatography spectra and retention time measurements for small molecules, and you want to improve structural identification accuracy by predicting retention times.
   9 installs
8. ▌
   Molecular Structure Prediction Evaluation 3 · holobiomicslab

   Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
   11 installs
9. ▌
   Molecular Structure Prediction Validation 2 · holobiomicslab

   Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular structures, and you need to assess prediction accuracy and structural correctness against ground-truth or reference.
   9 installs
10. ▌
    Software Feature Inventory And Comparison 4 · holobiomicslab

    Use when you need to assess whether a newly developed FT-ICR MS pipeline (e.
    6 installs
11. ▌
    Stable Isotope Probing Abundance Modeling 2 · holobiomicslab

    Use when you have a high-resolution mass spectrum (FT scan) containing a peptide precursor at known charge state with known or suspected stable isotope labeling (e.
    9 installs
12. ▌
    Structural Similarity Scoring Metabolites 3 · holobiomicslab

    Use when when you have paired MS/MS spectra from unknown metabolites and a reference database of known metabolites, and you want to rank candidate structures for unknown compounds by their predicted structural similarity rather than exact spectral matching.
    11 installs
13. ▌
    Ms Vendor Documentation Extraction 3 · 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.
    14 installs
14. ▌
    File Format Conversion Validation 2 · holobiomicslab

    Use when when you have raw mzML or mzXML mass spectrometry data files that need to be archived or transmitted with minimal storage footprint, and you must verify that the decompressed output exactly reproduces the original input at the byte level.
    8 installs
15. ▌
    Model Generalizability Evaluation 2 · holobiomicslab

    Use when you have a pre-trained or newly retrained graph neural network for collision cross section prediction and need to measure whether its performance generalizes across different molecular datasets (e.g., training on METLIN but evaluating on CCSBase).
    10 installs
16. ▌
    Quality Control Metric Evaluation 3 · holobiomicslab

    Use when you have measured IM-MS lipidomics data spiked with U13C labeled internal standards and need to assess whether CCS bias remains within acceptable limits for each lipid class-adduct combination.
    10 installs
17. ▌
    Breath Volatile Peak Classification 2 · holobiomicslab

    Use when after feature extraction and alignment when you have a numerical feature table (CSV or dataframe) with intensity values across retention time or m/z dimensions, and you need to identify and rank peaks by signal quality and prominence rather than relying on all extracted features equally.
    11 installs
18. ▌
    Chromatographic Peak Classification 2 · holobiomicslab

    Use when you have (1) a benchmark dataset of reference peaks with validated m/z, retention time boundaries, and isotopologue assignments, and (2) NPP output feature tables (unaligned and aligned) from tools like XCMS, MZmine 2, or MS-DIAL that you wish to evaluate.
    12 installs
19. ▌
    Functional Trait Diversity Analysis 3 · holobiomicslab

    Use when when you have abundance-normalized FT-ICR MS peak data with assigned molecular formulas and need to distinguish between richness (total number of distinct metabolites) and functional diversity (diversity in metabolic potential).
    4 installs
20. ▌
    Interactive Plot Backend Evaluation 2 · holobiomicslab

    Use when you have mass spectrometry data (chromatograms, spectra, peak maps, mobilograms) that you want to visualize interactively using pyOpenMS-viz, and you need to select between bokeh and plotly backends based on execution time and feature parity.
    12 installs
21. ▌
    Metabolite Abundance Stratification 3 · holobiomicslab

    Use when you have a peak-abundance matrix from FT-ICR MS (peaks as rows, samples as columns with raw peak intensities) and need to compute abundance-based diversity indices or functional diversity metrics that are sensitive to relative vs. absolute peak heights.
    8 installs
22. ▌
    Pubchem Compound Database Retrieval 2 · holobiomicslab

    Use when you need to supply candidate metabolite structures for mass spectrometry annotation when working within an integrative metabolomics data analysis workflow (such as MAGMa).
    11 installs
23. ▌
    Retention Time Alignment Evaluation 2 · holobiomicslab

    Use when you have run an NPP tool (XCMS, MZmine 2, etc.) on mzML files and need to assess whether the alignment stage preserved peak detection fidelity and isotopologue abundance ratios.
    11 installs
24. ▌
    Retention Time Intensity Extraction 2 · holobiomicslab

    Use when when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to generate a TIC plot to visualize overall sample ionization intensity as a function of retention time.
    11 installs
25. ▌
    Mass Spectrometry Adduct Annotation 3 · holobiomicslab

    Use when you have tabulated pairwise mass differences from a MALDI-MS imaging dataset (via massdiff()) and need to identify which observed mass differences correspond to known chemical adducts (e.g., [M+H]+, [M+Na]+, [M-H2O]+).
    8 installs
26. ▌
    Chemical Graph Connectivity Validation 2 · 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.
    17 installs
27. ▌
    Dataframe And Numericlist Manipulation 2 · holobiomicslab

    Use when you are implementing a new MsBackend subclass and need to store spectra metadata (sample names, retention times, precursor m/z, etc.) separately from peak data (m/z and intensity pairs) while maintaining row-wise alignment.
    14 installs
28. ▌
    Feature Group Refinement Multicriteria 3 · holobiomicslab

    Use when after initial retention-time-based feature grouping (e.g., ±20 s window) when you need to separate co-eluting features that are chemically distinct. Triggers include: (1) large feature groups (>2–3 members) suspected to contain multiple compounds;
    13 installs
29. ▌
    Retention Time Alignment Index Mapping 3 · holobiomicslab

    Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
    11 installs
30. ▌
    Spectral Features Module Integration 2 · holobiomicslab

    Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than scalar molecular properties.
    5 installs
31. ▌
    Spectral Library Matching Evaluation 2 · holobiomicslab

    Use when you have a trained spectral embedding model (e.g., MSBERT, Spec2Vec) and need to benchmark its library matching accuracy against reference spectra on a test dataset.
    9 installs
32. ▌
    Spectral Similarity Network Building 3 · holobiomicslab

    Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical hierarchy for comparative metabolomic analysis.
    12 installs
33. ▌
    Spectrum Filtering And Normalization 3 · holobiomicslab

    Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or quantitative analysis.
    11 installs
34. ▌
    Chemical Class Novelty Detection 2 · holobiomicslab

    Use when when you have CANOPUS chemical class predictions for your samples and need to identify which extracts contain chemical classes absent from the literature for their species or genus.
    11 installs
35. ▌
    Abstract Base Class Implementation 2 · 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.
    10 installs
36. ▌
    Adduct Mass Adjustment Calculation 2 · 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.
    8 installs
37. ▌
    CSV File Parsing And Peak Indexing 2 · 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.
    8 installs
38. ▌
    Datatype Validation Helper Methods 2 · 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.
    5 installs
39. ▌
    Ft Icr Ms Analysis Tool Evaluation 3 · 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).
    10 installs
40. ▌
    Graph Clustering Community Detection 3 · holobiomicslab

    Use when after constructing a spectral similarity network from pairwise cosine similarity scores between deconvolved GC-MS spectra.
    9 installs
41. ▌
    Hydrogen Rearrangement Rules Scoring 2 · holobiomicslab

    Use when after MS-CleanR has filtered and clustered LC-MS features and formatted them for MS-FINDER input (m/z, retention time, MS/MS spectra).
    11 installs
42. ▌
    Interactive Visualization Inspection 2 · holobiomicslab

    Use when after msFeaST pipeline execution has produced a dashboard_data.json file containing quantification, metadata, and spectral matrices, or when you need to validate that preprocessing steps correctly loaded and rendered ms/ms feature data before downstream statistical or network analysis.
    8 installs
43. ▌
    Internal Standard Feature Extraction 2 · holobiomicslab

    Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications and need to monitor internal standard retention time, m/z, and intensity variation across samples as part of automated or user-defined QC checks during instrument runs.
    12 installs
44. ▌
    Ion Mobility Arrival Time Conversion 2 · holobiomicslab

    Use when you have a feature table containing raw ion mobility arrival time measurements paired with experimentally assigned biomolecular class labels (e.g., lipid, protein, carbohydrate), and you need to compute CCS values for downstream structural or comparative analysis.
    9 installs
45. ▌
    Isotopologue Mass Offset Calculation 2 · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format with m/z, drift_time, retention_time, intensity columns) and need to identify and label isotopic signatures within singly charged species.
    9 installs
46. ▌
    Jupyter Notebook Workflow Automation 3 · holobiomicslab

    Use when when you have raw LC-MS/MS spectral data in .
    7 installs
47. ▌
    Lc Hrms Metabolomics Data Processing 3 · holobiomicslab

    Use when you have LC-HRMS raw data files (.mzML or .abf format) from metabolomics experiments and need to extract, align, and annotate features in a reproducible manner across multiple computational environments.
    8 installs
48. ▌
    Lc Ms Scan Acquisition Orchestration 3 · holobiomicslab

    Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that strategy will acquire MS1 and MS2 scans over a defined retention-time window.
    12 installs
49. ▌
    Mass Spectral Fingerprint Generation 3 · holobiomicslab

    Use when you have unaligned MS2 spectra from one or more samples (in formats like .mgf, .mzML, or .mzXML) and need to compare them in a retention-time-agnostic manner.
    11 installs
50. ▌
    Mass Spectral Metadata Harmonization 3 · holobiomicslab

    Use when you have multiple mass spectral libraries in different formats (NIST MSP + MOL folder, MoNA MSP, RIKEN MSP, SWGDRUG MSP) and need to merge them into a single, MS-DIAL-compatible MSP file with consistent SMILES assignments, Kovats retention indices (RI), and polarity annotations across all.
    10 installs
51. ▌
    Mass Spectrometry Benchmark Analysis 3 · holobiomicslab

    Use when you have implemented or modified a tandem mass spectrometry formula inference model and need to measure whether a specific architectural change (e.
    9 installs
52. ▌
    Mass Spectrometry Data Visualization 3 · holobiomicslab

    Use when after applying retention time, abundance correlation, or EIC similarity-based feature grouping (e.g., via SimilarRtimeParam, AbundanceSimilarityParam, or EicSimilarityParam). Use when you need to visually confirm that grouped features belong to the same compound—i.
    13 installs
53. ▌
    Mass Spectrometry Metric Engineering 3 · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to quantify file quality for automated quality control, longitudinal instrument monitoring, or training a quality prediction classifier.
    9 installs
54. ▌
    Metabolite Identification Validation 2 · holobiomicslab

    Use when you have extended a metabolite identification tool (such as Met-ID) to support a new derivatizing matrix beyond the default (e.
    11 installs
55. ▌
    Metabolomic Feature Table Imputation 3 · holobiomicslab

    Use when after feature detection and peak alignment have produced a feature table with zero or missing values across samples.
    9 installs
56. ▌
    Spectrum Preprocessing Precursor Masking 2 · holobiomicslab

    Use when when training a formula-prediction model with a frozen pretrained TCN spectrum encoder and unfrozen FormulaEncoder and RescoreHead components, or when you suspect the model may use precursor intensity as a spurious feature rather than fragment-pattern information for molecular formula.
    12 installs
57. ▌
    Tandem Mass Spectra Embedding Generation 2 · holobiomicslab

    Use when you have tandem mass spectra (in .msp or compatible format) from instruments like Orbitrap, and you need to compute library matching scores, cluster spectra by chemical similarity, or embed spectra into a learned vector space for downstream similarity or clustering tasks.
    10 installs
58. ▌
    Graph Neural Network Model Inference 3 · holobiomicslab

    Use when you have a trained GNN model (stored as .h5 weights) and molecular graph representations (SMILES strings and/or 3D coordinates), and you need to compute predicted CCS values or perform feature importance analysis via ablation or gradient-based saliency mapping.
    13 installs
59. ▌
    Batch Effect Correction And Adjustment 2 · holobiomicslab

    Use when your m/z peak data spans multiple batches (recorded in metadata as a batch ID column) or samples have varying concentrations that are documented in metadata.
    9 installs
60. ▌
    Chemical Structure Similarity Matching 3 · holobiomicslab

    Use when you have a set of query chemical compounds (as SMILES, names, or ChemMine objects) and a reference library organized into type groups (e.g., Type A–E chemical sets), and you need to assign each query compound to its -matching type based on structural similarity.
    6 installs
61. ▌
    Quality Control Threshold Optimization 2 · holobiomicslab

    Use when when you have extracted a peak feature table (CSV or tabular format) with mass-to-charge ratios, retention times, and intensity values across multiple samples, and you need to distinguish genuine differential metabolic signals from instrumental noise or low-abundance background before.
    10 installs
62. ▌
    Spectra Data Extraction And Subsetting 3 · holobiomicslab

    Use when when you need to extract m/z and intensity peak values from a Spectra object backed by MsBackendMzR or similar on-disk backends; when analyzing subsets of spectra without loading all peaks into memory;
    11 installs
63. ▌
    Spectrum Record Consistency Validation 3 · holobiomicslab

    Use when when you have a mass spectrometry data file (such as mzPeak) that has been read by two or more independent implementations (e.g., Rust, Python/pyarrow, R/arrow) and need to verify that all implementations produce identical spectrum metadata, data types, row counts, and numerical values.
    11 installs
64. ▌
    Hierarchical Spectrum Object Construction 2 · holobiomicslab

    Use when immediately after parsing and validating raw LC-MS/MS data files (mzML, mzXML, or vendor formats) when you need to prepare spectral data for fragmentation tree computation, isotope pattern analysis, or molecular formula ranking within the SIRIUS framework.
    13 installs
65. ▌
    Mass Spectrometry Metadata Interpretation 2 · holobiomicslab

    Use when when integrating LC-MS/MS data from diverse sources (e.g., public repositories like MSV000080102, instrument outputs, or precomputed workflows) into NPDtools pipelines.
    8 installs
66. ▌
    Signal Trend Assessment Across Injections 2 · holobiomicslab

    Use when you have QCpool (pooled quality control) samples measured at regular intervals across one or more LC-MS/MS sequences and need to detect whether instrument performance degrades, drifts, or destabilizes during the analytical run.
    9 installs
67. ▌
    Top N Accuracy And Auc Metric Calculation 2 · holobiomicslab

    Use when you have a ranked candidate list (e.g., BGCs sorted by IOKR or strain-correlation score) for each test spectrum, a known ground-truth BGC for each spectrum, and you want to measure retrieval performance across multiple recall depths (top-1 through top-200) and overall discrimination.
    11 installs
68. ▌
    Bgc Spectrum Ranking By Kernel Similarity 3 · holobiomicslab

    Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or predicted structures (e.
    11 installs
69. ▌
    Chemical Structure Fingerprint Comparison 4 · holobiomicslab

    Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method actually reflects true chemical structural similarity.
    9 installs
70. ▌
    Chemo Informatics Workflow Reconstruction 2 · holobiomicslab

    Use when when you have access to the source code of a chemo-informatics tool (e.
    9 installs
71. ▌
    Comparative Machine Learning Benchmarking 3 · holobiomicslab

    Use when you have developed a new machine learning model for predicting metabolomic profiles from microbiome data and need to quantify its performance improvement over existing methods.
    14 installs
72. ▌
    Precursor Ion Chromatogram Extraction 3 · holobiomicslab

    Use when you have raw DIA mass spectrometry data files (.raw, .d, or .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to extract precursor ion chromatograms for quality assessment or downstream analysis.
    13 installs
73. ▌
    Precursor Peak Removal Mass Tolerance 3 · holobiomicslab

    Use when after loading an MsmsSpectrum object but before intensity filtering or spectral annotation.
    7 installs
74. ▌
    Reaction Propensity Score Computation 3 · holobiomicslab

    Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with reaction-metabolite associations) to estimate how differences in substrate availability—independent of gene expression—translate into.
    8 installs
75. ▌
    Retention Time And Mz Based Alignment 3 · holobiomicslab

    Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each sample.
    10 installs
76. ▌
    Routing Module Testing And Validation 3 · holobiomicslab

    Use when when you have implemented conditional routing logic in the GNPS_MASST codebase and need to verify that spectrum submissions with explicit domain-context selections (e.
    9 installs
77. ▌
    Sparse Distance Matrix Interpretation 2 · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from nearest neighbor indexes (containing only cosine distances between neighboring spectra, not exhaustive pairwise comparisons) and need to partition spectra into groups of similar ions or peptides.
    6 installs
78. ▌
    Spectral Peak Intensity Normalization 2 · holobiomicslab

    Use when after loading raw m/z peak data (in MetaboAnalyst, MetaboShiny native, or Metabolights format) and merging it with sample metadata (batch IDs, concentration values, experimental group labels).
    14 installs
79. ▌
    Spectral Peak Matching With Tolerance 2 · holobiomicslab

    Use when when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks. Use this skill before calculating similarity scores (cosine, entropy, Bhattacharyya) or when applying penalty factors to unmatched peaks.
    10 installs
80. ▌
    Spectral Similarity Scoring Ei Simple 2 · holobiomicslab

    Use when you have a query electron ionization (EI) mass spectrum and need to search it against a library of known EI mass spectra to identify unknown compounds. Use it when exact identity matching (e.
    7 installs
81. ▌
    Subformula Assignment Neural Networks 3 · holobiomicslab

    Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational overhead of generating full SIRIUS fragmentation trees or do not have access to spectrum databases.
    11 installs
82. ▌
    Substrate Concentration Normalization 2 · holobiomicslab

    Use when you have LC-MS normalized intracellular metabolite abundance data from multiple cell lines (or samples) and need to compute reaction-level propensity scores that account for substrate availability as a predictor of metabolic flux.
    11 installs
83. ▌
    Tanimoto Score Threshold Optimization 3 · holobiomicslab

    Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision threshold for classifying spectrum pairs as 'chemically related' or 'unrelated'.
    8 installs
84. ▌
    Temporal Profile Correlation Analysis 3 · holobiomicslab

    Use when you have time-resolved direct injection mass spectrometry data (e.
    9 installs
85. ▌
    Transformer Encoder Decoder Inference 2 · holobiomicslab

    Use when when you have preprocessed MS/MS spectra (normalized intensities, filtered for quality, with top peaks retained) that have been encoded using a spectral representation method (e.
    13 installs
86. ▌
    Atom Feature Extraction Chemistry 3 · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical database (e.
    6 installs
87. ▌
    Metabolomics Feature Table Filtering 3 · holobiomicslab

    Use when when you have a raw LC-MS peak table imported from vendor software (e.
    7 installs
88. ▌
    Molecular Formula Quality Assessment 2 · holobiomicslab

    Use when immediately after formula assignment from raw FT-ICR MS peak detection, when you have a peak intensity matrix with assigned molecular formulas and need to remove spurious or low-confidence assignments before calculating thermodynamic indices, determining compound classes, or performing.
    7 installs
89. ▌
    Molecular Network Graph Manipulation 3 · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you need to embed substructural motif identifiers, confidence scores, or chemical class labels as node/edge attributes for.
    8 installs
90. ▌
    Msconvert Integration And Invocation 2 · holobiomicslab

    Use when when you have vendor-format LC-MS acquisition files (Thermo .raw, Bruker .d, Sciex .ms, Agilent, Waters formats) that need to be ingested into a quality control or data processing pipeline that requires open, standardized spectral formats.
    12 installs
91. ▌
    Multi Dataset Integration Mzrt Space 2 · holobiomicslab

    Use when you have multiple CSV feature tables from independent metabolomic experiments, each with RT and m/z annotations, and you need to produce a single consolidated feature matrix for comparative analysis across all samples.
    12 installs
92. ▌
    Multi Task Loss Function Formulation 2 · holobiomicslab

    Use when when training an object detection network that must predict both discrete labels (e.g., true peak vs. false peak) and continuous coordinates (e.
    11 installs
93. ▌
    Neural Network Architecture Training 2 · holobiomicslab

    Use when you have a pretrained TCN spectrum encoder from formula prediction and need to train a rescoring model that ranks formula candidates by confidence. The input is a set of spectra with ground-truth formula labels and multiple candidate formulas per spectrum.
    7 installs
94. ▌
    Prm Acquisition Event Identification 4 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is happening at regular intervals consistent with your instrument method design.
    8 installs
95. ▌
    Qc Reference Chromatogram Extraction 2 · holobiomicslab

    Use when when processing a batch of LC-MS samples in mzML or mzXML format where at least one file has been designated as a quality control (QC) file, extract its TIC or BPC before performing retention time correction.
    11 installs
96. ▌
    Retention Time Prediction Validation 2 · holobiomicslab

    Use when after training a GNN-RT model on preprocessed molecular graph data (from Train.py) or after applying transfer learning to an in-house dataset (from Transferlearning.
    11 installs
97. ▌
    Sample Centric Metabolite Annotation 3 · holobiomicslab

    Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra) and sample-level taxonomical metadata, and you want to assign both spectral identity and predicted chemical structure to.
    9 installs
98. ▌
    Sampledata Annotation And Assignment 2 · holobiomicslab

    Use when after loading multiple LC-MS .mzML files into an MsExperiment object using MsBackendMzR backend, when you have a documented injection sequence (e.
    12 installs
99. ▌
    Search Results Filtering And Parsing 2 · holobiomicslab

    Use when you have loaded DIA mass spectrometry search results containing feature identification data with associated Q-value scores, and you need to restrict the analytes available in selection drop-downs to those meeting a quality cutoff (typically 1% FDR equivalent) before visualization or manual.
    6 installs
100. ▌
     Simulation Control Loop Architecture 4 · holobiomicslab

     Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic window selection) would perform without access to real instrument time.
     6 installs