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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Quality Control Summary Generation · holobiomicslab

   Use when after applying one or more mpactr filters (mispicked, group, CV, or insource) to a peak table in a chained filtering workflow.
   0 installs
2. ▌
   Reaction Flux Concordance Analysis · holobiomicslab

   Use when you have computed RAS (Reaction Activity Scores) from transcriptomics and GPR rules, RPS (Reaction Propensity Scores) from intracellular metabolomics via mass-action kinetics, and flux distribution differences (FFD) from constraint-based sampling across multiple biological samples.
   0 installs
3. ▌
   Rescore Training Data Augmentation · holobiomicslab

   Use when when you have TCN-predicted candidate formulas with ranked scores and need to train a Siamese rescore model to re-rank those candidates.
   0 installs
4. ▌
   Sample Batch Metadata Organization · holobiomicslab

   Use when you have tab-delimited metabolomics data with columns for aliquot identifiers, compound names, peak areas (primary and internal standard), sample type (QC, study sample, calibration), batch labels, and injection times, and need to construct a single unified object for batch correction.
   0 installs
5. ▌
   Sample Metadata Integration For Qc · holobiomicslab

   Use when when you have an aligned MemoMatrix (sample-by-feature occurrence matrix where features are MS2 peaks and neutral losses) and corresponding sample annotations (especially blank/control sample labels), and you need to exclude background-derived peaks and losses before applying visualization.
   0 installs
6. ▌
   Sample Spectrum Metadata Alignment · holobiomicslab

   Use when you have a GNPS task ID from a completed molecular networking workflow (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING on GNPS1, or classical_networking_workflow / feature_based_molecular_networking_workflow on GNPS2) and need to access the resulting spectral.
   0 installs
7. ▌
   Simulation Evaluation Data Capture · holobiomicslab

   Use when when you have simulated DDA (data-dependent acquisition) scans from a ViMMS Environment and need to (1) quantify how well the simulated acquisition matched real or reference data (via evaluation metrics), and (2) export the results as standards-compliant mzML files for comparison with.
   0 installs
8. ▌
   Spectral Feature Vector Generation · holobiomicslab

   Use when you have a collection of MS/MS spectra in standard formats (mzML, MGF) and need to perform rapid similarity search, clustering, or joint analysis across millions of spectra without repeated peptide database searches.
   0 installs
9. ▌
   Spectral Fingerprint Vectorization · holobiomicslab

   Use when you have MS2 fragmentation spectra from multiple metabolomics samples and need to compare them in a retention time-agnostic manner, especially when samples are chemically diverse, acquired with different LC methods or mass spectrometer technologies (e.
   0 installs
10. ▌
    Spectral Library Candidate Ranking · holobiomicslab

    Use when after MS2Deepscore has selected the top 2000 candidate spectra from a library based on spectral similarity, and you need to re-rank these candidates to surface the single match (either exact or analogue) rather than rely on raw spectral similarity alone.
    0 installs
11. ▌
    Spectral Library Database Querying · holobiomicslab

    Use when you have one or more MS/MS query spectra (in mzML, mgf, msp, mzxml, json, or pickled matchms format) and a pre-built spectral library stored in SQLite with precomputed MS2Deepscore embeddings.
    0 installs
12. ▌
    Spectral Library Format Conversion · holobiomicslab

    Use when when you have mass spectral libraries from multiple sources (NIST, MoNA, RIKEN, GNPS) in disparate formats (MSP, MGF, MOL folder structures) or with misaligned metadata (e.
    0 installs
13. ▌
    Spectral Library Msp Serialization · holobiomicslab

    Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those spectra as a reusable MSP-format spectral library for downstream identification tasks in Excalibur, Skyline, or NIST MS.
    0 installs
14. ▌
    Spectral Library Schema Validation · holobiomicslab

    Use when after harmonizing MS/MS spectra and metadata fields (compound identifiers, adduct annotations, collision energies, instrument types) to a common schema, and before exporting the spectral library to standardized formats (mzML, mzTab, or repository-native format).
    0 installs
15. ▌
    Spectral Search Logic Control Flow · holobiomicslab

    Use when when you need to understand or modify how MS2Query routes query spectra through its dual-pathway architecture, or when integrating MS2Query into another tool and need to trace how spectral similarity scores (MS2Deepscore) feed into library-match versus analogue-search branches with.
    0 installs
16. ▌
    Spectral Similarity Scoring Cosine · holobiomicslab

    Use when you have a collection of preprocessed and cleaned mass spectrometry spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to compute all-pairs or targeted spectral similarity scores to identify related spectra, perform spectral library searches, or build a similarity network.
    0 installs
17. ▌
    Spectrum Binning And Normalization · holobiomicslab

    Use when you have raw, high-resolution MS/MS spectra in mzML, mzXML, or MGF format that need to be prepared for fast similarity searching or clustering.
    0 installs
18. ▌
    Stable Isotope Labeling Proteomics · holobiomicslab

    Use when when you have mass spectrometry data (MS1/MS2 scans from ThermoFisher .raw files, mzML, or MGF) from cells or organisms cultured with stable isotope-enriched substrates (e.g., 13C, 15N, 2H) at any enrichment level (natural 1.
    0 installs
19. ▌
    System Call Invocation Via System2 · holobiomicslab

    Use when you need to query or extract data from Thermo Fisher Scientific .raw files or other proprietary binary formats accessible only through a compiled external executable (e.g., RawFileReader .NET assembly). The executable returns text or structured output (e.
    0 installs
20. ▌
    Tandem Mass Spectra Interpretation · holobiomicslab

    Use when you have an unknown MS/MS spectrum (tandem mass spectrum) with a measured precursor m/z and fragment peaks, and you need to assign the most likely molecular formula and ionization adduct (e.g., [M+H]+, [M+Na]+, [M+K]+).
    0 installs
21. ▌
    Tandem Mass Spectrum Normalization · holobiomicslab

    Use when preparing tandem MS/MS datasets for cross-dataset similarity analysis or spectral matching, particularly when datasets originate from different instruments, acquisition dates, or sample preparation protocols that may introduce systematic variations in peak intensities.
    0 installs
22. ▌
    Target List Matching And Alignment · holobiomicslab

    Use when you have LC-MS data (mzML or netCDF format) and a predefined list of target metabolites with known m/z values and retention time windows that you wish to extract and quantify.
    0 installs
23. ▌
    Tensor Preprocessing Normalization · holobiomicslab

    Use when when you have raw MS/MS spectral data in the form of intensity arrays indexed by m/z values and need to feed them into the Spec2Mol encoder neural network. Apply this skill before encoder inference to ensure spectral inputs conform to the encoder's expected dimensionality and value ranges.
    0 installs
24. ▌
    Threshold Based Library Validation · holobiomicslab

    Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both molecular diversity (distinct species count) and chemical classification (lipid-type category count).
    0 installs
25. ▌
    Lcms Peak Detection And Alignment · holobiomicslab

    Use when you have one or more raw mzXML or mzML LCMS data files (from DDA, DIA, or fullscan acquisition) and need to extract quantitative metabolite features for multi-sample comparative analysis.
    0 installs
26. ▌
    Lcms Spectral Peak Classification · holobiomicslab

    Use when you have raw LC-MS spectral peak data (in the format provided by DOI 10.25345/C5FD2F) and need to build a classifier that can distinguish valid peaks from false positives or background noise without manual feature engineering.
    0 installs
27. ▌
    Library Analogue Search Branching · holobiomicslab

    Use when when you need to reconstruct or validate the control-flow architecture of a spectral search system that must handle both exact-match library lookups and analogue discovery in a single pass, particularly when the system uses pre-computed embeddings for efficiency and machine learning for.
    0 installs
28. ▌
    Link Graph Assembly And Traversal · holobiomicslab

    Use when after running a scoring algorithm (e.g., MetcalfScoring) on paired genomic and metabolomic datasets.
    0 installs
29. ▌
    M Z Metabolite Annotation Mapping · holobiomicslab

    Use when when you have a spatial metabolomics or LC-MS dataset with detected m/z features (as a feature matrix or SpaMTP Seurat object) and need to assign metabolite identities. Specifically: you have observed m/z values, you know the ionization polarity and expected adduct form (e.
    0 installs
30. ▌
    Machine Learning Model Evaluation · holobiomicslab

    Use when you have a trained NeatMS neural network model and a labelled validation dataset of MS1 peaks (annotated as 'High_quality' or 'Low_quality'), and you need to identify the scalar probability threshold that separates true positive from false positive peak classifications in your specific.
    0 installs
31. ▌
    Mass Accuracy Tolerance Filtering · holobiomicslab

    Use when when you have a peaklist from IDSL.IPA or similar peak-picking tools (containing observed m/z and intensity values) and need to assign molecular formulas from a prioritized chemical space.
    0 installs
32. ▌
    Mass Isotopologue Adduct Grouping · holobiomicslab

    Use when after sample alignment has established consensus retention time and m/z coordinates across all samples, and you need to identify and merge peaks that represent isotopologues (e.g., ¹³C variants) or adducts (e.
    0 installs
33. ▌
    Mass Range Constraint Application · holobiomicslab

    Use when when generating a virtual chemical mixture for LC-MS/MS simulation, or when sampling molecular formulas from a metabolite database (such as HMDB), you need to restrict the sample to a specific m/z window that matches your instrument's acquisition range or your analytical focus.
    0 installs
34. ▌
    Mass Spectra Embedding Extraction · holobiomicslab

    Use when you have tandem mass spectra (MS/MS) in .msp format and need dense, chemically meaningful vector representations for library matching, similarity computation, or structural clustering. Apply this when comparing spectra across large reference databases (e.
    0 installs
35. ▌
    Mass Spectrometry Data Extraction · holobiomicslab

    Use when you have native Thermo Fisher RAW mass spectrometry files and need to extract scan-level metadata (retention time, total ion current, scan mode), MS1/MS2 peak lists with m/z and intensity arrays, or instrument/LC/MS method details for downstream computational analysis, QC, or cross-sample.
    0 installs
36. ▌
    Mass Spectrometry Data Validation · holobiomicslab

    Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and post-filter counts of spectra and fragments at each major step (TIC cutoff, intra-spectrum grouping, frequency-based labeling).
    0 installs
37. ▌
    Mass Spectrometry Database Search · holobiomicslab

    Use when you have an unknown mass spectrum (or a representative metabolite spectrum from public data) and need to identify it by comparing it against a large reference library—particularly when the database contains billions of spectra and earlier tools like MASST are too slow or resource-intensive.
    0 installs
38. ▌
    Mass Spectrometry Feature Mapping · holobiomicslab

    Use when you have (1) aligned LC-MS/MS feature quantification matrix (features × fractions with m/z and RT for each feature), (2) bioassay activity measurements across the same fractions, and (3) need to assign bioactivity values to individual molecular network nodes to identify bioactive compounds.
    0 installs
39. ▌
    Mass Spectrometry File Validation · holobiomicslab

    Use when after MSConvert has converted vendor-specific raw mass spectrometry data (ThermoFisher, Agilent, or equivalent formats) on a Linux system and before initiating analysis in MSThunder.
    0 installs
40. ▌
    Mass Spectrometry Library Ranking · holobiomicslab

    Use when you have a set of unidentified tandem mass spectra (queries) and need to identify them by matching against a curated reference library (e.g., GNPS Orbitrap dataset).
    0 installs
41. ▌
    Mass Spectrum Basepeak Extraction · holobiomicslab

    Use when when you have Thermo Fisher Scientific .raw files from Orbitrap instruments and need to build a quantitative summary of MS1 acquisition intensity dynamics across a run—specifically, the m/z and intensity of the most intense peak in each MS1 scan.
    0 installs
42. ▌
    Mass Spectrum Prediction Modeling · holobiomicslab

    Use when you have a collection of molecular structures (SMILES or chemical graphs) with paired experimental tandem mass spectra and want to build or benchmark a predictive model.
    0 installs
43. ▌
    Mass To Charge Tolerance Matching · holobiomicslab

    Use when you have statistically significant LC-MS features and need to group them into structural clusters. Specifically, use it after selecting features by p-value threshold (e.g., p < 0.
    0 installs
44. ▌
    Mass Tolerance Window Calibration · holobiomicslab

    Use when when implementing adduct detection in LC-MS metabolomics workflows, after defining theoretical adduct mass offsets (e.g., [M+NH4]+ at +17.0266 Da, [M+K]+ at +38.9815 Da), and before assigning adduct labels to a feature table.
    0 installs
45. ▌
    Mass Track Extraction And Binning · holobiomicslab

    Use when when you have centroid mzML files from LC-MS metabolomics acquisition and need to construct sample-level mass tracks before cross-sample alignment. Specifically: you are starting fresh with vendor-converted or pre-processed mzML input;
    0 installs
46. ▌
    Mass2motif Parameter Optimization · holobiomicslab

    Use when when you have a preprocessed bag-of-fragments corpus from tandem mass spectrometry spectra and need to train an MS2LDA model to discover Mass2Motifs.
    0 installs
47. ▌
    Mb Vip Feature Importance Ranking · holobiomicslab

    Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify which features drive model performance and warrant further statistical validation or biological interpretation.
    0 installs
48. ▌
    Metabcombiner Object Construction · holobiomicslab

    Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to identify overlapping <m/z, retention time> features across them.
    0 installs
49. ▌
    Metabolite Feature Anova Analysis · holobiomicslab

    Use when you have normalized abundance data from LC-MS/MS for multiple samples classified into three or more discrete groups (e.
    0 installs
50. ▌
    Metabolite Feature Column Mapping · holobiomicslab

    Use when you have peak-picked LC-MS metabolomics data in a tabular format (R data frame) with columns for mass-to-charge ratio, retention time, feature identifiers, adduct annotations, and sample measurements, but the column names do not follow a standard naming convention.
    0 installs
51. ▌
    Metabolite Mass Database Matching · holobiomicslab

    Use when after features have been grouped into empirical compounds (empCpds) with inferred molecular formulas and adduct assignments by khipu, and you need to assign putative metabolite identities at the formula level.
    0 installs
52. ▌
    Metabolite Ratio Batch Correction · holobiomicslab

    Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with measured ion areas for compounds and assigned internal standards.
    0 installs
53. ▌
    Metabolite Set Annotation Mapping · holobiomicslab

    Use when you have a metabolomics peak intensity matrix with feature IDs (m/z, retention time, or arbitrary peak identifiers) and need to assign these peaks to standardized metabolite databases or spectral groupings (KEGG compounds, ChEBI IDs, GNPS Molecular Families, or MS2LDA Mass2Motifs) before.
    0 installs
54. ▌
    Metabolomic Heatmap Visualization · holobiomicslab

    Use when after completing feature annotation and reaction assignment in an untargeted metabolomics workflow, specifically when you have a feature-by-sample intensity matrix aligned with metabolite identities and want to communicate cluster structure, reaction pathway groupings, and feature.
    0 installs
55. ▌
    Metabolomic Signal Quantification · holobiomicslab

    Use when you have raw untargeted LC/MS data in open mzML or mzXML format and need to extract a quantified feature matrix (m/z and retention time coordinates with sample intensities) without prior knowledge of optimal signal detection parameters, batch effects, or quality control samples.
    0 installs
56. ▌
    Metabolomics Data Format Handling · holobiomicslab

    Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into MetaboAnalystR 4.0 for unified LC-MS1 feature detection and MS/MS spectra processing.
    0 installs
57. ▌
    Metabolomics Data Quality Metrics · holobiomicslab

    Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high technical variability or signal degradation before proceeding to statistical analysis or interpretation of.
    0 installs
58. ▌
    Missing Peak Imputation Fillpeaks · holobiomicslab

    Use when apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection failures.
    0 installs
59. ▌
    Molecular Network Node Annotation · holobiomicslab

    Use when you have a GNPS-generated molecular network (classical or feature-based workflow) and corresponding MS2LDA LDA experiment results (Mass2Motif assignments and/or chemical class predictions), and you need to propagate those annotations to individual network nodes to support visual and.
    0 installs
60. ▌
    Molecular Networking Construction · holobiomicslab

    Use when you have LC-MS/MS DDA data from one or more samples and need to organize fragmentation spectra by similarity relationships to support compound annotation, enable cross-sample comparisons, and identify known and unknown metabolites sharing structural features.
    0 installs
61. ▌
    Molecular Representation Encoding · holobiomicslab

    Use when when you have a molecular target compound defined by SMILES, InChI, or chemical formula and need to feed it into a pretrained spectrum prediction model (ICEBERG or SCARF) to generate tandem mass spectra or conduct structural elucidation.
    0 installs
62. ▌
    Ms Dial Export File Specification · holobiomicslab

    Use when you have MS-DIAL 4 or MS-DIAL 5 alignment results and need to configure LipoCLEAN for quality filtering of lipid identifications. Use this skill at the start of a LipoCLEAN analysis when you need to specify which MS-DIAL export files to analyze and how to locate them.
    0 installs
63. ▌
    Ms Dial Peak Character Estimation · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering, containing m/z, retention time, and peak intensity metrics for each feature) and need to group features into clusters that represent true metabolite signals rather than instrumental or chemical artifacts.
    0 installs
64. ▌
    Ms Ms Spectral Data Preprocessing · holobiomicslab

    Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for MS/MS-to-structure inference.
    0 installs
65. ▌
    Ms1 Scan Extraction And Filtering · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file from an Orbitrap instrument and need to programmatically retrieve MS1 spectral attributes (base-peak m/z, intensity, retention time) for downstream statistical analysis or quality control in R, rather than relying on external preprocessing.
    0 installs
66. ▌
    Ms2 Fingerprint Vector Generation · holobiomicslab

    Use when you have LC-MS/MS data in mzML, mzXML, or MGF format from one or more metabolomics samples and need to compare samples that may have poor overlap in detected features, strong retention time shifts between runs, or were acquired on different LC methods or MS technologies (e.
    0 installs
67. ▌
    Msconvert Parameter Configuration · holobiomicslab

    Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it for nontargeted analysis using MSThunder on a Linux system.
    0 installs
68. ▌
    Multi Instrument Data Integration · holobiomicslab

    Use when you have DIA mass spectrometry raw files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) in their native formats (.raw, .d, .
    0 installs
69. ▌
    Mzml Format Export From Simulator · holobiomicslab

    Use when after running an Environment simulation in ViMMS that has generated MS1 and/or MS/MS scans from a virtual mass spectrometer and controller pair. Use this skill when you need to preserve the generated scans in a standard format compatible with existing metabolomics software (e.
    0 installs
70. ▌
    Mzml Mzxml File Format Processing · holobiomicslab

    Use when your raw LC-MS data are in vendor-specific binary formats (e.g., .raw, .d, .
    0 installs
71. ▌
    Neighbourhood Density Computation · holobiomicslab

    Use when after library-matching has produced ranked candidate spectra with MS2Deepscore embeddings.
    0 installs
72. ▌
    Network Graph Manipulation Python · holobiomicslab

    Use when you have a molecular network graph exported from GNPS (as GraphML, JSON, or adjacency format) and separate experimental data (bioassay activity matrix, feature quantification table, or MS/MS annotations) indexed by feature ID, retention time, or m/z.
    0 installs
73. ▌
    Network Node Attribute Assignment · holobiomicslab

    Use when you have constructed a NetworkX graph with LC-MS features as nodes and need to annotate each node with metadata derived from the MamsiStructSearch output (assay source, isotopologue group, adduct group, structural cluster ID, correlation cluster ID, and optional compound annotation).
    0 installs
74. ▌
    Neutral Loss Composition Matching · holobiomicslab

    Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries from a MotifDB reference database.
    0 installs
75. ▌
    Peak Detection And Mass Alignment · holobiomicslab

    Use when when you have raw LC-MS/MS data files (.mzML, .raw, or vendor formats) from multiple samples and need to identify reproducible molecular features across the cohort before annotation or statistical analysis.
    0 installs
76. ▌
    Peak Quality Label Stratification · holobiomicslab

    Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
    0 installs
77. ▌
    Peak Table Filtering Metabolomics · holobiomicslab

    Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples (SampleType='LQC') and you want to exclude noisy or unstable EICs before building a peak quality classifier.
    0 installs
78. ▌
    Peptide Spectrum Match Annotation · holobiomicslab

    Use when when you have a peptide sequence, observed MS2 spectrum peaks (m/z, intensity, charge state), and need to determine which theoretical fragment ions (B and Y ions) match the observed data—particularly in stable isotope probing (SIP) experiments where peptides carry heavy isotope labels (e.
    0 installs
79. ▌
    Peptidoform Scoring And Filtering · holobiomicslab

    Use when after a transformer-based de novo sequencing model (such as Casanovo) generates candidate peptide sequences from MS/MS spectra, before exporting results or using them in database matching or visualization workflows.
    0 installs
80. ▌
    Positive Mode Ionization Analysis · holobiomicslab

    Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
    0 installs
81. ▌
    Positive Negative Class Balancing · holobiomicslab

    Use when when training a formula rescoring model on MS/MS spectra where positive examples (correct molecular formulas) are unevenly distributed across molecular formula groups or vastly outnumbered by negative examples (incorrect candidates), resulting in class imbalance that degrades model.
    0 installs
82. ▌
    Ppm Tolerance Scoring And Ranking · holobiomicslab

    Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
    0 installs
83. ▌
    Precursor Ion Isolation Windowing · holobiomicslab

    Use when processing SWATH-MS (Sequential Windowed Acquisition of all Theoretical Mass-spectra) raw data files (mzML or vendor format) for untargeted metabolomics, specifically before attempting to deconvolute overlapping MS/MS spectra.
    0 installs
84. ▌
    Precursor List Formatting For Dda · holobiomicslab

    Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software.
    0 installs
85. ▌
    Probability Threshold Calibration · holobiomicslab

    Use when after training or loading a NeatMS neural network model, apply this skill when you have a labelled validation dataset and need to determine the optimal probability threshold that maximizes classification performance (true positives minus false positives).
    0 installs
86. ▌
    Proteomics Data Format Conversion · holobiomicslab

    Use when you have vendor raw files (e.g., .raw from Thermo, .d from Agilent, .wiff2 from Sciex) that need to be converted to a standard format for analysis pipelines, data sharing, or when you require the high compression rates and fast decoding provided by Aird format.
    0 installs
87. ▌
    Public Database Query Integration · holobiomicslab

    Use when you have an experimental MS/MS spectrum (m/z and intensity pairs with known precursor m/z) and need to identify the compound by searching against public repositories or a local reference library.
    0 installs
88. ▌
    Qc Sample Classification Labeling · holobiomicslab

    Use when when loading multiple LC-MS runs (mzML files) into an MsExperiment object and the injection sequence contains an interleaved or documented pattern of QC and sample runs (e.g., two QC, four sample, two QC, four sample, two QC).
    0 installs
89. ▌
    Quality Control Report Generation · holobiomicslab

    Use when after completing doAnalysis on an mzQuality SummarizedExperiment object with outlier detection, batch correction, and compound reliability filtering applied.
    0 installs
90. ▌
    Query Result Serialization To CSV · holobiomicslab

    Use when after executing a MassQL query against mzML mass spectrometry files and obtaining a tabulated result DataFrame in memory.
    0 installs
91. ▌
    R Script Validation And Execution · holobiomicslab

    Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
    0 installs
92. ▌
    R Statistical Model Serialization · holobiomicslab

    Use when after training a customized R statistical or machine learning model on annotated training data, you need to persist the trained model object for reuse in downstream analysis workflows without retraining.
    0 installs
93. ▌
    R6 Reference Semantics Comparison · holobiomicslab

    Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it.
    0 installs
94. ▌
    Retention Time Prediction Scoring · holobiomicslab

    Use when you have a list of candidate metabolites for an unknown compound (from mass-to-structure search or library matching), experimental retention time(s) from one or more chromatographic methods, and access to a trained DNN RT predictor and meta-learned RT projection model.
    0 installs
95. ▌
    Rippp Structure Database Matching · holobiomicslab

    Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or mzData format from LC-MS/MS analysis; (2) a set of predicted RiPP precursor peptides derived from genomic biosynthetic gene cluster mining (via antiSMASH, BOA, or raw FASTA);
    0 installs
96. ▌
    Sample Relationship Visualization · holobiomicslab

    Use when after generating aligned MS2 fingerprints (sample-by-fingerprint matrices) from metabolomics data when you need to visually inspect sample clustering, identify sample similarities, or detect batch effects and RT shifts across different LC methods or mass spectrometer technologies.
    0 installs
97. ▌
    Search Results Loader Integration · holobiomicslab

    Use when you have search result files from one or more DIA-MS analysis tools and need to load them into a unified environment for Q-value filtering, cross-tool comparison (upset plots), and interactive visualization of identifications, quantifications, and coefficient of variation metrics across.
    0 installs
98. ▌
    Signal Noise Trade Off Evaluation · holobiomicslab

    Use when after generating consensus spectra with fragment recurrence frequencies, when you have replicate MS/MS spectra for features and need to choose a single frequency cutoff for denoising. Triggers include: (1) uncertainty about which frequency threshold to apply across all features;
    0 installs
99. ▌
    Signal To Noise Ratio Computation · holobiomicslab

    Use when after peak detection in nontargeted LC-MS workflows when you have a feature table with detected peaks and need to assign quality scores or filter low-confidence features.
    0 installs
100. ▌
     Spectral Candidate Classification · holobiomicslab

     Use when after performing spectral library matching of mass spectrometry peaks against a fragmentation library (e.
     0 installs