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HolobiomicsLab

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1. ▌
   Vendor Format Routing Dispatch 2 · holobiomicslab

   Use when you have a collection of raw mass spectrometry data files from multiple instrument vendors (Agilent, Bruker, Thermo) and/or mzML exports that need to be converted to a standardized, cross-platform format for downstream software development, AI research, or multi-vendor meta-analysis.
   4 installs
2. ▌
   Binary Representation Generation 2 · holobiomicslab

   Use when you have raw mass spectra data (MGF format with m/z/intensity pairs) that need to be clustered rapidly, especially on large-scale proteomics datasets (millions of spectra).
   6 installs
3. ▌
   Building Block Annotation Export 2 · holobiomicslab

   Use when you have retrieved a user database entry (sequence or building-block structure record) from the MassSpecBlocks backend and need to generate a file in CycloBranch format for mass spectra analysis, interpretation, or sharing with collaborators using the CycloBranch software.
   4 installs
4. ▌
   Chemical Structure Serialization 2 · holobiomicslab

   Use when you need to export a stored chemical structure (sequence or building-block entry) from the MassSpecBlocks database to enable mass spectra analysis in CycloBranch or when preparing structures for import into other cheminformatics workflows that require a standardized structure interchange.
   4 installs
5. ▌
   Cheminformatics Library Querying 3 · holobiomicslab

   Use when you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to assess which library compounds are structurally similar to your queries, retrieve their categorical annotations (e.
   4 installs
6. ▌
   Domain Specific Language Parsing 2 · holobiomicslab

   Use when when you have SQL-inspired query strings that encode domain-specific assumptions and need to validate, transform, or execute them against data repositories. Specifically: input is human-readable DSL text containing mass spectrometry-specific clauses (e.
   8 installs
7. ▌
   Multiclass Metabolite Comparison 2 · holobiomicslab

   Use when when you have a normalized metabolite abundance matrix with sample metadata assigning each sample to one of three or more distinct biological classes (e.
   3 installs
8. ▌
   Neutral Loss Peak Interpretation 3 · holobiomicslab

   Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.
   5 installs
9. ▌
   Orchestrator Architecture Design 2 · holobiomicslab

   Use when when building a multi-backend visualization library where users specify both a plot type (spectrum, chromatogram, peakmap) and a backend (matplotlib for static output, Bokeh or Plotly for interactive), and you need to avoid code duplication across backends while keeping the user-facing API.
   4 installs
10. ▌
    Peak Detection Optimization Free 2 · holobiomicslab

    Use when when processing raw untargeted LC/MS data in mzML or mzXML format and you need to detect peaks across mass-to-charge (m/z) and retention time (rt) dimensions without prior knowledge of optimal signal detection parameters, QC samples, or domain expertise in LC/MS preprocessing.
    4 installs
11. ▌
    Peak List Filtering And Cleaning 2 · holobiomicslab

    Use when you have acquired MS/MS spectra containing suspect noise ions—either electronic noise (ions with identical intensities occurring >4 times in a single peak list, a signature of detector artifacts) or chemical noise (fragment ions chemically implausible given the precursor molecule's.
    4 installs
12. ▌
    Peptide Mass Calculation Average 2 · holobiomicslab

    Use when you have a list of polypeptide sequences (one per line or CSV format) and need to compute average mass (weighted by natural isotope abundances) to compare against experimental LC-MS or MS/MS data where the full isotopic distribution—not just the most abundant peak—is relevant for peptide.
    4 installs
13. ▌
    Pfas Homologous Series Detection 3 · holobiomicslab

    Use when you have an m/z-resolved feature list from LC- or GC-HRMS analysis (either detected by pyOpenMS or provided as a custom Excel table) and need to prioritize potential PFAS compounds by identifying clusters of homologous structures.
    5 installs
14. ▌
    Qc Sample Batch Drift Correction 3 · holobiomicslab

    Use when you have a QC-annotated feature table (samples × features with QC sample identifiers) from LC-MS untargeted metabolomic profiling and observe systematic signal drift across the run sequence or between batch blocks.
    4 installs
15. ▌
    Qc Sample Variability Assessment 2 · holobiomicslab

    Use when after batch correction of a metabolomics dataset using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to systematically evaluate which one produces the most stable compound quantification (lowest QC variability) for each compound.
    4 installs
16. ▌
    R6 Class Object Mutation Testing 2 · holobiomicslab

    Use when when applying a series of mpactr filter functions (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) with copy_object=FALSE to confirm that the original peak table object is mutated as intended, not silently copied.
    7 installs
17. ▌
    Raw Data Throughput Benchmarking 2 · holobiomicslab

    Use when when you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.
    3 installs
18. ▌
    Raw File Data Extraction Via API 3 · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.
    7 installs
19. ▌
    S4 Class Object Memory Profiling 2 · holobiomicslab

    Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures or defer initialization until data access.
    6 installs
20. ▌
    Score Distribution Visualization 3 · holobiomicslab

    Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient separation between validated links and the background population.
    7 installs
21. ▌
    Smoothing Spline Basis Selection 2 · holobiomicslab

    Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction spline.
    2 installs
22. ▌
    Spatial Overlap Analysis Imaging 3 · holobiomicslab

    Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit overlapping spatial distributions across the tissue image that could confound downstream annotation filtering.
    4 installs
23. ▌
    Neutral Loss Composition Matching 3 · 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.
    4 installs
24. ▌
    Nmr Spectral Comparative Analysis 2 · holobiomicslab

    Use when you have 2D NMR spectral data (heteronuclear and/or homonuclear experiments) from multiple samples in a natural products library or mixture, and you need to identify common structural scaffolds, correlate features across samples, or prioritize samples for further structural annotation.
    4 installs
25. ▌
    Peak Extraction Rescue Algorithms 3 · holobiomicslab

    Use when traditional peak extraction algorithms have produced a feature table that you suspect is incomplete or missing known suspects from your target database (e.g., T3DB).
    4 installs
26. ▌
    Peptidoform Scoring And Filtering 2 · 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.
    4 installs
27. ▌
    Positive Mode Ionization Analysis 2 · holobiomicslab

    Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
    5 installs
28. ▌
    Python Class Discovery Reflection 2 · holobiomicslab

    Use when when building an extensible converter framework where new converter implementations (e.g., WebConverters or ComputeConverters for external chemical services) should be automatically discovered and registered without modifying a central registry.
    6 installs
29. ▌
    Quality Control Report Generation 2 · holobiomicslab

    Use when after completing doAnalysis on an mzQuality SummarizedExperiment object with outlier detection, batch correction, and compound reliability filtering applied.
    4 installs
30. ▌
    R6 Reference Semantics Comparison 3 · 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.
    4 installs
31. ▌
    Retention Time Feature Clustering 3 · holobiomicslab

    Use when after chromatographic peak detection (findChromPeaks) when you have a processed XcmsExperiment object with detected peaks and need to perform initial feature grouping. Use it when features of the same compound are expected to co-elute within a narrow retention-time window (e.
    4 installs
32. ▌
    Sample Relationship Visualization 3 · 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.
    5 installs
33. ▌
    Spectral Candidate Classification 2 · holobiomicslab

    Use when after performing spectral library matching of mass spectrometry peaks against a fragmentation library (e.
    4 installs
34. ▌
    Spectral Clustering Density Based 3 · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically when clustering bottom-up proteomics data with the goal of grouping spectra from the same peptide sequence or when you.
    5 installs
35. ▌
    Spectral Denoising Formula Method 2 · holobiomicslab

    Use when you have a noisy MS/MS spectrum and need to identify and remove chemical noise ions (as opposed to electronic noise). You have the precursor compound's SMILES string or molecular formula and its adduct type.
    4 installs
36. ▌
    Spectral Feature Table Generation 2 · holobiomicslab

    Use when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to identify and quantify metabolic features before multi-sample alignment. Use MS1 peak picking for full-scan or DDA data to extract Gaussian and non-Gaussian shaped peaks;
    4 installs
37. ▌
    Spectral Library Entry Generation 3 · holobiomicslab

    Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for a known metabolite.
    3 installs
38. ▌
    Spectral Metadata Standardization 3 · holobiomicslab

    Use when you have mass spectrometry spectra stored across multiple, disparate metabolomics repositories (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA) and need to retrieve them using a single identifier scheme, or you are publishing spectrum figures and need.
    6 installs
39. ▌
    Conditional Logic Implementation 3 · holobiomicslab

    Use when you have a user-submitted spectrum with domain-context metadata (e.
    4 installs
40. ▌
    Detection Network Output Parsing 2 · holobiomicslab

    Use when you have raw LC-MS data in mzML format with regions of interest (ROI) already identified, and a trained detection model (e.g., checkpoint0029.pth) has produced bounding box predictions with confidence scores.
    6 installs
41. ▌
    Docker Environment Configuration 2 · holobiomicslab

    Use when you need to deploy CloMet for the first time on a new system, or when you want to ensure reproducible execution of metabolomics data harmonization tasks without manual dependency management.
    5 installs
42. ▌
    Docker Image Registry Inspection 2 · holobiomicslab

    Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's size falls within documented ranges (e.g., cli 6–7 GB, dev 9–11 GB, linux 8–10 GB, windows 4–5 GB).
    4 installs
43. ▌
    Embedding Similarity Computation 2 · holobiomicslab

    Use when when you have pre-computed embeddings (from MSBERT, Spec2Vec, or other deep learning models) for a query spectrum dataset and a reference library, and need to measure how well the embedding space ranks correct library matches.
    4 installs
44. ▌
    Feature Annotation Consolidation 3 · holobiomicslab

    Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to consolidate redundant or related ion signals into compound-level feature groups before downstream statistical or.
    4 installs
45. ▌
    Feature Intensity Quantification 2 · holobiomicslab

    Use when after features have been identified in LC-MS data via peak picking, MS2 recognition, or targeted-list matching, and you need to measure their signal magnitude (peak height or area) across samples for quantitative comparison, normalization, or statistical testing in metabolomics studies.
    6 installs
46. ▌
    Feature Table Moniker Management 3 · holobiomicslab

    Use when when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to track which version of the table is being used at each step.
    5 installs
47. ▌
    Field Mapping And Transformation 2 · holobiomicslab

    Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.
    4 installs
48. ▌
    File API Endpoint Implementation 2 · holobiomicslab

    Use when when you need to construct a POST endpoint that ingests raw spectral data files from multiple vendor formats (jcamp, RAW, mzML) and must standardize them for downstream processing.
    6 installs
49. ▌
    Fragment Ion Difference Counting 3 · holobiomicslab

    Use when when preparing tandem MS/MS data for spectral alignment and similarity comparison, particularly when you have loaded raw fragmentation spectra and need to extract and quantify mass difference patterns that capture the fragmentation process.
    4 installs
50. ▌
    Fragment Ion Type Interpretation 2 · holobiomicslab

    Use when you have an tandem MS spectrum with unidentified peaks and a known or hypothesized peptide sequence (in ProForma 2.0 format, including post-translational modifications).
    4 installs
51. ▌
    Gc Ims Peak Alignment Evaluation 3 · holobiomicslab

    Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using hierarchical clustering.
    4 installs
52. ▌
    Gcxgc Preprocessed Data Handling 2 · holobiomicslab

    Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a reference using 2D correlation optimized warping) and need to consolidate them into a single analytical object for.
    5 installs
53. ▌
    Ion Count Percentage Calculation 3 · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to an mpactr object and generating a qc_summary() data.
    2 installs
54. ▌
    Ion Type Assignment Verification 3 · holobiomicslab

    Use when after calling MsmsSpectrum.annotate_proforma() to assign fragment ions to a mass spectrum, verify that each annotated peak has the correct ion_type ('b' or 'y'), charge state, and m/z deviation from the theoretical mass computed for that peptidoform.
    4 installs
55. ▌
    Disease Classification Prediction 2 · holobiomicslab

    Use when you have raw LC-MS metabolomics data from multiple disease groups (in .npy or .
    3 installs
56. ▌
    Docker Multistage Build Execution 2 · holobiomicslab

    Use when you need to containerize a C#-based Windows application (like AirdPro CLI) for Linux deployment, require Wine and .NET Framework 4.
    5 installs
57. ▌
    Environment Variable Provisioning 2 · holobiomicslab

    Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb, joblauncher, job, pubchem) receives the correct configuration—such as port mappings, service URLs, and data paths—without.
    4 installs
58. ▌
    Feature Grouping By Molecular Ion 3 · holobiomicslab

    Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
    5 installs
59. ▌
    File Format Export And Validation 2 · holobiomicslab

    Use when after executing MassQL queries on mass spectrometry data that produce tabulated results (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to persist those results for archival, sharing, or downstream statistical analysis.
    5 installs
60. ▌
    Ftms Mass Spectrum Peak Detection 2 · holobiomicslab

    Use when you have loaded an FT-ICR raw spectrum (e.g., ESI_NEG_SRFA.d in Bruker or ThermoFisher .raw format) and need to identify the m/z positions and intensities of individual mass spectral peaks.
    6 installs
61. ▌
    Github Actions Artifact Retrieval 2 · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers, portable binaries, or packages), and document the workflow run metadata.
    4 installs
62. ▌
    Installation Validation Reporting 2 · holobiomicslab

    Use when when deploying a new Python package in a reproducible analysis environment or continuous integration pipeline, and you need to confirm that all required core modules (e.g., pyteomics.mass, pyteomics.pepxml, pyteomics.mzid, pyteomics.tandem, pyteomics.
    8 installs
63. ▌
    Intensity Distribution Simulation 2 · holobiomicslab

    Use when when you need to create synthetic noisy MS/MS spectra from clean baseline spectra to validate denoising algorithms, compare denoising performance across noise levels, or generate ground-truth test datasets where the true signal and noise composition are known and controllable.
    4 installs
64. ▌
    Inter Sample Variance Calculation 2 · holobiomicslab

    Use when after applying batch correction (e.g., via pycombat) to a multi-batch feature table, to validate whether the correction has reduced systematic intensity differences between batches.
    4 installs
65. ▌
    Keras Regularizer API Integration 2 · holobiomicslab

    Use when when extending an existing neural network class (e.g., SiameseModel) that lacks user-configurable regularization, and you need to prevent overfitting on moderate-sized training datasets (e.
    6 installs
66. ▌
    Library Analogue Search Branching 3 · 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.
    3 installs
67. ▌
    Link Graph Assembly And Traversal 2 · holobiomicslab

    Use when after running a scoring algorithm (e.g., MetcalfScoring) on paired genomic and metabolomic datasets.
    4 installs
68. ▌
    Mass Accuracy Tolerance Filtering 2 · 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.
    5 installs
69. ▌
    Mass Spectrometry Library Ranking 2 · 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).
    4 installs
70. ▌
    Ms Ms Spectrum Pairwise Comparison 3 · holobiomicslab

    Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format that have been converted to low-dimensional vectors via feature hashing, and you need to identify which spectra are similar enough to cluster together.
    2 installs
71. ▌
    Msexperiment Backend Configuration 2 · holobiomicslab

    Use when you have multiple centroided .mzML LC-MS files that need to be loaded into a unified object for targeted peak integration, and you need to distinguish QC runs from sample runs to compute per-group quality metrics (e.g., average SNR, peak correlation, area under curve per QC cohort).
    3 installs
72. ▌
    Network Module Interaction Scoring 2 · holobiomicslab

    Use when after biclustering a normalized microbe-metabolite feature attribution score matrix into distinct functional modules, use this skill to summarize pairwise module interactions by aggregating scores between all microbe-metabolite pairs from different modules.
    4 installs
73. ▌
    Neural Network Architecture Design 3 · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV from mzMine or XCMS) for LCMS data, have generated training/validation/test batches with known class imbalance, and need to train a CNN model from scratch to achieve AUC ROC > 0.9 for distinguishing true from false positive MS1 peaks.
    7 installs
74. ▌
    Numerical Equivalence Verification 2 · holobiomicslab

    Use when when you have reimplemented an algorithm in a new package or optimized an existing algorithm and need to verify that the new version produces the same numerical results as the original or reference implementation.
    5 installs
75. ▌
    Peak Height Threshold Optimization 2 · holobiomicslab

    Use when you have raw metabolomic LC-MS data processed through XCMS CentWave feature extraction and want to improve true positive feature recovery while controlling false positive rate and crash likelihood.
    4 installs
76. ▌
    Peak Network Clustering Inadequate 2 · holobiomicslab

    Use when you have picked peaks (coordinates and intensities) from INADEQUATE spectra and need to distinguish which peaks likely originate from the same metabolite before matching to a reference database.
    4 installs
77. ▌
    Peak To Formula Assignment Mapping 2 · holobiomicslab

    Use when when you have a fragment peak list (m/z values and intensities) from MS/MS data and need to assign candidate chemical subformulae to each peak as part of a de novo chemical formula inference pipeline.
    3 installs
78. ▌
    Q Value Based Confidence Filtering 2 · holobiomicslab

    Use when after loading feature identification results (e.g., from OpenSwath or other DIA search engines) when you need to display only confident peptide precursors and their chromatograms.
    5 installs
79. ▌
    Quality Control Sample Aggregation 2 · holobiomicslab

    Use when you have a feature intensity matrix (peak vector) and a corresponding set of QC sample indices from a multi-batch LC/GC-MS experiment, and you need to establish batch-invariant reference statistics before applying QC-based batch correction methods such as bcpareto(), bccenter(), or.
    6 installs
80. ▌
    Quality Control Sample Designation 2 · holobiomicslab

    Use when when importing a new batch of centroided mzML or mzXML LC-MS files into MetCohort, before any data alignment or feature detection is performed. At least one file must be designated as QC to enable ROA detection and alignment;
    4 installs
81. ▌
    Quality Control Summary Generation 2 · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, CV, or insource) to a peak table in a chained filtering workflow.
    7 installs
82. ▌
    Reaction Flux Concordance Analysis 3 · 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.
    4 installs
83. ▌
    Rescore Training Data Augmentation 3 · 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.
    2 installs
84. ▌
    Sample Spectrum Metadata Alignment 2 · 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.
    3 installs
85. ▌
    Isotopologue Signature Detection 3 · holobiomicslab

    Use when you have preprocessed, statistically significant LC-MS features (from multiple assays or a single assay) and need to group features that represent the same metabolite in different isotopic labeling states.
    4 installs
86. ▌
    JSON Parsing Motifset Extraction 3 · holobiomicslab

    Use when you have completed the MS2LDA LDA modeling phase and possess motifset.json or motifset_optimized.json files containing inferred Mass2Motifs.
    4 installs
87. ▌
    Kendrick Mass Defect Calculation 2 · holobiomicslab

    Use when you have a feature list from LC- or GC-HRMS analysis (with m/z, retention time, and exact mass columns) and you want to detect homologous series of PFAS compounds that repeat by CF₂ mass increments (typically ≈34 Da).
    3 installs
88. ▌
    Lantibiotic Structure Annotation 3 · holobiomicslab

    Use when you have (1) genomic data from a Streptomyces or other RiPP-producing organism in raw FASTA format or annotated GenBank format, (2) high-resolution LC-MS/MS spectra in centroided MGF, mzML, mzXML, or mzData format, and (3) a known or predicted lantibiotic core peptide sequence you wish to.
    3 installs
89. ▌
    Lc Ms Data Pipeline Architecture 2 · holobiomicslab

    Use when you have vendor-format LC-MS acquisition files (.raw, .d, .ms) from instrument runs and need to set up an end-to-end data quality control system that converts proprietary formats into open mzML, processes spectral data, and surfaces QC failures in real time.
    6 installs
90. ▌
    Lc Ms Feature Quality Assessment 2 · holobiomicslab

    Use when you have generated feature tables from LC-MS data using different parameter combinations (e.g., varying Centwave, FeatureFinderMetabo, or ADAP peak picking settings) and need to objectively compare their outputs to select the -performing configuration for your dataset.
    4 installs
91. ▌
    Lc Ms Quality Metric Computation 3 · holobiomicslab

    Use when after performing peak detection on centroided .mzML LC-MS data with screening_mode=FALSE in TARDIS.
    4 installs
92. ▌
    Lcms Feature Relationship Export 2 · holobiomicslab

    Use when after ISFrag has completed identification of in-source fragment features (Part 4 output), when you need to serialize and inspect the hierarchical fragmentation relationships among identified ISF features, or when preparing data for visualization or external analysis of fragment lineage and.
    3 installs
93. ▌
    Lcms Target Visibility Screening 3 · holobiomicslab

    Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.
    5 installs
94. ▌
    Lipid Library Annotation From Mz 3 · holobiomicslab

    Use when you have experimental peaklist data (CSV or mzML-derived tables) from UHPLC-HRMS/MS instruments (Q-Exactive, Agilent/Bruker/SCIEX Q-TOF) with fragment m/z values and want to annotate them to known lipid identities.
    4 installs
95. ▌
    Machine Learning Model Inference 2 · holobiomicslab

    Use when you have molecular descriptors or fingerprints for a set of compounds (e.g., from LC-MS metabolomics) and need to predict a continuous property—such as HPLC retention time—to support compound identification or filter out false positive annotations.
    4 installs
96. ▌
    Mass Difference Pattern Matching 3 · holobiomicslab

    Use when after peak picking and sample alignment when you have an aligned feature table containing m/z and retention time coordinates. Use it when your untargeted LC-MS workflow needs to reduce feature redundancy caused by naturally occurring stable isotope patterns and common adduct formation.
    4 installs
97. ▌
    Metabolite Spectral Data Merging 3 · holobiomicslab

    Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of in-house standards in separate MSP files) and need to combine them with consistent metadata (SMILES, InChIKey, molecular.
    4 installs
98. ▌
    Metabolomics File Format Parsing 2 · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and tabular data sections (e.g., METABOLITES, DATA blocks), and need to load them into memory for downstream conversion, validation, or analysis rather than manual text parsing.
    6 installs
99. ▌
    Molecular Fingerprint Generation 2 · holobiomicslab

    Use when when you have annotated chemical structures (SMILES or InChI strings) from a curated MS/MS dataset and need to compute pairwise structural similarity scores (Tanimoto or other metrics) as training labels, or when preparing molecular representations for comparison against mass spectral data.
    6 installs
100. ▌
     Ms2 Diagnostic Fragment Matching 3 · holobiomicslab

     Use when you have centroided MS2 spectra from data-dependent LC- or GC-HRMS measurements and need to rapidly prioritize potential PFAS features within a larger feature set.
     4 installs