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HolobiomicsLab

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1. ▌
   Binary Cross Entropy Loss Optimization · holobiomicslab

   Use when when you have a pretrained spectrum encoder (TCN) and need to train a formula rescoring module that ranks candidate molecular formulas against MS/MS spectra.
   1 install
2. ▌
   Cardinal Peak Processing Snr Filtering · holobiomicslab

   Use when when you have loaded an unprocessed Cardinal object from MS imaging data (e.g., from Zenodo or native formats) containing thousands of m/z features across many spectra, and you need to produce a curated peak list with known expected peak count (e.g., 687 cleaned peaks from PIGII_206).
   2 installs
3. ▌
   Chemical Similarity Metrics Evaluation · holobiomicslab

   Use when after training a sequence-to-sequence decoder that reconstructs SMILES strings from fixed-size embeddings (e.g., from MS/MS spectra), use this skill to measure reconstruction fidelity on held-out test embeddings.
   0 installs
4. ▌
   Chemical Valence Constraint Validation · holobiomicslab

   Use when when you have enumerated a large pool of candidate chemical subformulae for observed fragment peaks (m/z values) within a mass tolerance window and need to eliminate chemically invalid candidates before ranking.
   1 install
5. ▌
   Chromatographic Misalignment Detection · holobiomicslab

   Use when after running XCMS-based alignment on LC-MS datasets with hundreds of samples or data acquisition periods longer than a week, when the assumption that all m/z bins in the same sample share a single warping function is likely to fail.
   0 installs
6. ▌
   Cluster Based Candidate Prioritization · holobiomicslab

   Use when after mass-to-charge matching has produced a large table of candidate KEGG metabolites with multiple adduct assignments per feature. Use it when you observe that multiple candidate ions co-elute and share similar intensity profiles, suggesting they derive from the same parent metabolite;
   0 installs
7. ▌
   Clustering Solution Comparison Metrics · holobiomicslab

   Use when you have applied two different clustering or dendrogram-flattening methods (e.g., constant-threshold vs. silhouette-score optimization) to the same feature set and need to assess whether the two solutions assign features to clusters consistently.
   0 installs
8. ▌
   Compound List Annotation And Filtering · holobiomicslab

   Use when after marker identification or feature selection has produced a list of discriminatory m/z features, and before pathway enrichment analysis (e.g., KEGG).
   0 installs
9. ▌
   Compound Retrieval Hit At K Evaluation · holobiomicslab

   Use when when you have generated spectral embeddings for a query set and a reference spectral library, computed pairwise cosine similarity scores between them, and need to quantify retrieval performance across ranked candidates (top-1, top-5, top-10).
   0 installs
10. ▌
    Configuration File Validation Dynaconf · holobiomicslab

    Use when when setting up NPLinker for natural products data mining and you have a TOML configuration file (nplinker.toml) that specifies root_dir, mode (local or podp), and paths to GNPS, AntiSMASH, and MIBiG directories.
    0 installs
11. ▌
    Constraint Based Flux Balance Analysis · holobiomicslab

    Use when you have a generic genome-scale metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, extracellular flux measurements from bioanalyzer or similar) from multiple biological samples (cell lines, conditions).
    2 installs
12. ▌
    Container Image Selection And Mounting · holobiomicslab

    Use when when deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may differ. Choose this skill specifically when you need to process LC-HRMS .mzML or .
    1 install
13. ▌
    Cross Tool Result Concordance Analysis · holobiomicslab

    Use when you have executed multiple NPDtools database search pipelines (Dereplicator, VarQuest, Dereplicator+, or MetaMiner in different modes) on identical test spectra or RiPP sequence inputs and need to understand their relative sensitivity, specificity, and complementarity.
    1 install
14. ▌
    Dataframe And Numericlist Manipulation · 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.
    1 install
15. ▌
    Deep Learning Model Checkpoint Loading · holobiomicslab

    Use when when you have MS/MS spectra from GNPS or other libraries and need to apply a pre-trained FIDDLE model (TCN formula predictor or Siamese rescore architecture) without training from scratch. Use this skill before running inference on new samples or benchmarks.
    0 installs
16. ▌
    Directory Structure Schema Enforcement · holobiomicslab

    Use when you have raw or partially organized natural products data from multiple sources (GNPS molecular networking, AntiSMASH BGC predictions, BigScape clustering, MIBiG metadata) and need to prepare them for NPLinker integration.
    0 installs
17. ▌
    Distance Clustering In High Dimensions · holobiomicslab

    Use when when you have detected feature tables from two or more LC-IMS-MS/MS samples and need to establish correspondence between features across samples (i.e., which features in sample A match which features in sample B).
    1 install
18. ▌
    Drift Time To Ccs Correlation Modeling · holobiomicslab

    Use when you have tunemix or other reference standards with known m/z, drift-time, charge state, and CCS values, and you need to establish a predictive calibration model for your ion-mobility mass spectrometry instrument.
    2 installs
19. ▌
    Feature Abundance Correlation Analysis · holobiomicslab

    Use when after initial retention-time-based feature grouping (e.g., using SimilarRtimeParam with a 20-second window), apply this skill when you need to split large feature groups into more homogeneous sub-groups.
    2 installs
20. ▌
    Feature Abundance Threshold Comparison · holobiomicslab

    Use when after loading an MZmine3-exported feature quantification table and identifying blank sample columns, when you need to remove features with significant intensity in procedural blanks before proceeding to batch correction and statistical analysis.
    0 installs
21. ▌
    Feature Alignment Error Identification · holobiomicslab

    Use when you have completed peak detection and feature alignment in metabolomic LC-MS processing and suspect systematic errors in peak integration or feature misalignment across your sample cohort.
    0 installs
22. ▌
    Feature Correlation Graph Construction · holobiomicslab

    Use when after imputing missing values and before assigning Cluster_IDs in the notame preprocessing pipeline.
    0 installs
23. ▌
    Feature Flagging Threshold Calibration · holobiomicslab

    Use when after drift correction in non-targeted LC-MS metabolomics workflows, when you need to decide which molecular features are sufficiently reproducible (low instrument/QC variance) and biologically informative (high QC-versus-biological signal ratio) to retain for downstream statistical.
    0 installs
24. ▌
    Feature Grouping By Similarity Metrics · holobiomicslab

    Use when after LCMS feature alignment (e.g., Eclipse output) when you have a feature table with retention times and intensity profiles across multiple injections, and you need to collapse redundant features (e.
    0 installs
25. ▌
    Feature Retention Criteria Application · holobiomicslab

    Use when after signal drift correction and batch effect removal (step 4) have been completed and per-feature D-Ratio values are available, but before normalization (step 7).
    0 installs
26. ▌
    File Format Conversion Troubleshooting · holobiomicslab

    Use when when integrating MSConvert into an automated LC-MS QC workflow and you need to confirm that vendor acquisition files are properly converted to mzML format with intact spectral metadata. Apply this skill after each MSConvert invocation or when QC results appear incomplete or anomalous (e.
    2 installs
27. ▌
    File Path Normalization And Validation · holobiomicslab

    Use when when preparing to read Thermo Fisher Scientific .raw files using rawrr functions (readFileHeader, readSpectrum, readChromatogram, readIndex), or when retrieving cached assembly paths for the wrapped RawFileReader dependency.
    2 installs
28. ▌
    Fragmentation Pattern Query Validation · holobiomicslab

    Use when after converting a decision tree path into a MassQL query string, before deployment to production mass spectrometry workflows.
    0 installs
29. ▌
    Gnps Molecular Networking Data Parsing · holobiomicslab

    Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) or GNPS2 (https://gnps2.org) and need to programmatically load and validate its contents (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings.
    0 installs
30. ▌
    Ion Mode Specific Ccs Model Generation · holobiomicslab

    Use when you have tunemix reference data acquired in both positive and negative ion modes and need to establish independent CCS calibration curves for each mode. The skill is required when downstream CCS assignments must achieve R² ≥ 0.
    2 installs
31. ▌
    Isotope And Adduct Pattern Recognition · holobiomicslab

    Use when when processing MS1 mass tracks from a single sample and you have already constructed per-bin mass tracks with consensus m/z and intensity vectors.
    0 installs
32. ▌
    Isotopic Pattern Detection And Merging · holobiomicslab

    Use when your peak table contains features suspected of being artifacts of incorrect isotopic pattern splitting during preprocessing—particularly when you observe multiple ions with very similar mass-to-charge ratios and retention times, or when visual inspection of m/z vs. retention time plots.
    1 install
33. ▌
    Isotopologue Adduct Cluster Assignment · holobiomicslab

    Use when after sample alignment and peak picking have produced an aligned feature table with m/z and retention time coordinates.
    0 installs
34. ▌
    Isotopologue Grouping By Mass Accuracy · holobiomicslab

    Use when after PuInc_seeker has identified putative incorporations in a stable-isotope-labeled LC/MS dataset (e.g., CELL_Glc12 unlabeled vs. CELL_Glc13 labeled samples).
    2 installs
35. ▌
    Isotopologue Quantification Extraction · holobiomicslab

    Use when you have GC-CI-MS or LC-MS data in mzML format targeting a defined set of compounds with known monoisotopic mass, retention time, and chemical formula, and you need per-isotopologue (M+0, M+1, M+2, etc.) quantification metrics (area, maxo intensity, abundance).
    1 install
36. ▌
    Jpa Module Execution And Configuration · holobiomicslab

    Use when when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to extract metabolic features as the first major step of untargeted metabolomics analysis. Choose MS1 peak picking for DDA/full-scan data;
    2 installs
37. ▌
    JSON Serialization And Deserialization · holobiomicslab

    Use when after extracting header metadata from a Thermo Fisher Scientific .
    2 installs
38. ▌
    Laplacian Embedding Spectral Alignment · holobiomicslab

    Use when you have two or more MS/MS fragmentation spectra (with precursor m/z, fragment m/z values, and intensities) and need to identify which fragment ions match across spectra while quantifying the statistical confidence of those matches.
    2 installs
39. ▌
    Lc Ms Dataset Acquisition And Curation · holobiomicslab

    Use when when beginning an untargeted LC-MS metabolomics study and need to assemble a cohort of mzML files for processing; particularly when establishing performance baselines across sample counts (10, 50, 100+ samples), validating reproducibility, or preparing data for publication.
    2 installs
40. ▌
    Lc Ms Mass Matching Reference Building · holobiomicslab

    Use when at the start of an untargeted LC-MS annotation pipeline when you have a KEGG database with exact masses and need to prepare a mass-matching reference.
    0 installs
41. ▌
    Lipid Fragmentation Pattern Prediction · holobiomicslab

    Use when you have defined lipid species (class, chain composition, and adducts) and need to generate precursor–fragment transition pairs for targeted lipidomics experiments.
    2 installs
42. ▌
    Lipid Identification Quality Filtering · holobiomicslab

    Use when you have MS-DIAL lipid identification results (alignment exports in msp/txt format) and need to distinguish correct from incorrect lipid IDs before downstream analysis.
    0 installs
43. ▌
    Mass Spectrometry Data Format Handling · holobiomicslab

    Use when you have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM transition.
    0 installs
44. ▌
    Mass Spectrometry Embedding Generation · holobiomicslab

    Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert individual spectra into fixed-dimensional vector representations for similarity-based metabolite matching or comparative analysis.
    0 installs
45. ▌
    Mass Spectrometry File Format Handling · holobiomicslab

    Use when when you have Thermo Fisher Scientific Orbitrap .raw files (e.g., from Q Exactive HF instruments) and need to extract spectral, chromatographic, or metadata directly into R for downstream statistical analysis, benchmarking, or integration with Bioconductor workflows.
    0 installs
46. ▌
    Mass Spectrometry File Standardization · holobiomicslab

    Use when you have raw or semi-processed mass-spectrometry peak data from XCMS, MSnbase, or other peak-picking tools in non-standard formats (MetaboAnalyst-like, Metabolights, vendor-specific), and you need to load them into MetaboShiny for compound identification, normalization, and statistical.
    0 installs
47. ▌
    Mass Spectrometry Imaging Data Loading · holobiomicslab

    Use when you have raw or preprocessed MS imaging data archived as an RDS file or from a Zenodo deposit that includes the full m/z feature set (e.g., 10,200 m/z values spanning 150–1000 m/z range) and spectrum count (e.
    0 installs
48. ▌
    Mass Spectrum Averaging And Processing · holobiomicslab

    Use when you have loaded a Bruker Solarix transient file (.d format with .ser or .fid content) and need to generate a processed mass spectrum for peak picking and molecular formula annotation.
    0 installs
49. ▌
    Mass Spectrum Visualization Matplotlib · holobiomicslab

    Use when you have an annotated MsmsSpectrum object (with fragment assignments via ProForma 2.0) and need to produce a high-resolution, static PNG figure showing both the observed spectrum and color-highlighted fragment ion matches for inclusion in a manuscript or supplementary materials.
    2 installs
50. ▌
    Mass Tolerance Matching And Validation · holobiomicslab

    Use when you have an MS/MS spectrum with observed peaks and a peptidoform specification (e.g., ProForma 2.0 notation such as 'EM[Oxidation]EVEES[Phospho]PEK'), and you need to annotate which observed peaks correspond to known fragment ions.
    1 install
51. ▌
    Metabolite Ranking By Annotation Score · holobiomicslab

    Use when when you have generated a set of candidate metabolites for a given experimental MS/MS spectrum and need to determine which candidate is most likely to be the true metabolite.
    0 installs
52. ▌
    Metabolite Structure Format Conversion · holobiomicslab

    Use when when importing candidate metabolite structures from public chemical databases (PubChem, ChEBI, etc.) for use in MAGMa-based annotation workflows, or when integrating external structure datasets that may use divergent molecular representation formats or contain non-standard chemical.
    0 installs
53. ▌
    Metadata Batch Assignment Verification · holobiomicslab

    Use when after data merging and before applying batch correction algorithms (ComBat, SVA, or normalization techniques) to a merged feature table from non-targeted LC-MS/MS metabolomics data.
    0 installs
54. ▌
    Metadata Extraction From Spectral Data · holobiomicslab

    Use when you have raw mass spectrometry files in one of the supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to parse out metadata fields (e.
    0 installs
55. ▌
    Metadata Harmonization Standardization · holobiomicslab

    Use when when you have preprocessed MS/MS spectra from multiple source repositories or instruments with inconsistent metadata field naming, formats, or values (e.g., mixed adduct notations like '[M+H]+' vs '[M+H]⁺', variable instrument type strings, or non-standard collision energy units).
    0 installs
56. ▌
    Molecular Database Loading And Parsing · holobiomicslab

    Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1 only) before generating virtual LC-MS/MS data.
    0 installs
57. ▌
    Molecular Network Attribute Enrichment · holobiomicslab

    Use when you have a GNPS mass spectral molecular network (in .graphml or Cytoscape format) and wish to annotate its nodes and edges with chemical class assignments from the GNPS library and/or MS2LDA motif probabilities from an independent LDA experiment.
    0 installs
58. ▌
    Ms1 Spectral Annotation Chemical Space · holobiomicslab

    Use when you have (1) a peaklist from untargeted LC/HRMS analysis with m/z and intensity values (typically output from IDSL.IPA or similar peak-picking tools), (2) a need to assign molecular formulas to detected peaks, and (3) only MS1 spectral data available (MS/MS is not required).
    0 installs
59. ▌
    Multi Domain Search Result Aggregation · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST tools and need to synthesize results across domains (e.
    2 installs
60. ▌
    Multi Score Complementarity Evaluation · holobiomicslab

    Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine whether they capture complementary information that justifies combining them.
    0 installs
61. ▌
    Multidimensional Signal Smoothing Imms · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains jagged, low-abundance ion peaks or when saturation repair has been applied and the resulting reconstructed signals need artifact removal and enhancement.
    0 installs
62. ▌
    Mzml File Generation Mass Spectrometry · holobiomicslab

    Use when after frequency-based denoising and sample-level aggregation of replicate MS/MS spectra, when you need to export denoised spectra to a standardized, vendor-independent format compatible with spectral matching pipelines.
    0 installs
63. ▌
    Online Proteomics Resource Integration · holobiomicslab

    Use when your analysis requires MS/MS spectra from public proteomics datasets but you want to avoid manual download and format conversion.
    0 installs
64. ▌
    Pathway Activity Decomposition Via Svd · holobiomicslab

    Use when when you have a metabolite intensity matrix (samples × metabolites) with compound annotations and need to score pathway activity levels for pathway enrichment analysis.
    0 installs
65. ▌
    Pathway Activity Propagation Inference · holobiomicslab

    Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensity measurements, and p-values from statistical testing) and want to predict which metabolic pathways are active, but metabolite identification is incomplete, unreliable, or computationally expensive.
    1 install
66. ▌
    Peak Recovery From Filtered Candidates · holobiomicslab

    Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
    0 installs
67. ▌
    Peptide Sequence Prediction Comparison · holobiomicslab

    Use when when you have a pre-trained Casanovo model, annotated MS/MS spectra in MGF format, and want to benchmark whether beam search decoding improves peptide prediction quality over the default greedy decoding strategy.
    0 installs
68. ▌
    Qc Metric Visualization Across Samples · holobiomicslab

    Use when you have processed LC-MS peak detection output or feature tables containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to visually monitor whether internal standards are within acceptable QC.
    0 installs
69. ▌
    Retention Time Alignment Index Mapping · 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.
    2 installs
70. ▌
    Retention Time Calibration Integration · holobiomicslab

    Use when you have LC-MS data from authentic standards run in positive and negative ESI modes, converted to .mzML format, and you need to build an in-house metabolite reference library for untargeted identification workflows.
    0 installs
71. ▌
    Retention Time Drift Time M Z Querying · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format and need to retrieve specific spectra or chromatographic slices defined by one or more of: retention time (in minutes), ion mobility arrival time (in milliseconds for DT/SLIM or Vs/cm² for TimsTOF), or m/z value (as a float or.
    2 installs
72. ▌
    Retention Time Mass Proximity Matching · holobiomicslab

    Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for features that are detected in some samples but fall below the detection threshold in others.
    0 installs
73. ▌
    Sample Type Stratified Feature Masking · holobiomicslab

    Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that fail to show meaningful enrichment in actual study samples relative to blank contamination.
    0 installs
74. ▌
    Small Molecule Chromatography Modeling · holobiomicslab

    Use when when you have a set of small molecule structures (as SMILES or molecular graphs) and need to predict their elution order in RPLC systems with eluent pH around 2.
    2 installs
75. ▌
    Snakemake Dag Generation And Execution · holobiomicslab

    Use when you have multiple mzML or mzML.gz files from LC-IMS-MS/MS instruments and need to apply DEIMoS feature detection, alignment, and calibration operations in a reproducible, traceable manner.
    1 install
76. ▌
    Spectra Annotation Parsing And Pairing · holobiomicslab

    Use when when loading MS/MS spectra from MGF files for FIDDLE model training or evaluation, or when preparing spectrum–annotation pairs for rescore model data augmentation (TCN train/test sets).
    0 installs
77. ▌
    Spectra Variable And Peak Data Storage · holobiomicslab

    Use when when building a new mass spectrometry data backend for the Spectra package that must store and serve multiple spectra with their associated m/z and intensity peaks. Use this when you need a backend that combines efficient metadata lookup (via data.
    0 installs
78. ▌
    Spectral Consensus Spectrum Generation · holobiomicslab

    Use when after extracting and filtering top-TIC spectra for a given feature (e.
    0 installs
79. ▌
    Spectral Database Output Normalization · holobiomicslab

    Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON objects, TSV match tables) that need to be reconciled into a single normalized schema for downstream aggregation.
    0 installs
80. ▌
    Spectral Fingerprint Web Service Query · holobiomicslab

    Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural classification (compound class and subclass) with confidence estimates.
    0 installs
81. ▌
    Spectral Format Parsing And Validation · holobiomicslab

    Use when you have raw or unprocessed MS/MS spectral data in standard metabolomics formats (MGF, mzML, mzXML, msp, or JSON) and need to import them into a Python-based workflow for MS2 fingerprint generation, peak counting, or spectral similarity scoring.
    0 installs
82. ▌
    Spectral Library Export And Formatting · holobiomicslab

    Use when after theoretical spectra have been generated for lipid–adduct combinations with enumerated fragment masses and intensities, and you need to deploy them for downstream MS/MS analysis on Orbitrap (DDA via Excalibur) or SkyLine (targeted/PRM) workflows.
    2 installs
83. ▌
    Spectral Molecular Embedding Alignment · holobiomicslab

    Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures for an unknown compound spectrum by learning a joint embedding space rather than using traditional spectral similarity or.
    0 installs
84. ▌
    Spectral Noise Filtering Preprocessing · holobiomicslab

    Use when you have raw MS/MS spectral data and plan to calculate spectral similarity scores (whether using entropy distance, dot product, or other algorithms) for compound identification.
    0 installs
85. ▌
    Spectral Peak Intensity Interpretation · holobiomicslab

    Use when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict which fragments will appear with high intensity in a tandem MS spectrum, or when you are performing structural elucidation by ranking candidate molecules against experimental spectra and need.
    0 installs
86. ▌
    Spectral Similarity Matrix Computation · holobiomicslab

    Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and a reference library to identify similar or related spectra.
    2 installs
87. ▌
    Spectral Similarity Network Generation · holobiomicslab

    Use when after feature detection and alignment across LC-MS/MS runs (via MZmine2 or Optimus) have produced a feature quantification table and MGF file with MS/MS spectra, and you need to discover molecular relationships and detect unknown compounds through spectral clustering and library matching.
    0 installs
88. ▌
    Structure Prediction From Mass Spectra · holobiomicslab

    Use when you have GNPS-style MGF spectral files from MS/MS experiments and need to predict the molecular structure (as SMILES) of unknown compounds.
    0 installs
89. ▌
    Tandem Ms Data Annotation And Curation · holobiomicslab

    Use when you have an unknown tandem MS/MS spectrum (precursor m/z and fragment peaks) and need to infer the molecular formula and ionization mode (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+) in a de novo setting without access to spectral libraries.
    0 installs
90. ▌
    Tandem Ms Spectral Data Interpretation · holobiomicslab

    Use when you have untargeted MS2 spectral data in MS2MP-compatible format and need to assign KEGG pathway annotations to spectra without spectral library matching or manual compound identification.
    0 installs
91. ▌
    Time Resolved Dbdi Data Interpretation · holobiomicslab

    Use when you have time-resolved DBDI-MS data (intensity matrix with m/z features as rows and scan timepoints as columns) from direct injection analysis where chromatographic separation is unavailable and you need to identify which features represent fragments or adducts of the same parent compound.
    0 installs
92. ▌
    Transformation Product Data Extraction · holobiomicslab

    Use when after generating or obtaining a TP object (via generateTPs with library, in-silico, or BioTransformer algorithms) that contains SMILES, InChIKey, or formula information for transformation products, and you need to screen those TPs in LC-HRMS data or annotate them using MetFrag.
    0 installs
93. ▌
    Validated Link Proportional Comparison · holobiomicslab

    Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and IOKR), and you need to determine whether combining scores improves discrimination of true links from false positives.
    0 installs
94. ▌
    Vendor Format Recognition And Handling · holobiomicslab

    Use when when Rapid QC-MS receives vendor-format LC-MS acquisition files from instrument data folders and must prepare them for automated QC checks and MS-DIAL processing. Specifically: input files are in proprietary vendor formats (Thermo .raw, Bruker .d, Sciex .
    0 installs
95. ▌
    Workflow Pipeline Execution Validation · holobiomicslab

    Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically informed annotation pipeline, or after pipeline execution to verify all outputs were generated correctly.
    2 installs
96. ▌
    Xcms Object Handling And Preprocessing · holobiomicslab

    Use when you have raw gas or liquid chromatography–mass spectrometry data (in NetCDF or mzML format) and need to detect features, align them across samples by retention time and mass-to-charge ratio, correct for retention time drift, and fill missing values before downstream metabolite clustering.
    0 installs
97. ▌
    Xcms Ramclustr Data Object Integration · holobiomicslab

    Use when when you have raw LC-MS all-ion fragmentation (AIF) chromatograms in centroid mode and need to prepare them for metabolite annotation using fragment ion matching.
    0 installs
98. ▌
    Chemical Database Querying And Retrieval · holobiomicslab

    Use when you have BioTransformer-predicted metabolite structures (in SMILES or InChI format) and need to identify which known compounds in public databases match those structures.
    2 installs
99. ▌
    Fragmentation Pattern Similarity Scoring · holobiomicslab

    Use when after feature detection and alignment have produced a feature table with MS/MS spectra, and you have access to a reference spectral database (e.g., xenobiotic reaction libraries or public databases).
    0 installs
100. ▌
     Metabolomics Data Loading And Formatting · holobiomicslab

     Use when you have raw metabolomics count data (e.g., from mass spectrometry or NMR experiments) in tabular format and associated sample metadata (e.g., treatment groups, experimental factors) that need to be imported into R for analysis with packages like Omu.
     0 installs