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HolobiomicsLab

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1. ▌
   Numeric Variable Range Analysis · holobiomicslab

   Use when you have loaded a numeric column (e.g., H/C ratio, O/C ratio, m/z value, or intensity) from a CSV file into Punc'data and need to render a histogram with appropriate bar spacing. The skill is triggered when the range of the column is small enough that default bin widths (1.
   0 installs
2. ▌
   Object Oriented Design Analysis · holobiomicslab

   Use when you need to understand or document the extensibility architecture of a modular OOP codebase—specifically when developers must identify which classes, interfaces, or modules to extend or improve, or when onboarding contributors to a project whose documentation does not explicitly expose its.
   1 install
3. ▌
   Outlier Detection And Treatment · holobiomicslab

   Use when when you have a Metaboprep object with raw or batch-normalized metabolomics abundance data and need to detect samples that deviate significantly from the central distribution due to technical artifacts, processing errors, or biological extremes.
   2 installs
4. ▌
   Parameter Conditional Execution · holobiomicslab

   Use when when a post-processing step (such as dereplication) risks removing true positive signals due to overly strict thresholds, and you need the option to retain raw or unfiltered output without code branching.
   0 installs
5. ▌
   Pathway Robustness Benchmarking · holobiomicslab

   Use when when selecting a pathway analysis method for metabolomics peak data where noise and missing peaks are prevalent, or when validating that a chosen method performs consistently across realistic data quality variations.
   0 installs
6. ▌
   Peak Height Threshold Selection · holobiomicslab

   Use when when applying iterative peak detection (local-maximum or Gaussian-fit methods) to 1D extracted ion chromatograms (XICs), arrival time distributions (ATDs), or MS1 spectra from MZA-format files, and you need to decide which peaks to retain based on their intensity.
   2 installs
7. ▌
   Peak Shape Correlation Analysis · holobiomicslab

   Use when when extracting benchmark peaks from mzML files for multiple isotopologues of target molecules, after initial m/z and retention-time matching, to validate that detected isotopologue peaks exhibit consistent peak shape and expected abundance ratios before including them in a reliability.
   0 installs
8. ▌
   Peptide Charge State Prediction · holobiomicslab

   Use when you have raw mass spectrometry data in MS1 format and need to assign charge states to peptide ions without manual curation or rule-based heuristics.
   0 installs
9. ▌
   Performance Benchmark Execution · holobiomicslab

   Use when you have access to a tool with published performance claims (e.g., '~20 seconds on M2 Macbook') and want to validate those claims on your own hardware, or you need to benchmark processing speed before committing to a tool for production use on similarly sized datasets.
   0 installs
10. ▌
    Pfam Domain Pattern Recognition · holobiomicslab

    Use when when you have a set of Biosynthetic Gene Clusters (BGCs) in GenBank format and need to identify statistically significant or topic-modeled co-occurrence patterns of Pfam domains and subPfams across multiple genes.
    0 installs
11. ▌
    Plage Method Metabolite Scoring · holobiomicslab

    Use when use PLAGE when you have log2-transformed, standardized metabolite intensity data (rows = peak features, columns = samples) with compound annotations (peak ID → metabolite database ID mappings), and you want to rank metabolite groupings (pathways, GNPS Molecular Families, MS2LDA.
    2 installs
12. ▌
    Pretrained Model Weight Loading · holobiomicslab

    Use when you have a pretrained PyTorch model checkpoint (e.g., JESTR weights for NPLIB1) and wish to apply it to rank candidate molecules or score spectra without modifying model parameters.
    0 installs
13. ▌
    Python Filter Class Inheritance · holobiomicslab

    Use when you need to filter compounds during Pickaxe network expansion based on domain-specific criteria (e.g., mass matching, similarity thresholds, retention time windows) that are not covered by built-in filters.
    0 installs
14. ▌
    Python Scientific Visualization · holobiomicslab

    Use when you have per-sample model predictions and metabolite signal intensities from a trained deep learning model (e.g., DeepMSProfiler) and need to visualize which metabolites correlate most strongly with specific disease phenotypes.
    2 installs
15. ▌
    Pytorch Forward Pass Validation · holobiomicslab

    Use when after instantiating a PyTorch model (such as TransG-Net) with multimodal inputs (graph features and SMILES embeddings), and before beginning model training.
    1 install
16. ▌
    Pytorch Neural Network Training · holobiomicslab

    Use when you have a PyTorch model architecture (pretrained or freshly initialized), a dataset with molecular structures (as InChI strings or graph representations) and continuous target values (retention times in minutes), and you need to optimize model weights via supervised learning.
    0 installs
17. ▌
    Query Representation Validation · holobiomicslab

    Use when after parsing a MassQL query string into an abstract syntax tree or intermediate representation, before executing it against mass spectrometry data files (mzML, mzXML, etc.). Validation is essential when the query contains complex MS-specific patterns (e.
    2 installs
18. ▌
    R Syntax Validation And Linting · holobiomicslab

    Use when after editing R configuration scripts (e.g., Modular.r) that control execution modes (Modular vs Flow) or toggling analysis parameters (Lipid, TWeen_pos, PFAS). Apply this skill before integrating edited scripts into the LipidMatch-4.
    2 installs
19. ▌
    Raw Vendor File Format Handling · holobiomicslab

    Use when you have collected imaging mass spectrometry data in vendor-specific raw format (.raw files from Bruker, Waters, Thermo, or other instrument manufacturers) and need to convert it to the open, vendor-agnostic mzML XML format before downstream imzML construction and spatial alignment.
    0 installs
20. ▌
    Reaction Rule Coverage Analysis · holobiomicslab

    Use when when you need to decide how many reaction rules to include in a Pickaxe expansion run and want to quantify the coverage penalty of using a smaller subset; when benchmarking rule importance or frequency rankings;
    0 installs
21. ▌
    Reactive Pattern Implementation · holobiomicslab

    Use when when developing or extending a WPF-based GUI application (such as MsdialGuiApp) that requires declarative, composable handling of user interactions, real-time data binding, and asynchronous event streams.
    0 installs
22. ▌
    Record Filtering By Field Value · holobiomicslab

    Use when when you have a table of JSON records and need to select a subset matching a specific condition—for example, filtering records where 'status=active' before building a string value, or filtering 'experiment_type=MS' before constructing a matrix of dictionary objects.
    0 installs
23. ▌
    Reference Compound Verification · holobiomicslab

    Use when after formatting raw mass spectrometry transition data into the EISA-EXPOSOME schema (NAME, PrecursorMZ, ProductMZ, Intensity, RT, ID columns), and before exporting the final database file.
    2 installs
24. ▌
    Regex Capture Group Application · holobiomicslab

    Use when when you have PSM files (output from search engines like MaxQuant, MSGFPlus, or Sage) and spectrum files in mzML or MGF format with non-trivial or inconsistent naming schemes, and you need to establish which PSMs correspond to which spectra.
    2 installs
25. ▌
    Reproducibility Seed Management · holobiomicslab

    Use when before invoking random forest imputation (impute_rf) or any other stochastic algorithm on a MetaboSet expression matrix. Seed-setting is mandatory when reproducibility is required—either for method validation, peer review, or when sharing analysis code with collaborators.
    0 installs
26. ▌
    Search Performance Benchmarking · holobiomicslab

    Use when when you have two or more implementations of a spectral search tool (e.g., MASST vs. MASST+) and need to quantify whether claimed performance improvements (e.g., '100-fold speedup') are reproducible.
    1 install
27. ▌
    Shiny Plot Export Configuration · holobiomicslab

    Use when when building or maintaining a Shiny GUI for omics data analysis that must support interactive visualization download in multiple raster and vector formats, and when the current plot export backend (orca) is deprecated, unmaintained, or incompatible with your deployment environment (e.
    0 installs
28. ▌
    Spectral Dimension Verification · holobiomicslab

    Use when after reading an imzML file (continuous or processed format) using readMSIData() in Cardinal, verify the resulting MSImagingExperiment object before performing normalization, baseline reduction, peak-picking, or statistical analysis.
    0 installs
29. ▌
    Spectral Peak Intensity Scaling · holobiomicslab

    Use when after filtering and noise removal when you have a cleaned spectrum with m/z and intensity pairs and need to normalize the intensity distribution prior to peptide fragment annotation, spectral library matching, or machine learning-based spectrum analysis.
    0 installs
30. ▌
    Spectrum Metadata Title Parsing · holobiomicslab

    Use when when you have PSM files from a search engine (e.g., MaxQuant, MSGFPlus, Mascot) and corresponding spectrum files in mzML or MGF format, and the spectrum identifiers in both files use different naming conventions or formats.
    0 installs
31. ▌
    Taxon Identifier Resolution API · holobiomicslab

    Use when you have a metadata table with raw, non-standardized taxonomy strings (e.g. misspellings, deprecated nomenclature, or aliases) in separate species, genus, and family columns, and you need to standardize them before performing taxon-dependent scoring (e.
    2 installs
32. ▌
    Technical Heterogeneity Removal · holobiomicslab

    Use when your metabolomics matrix (log2-scaled, samples × features in .csv format) exhibits spatial or distributional separation by batch/analytical run, visible in PCA or RLA plots.
    0 installs
33. ▌
    Thermodynamic Index Calculation · holobiomicslab

    Use when after molecular formula assignment and filtering of FT-ICR MS peaks, when you have elemental composition (C, H, O, N, S, P counts) and need to characterize metabolite thermodynamic stability, degree of oxidation, aromaticity, and unsaturation to compare compound reactivity across samples.
    0 installs
34. ▌
    Threshold Based Match Filtering · holobiomicslab

    Use when after calculating similarity metrics (e.g. cosine similarity or spectral correlation) between query peak networks and a simulated INADEQUATE database, when you need to distinguish true metabolite matches from spurious or low-confidence assignments and generate a curated list of identified.
    0 installs
35. ▌
    Unified Vocabulary Construction · holobiomicslab

    Use when when you have parallel mass spectra and molecular structure data (e.g., CANOPUS or MassSpecGym datasets) and aim to train a single encoder-decoder model (e.g., BART) that must handle both modalities as input and output tokens.
    0 installs
36. ▌
    Visualization Format Conversion · holobiomicslab

    Use when you have generated exploratory data analysis plots (PCA, correlation heatmaps, missing-variable plots) in the pmartR Shiny interface and need to download them as static images for inclusion in reports, manuscripts, or presentations with specific width, height, and resolution requirements.
    1 install
37. ▌
    Web Service Health Verification · holobiomicslab

    Use when after deploying a containerized web application (e.g., via `docker run`), before proceeding to functional testing or integration. Use this skill to confirm the application server (Tomcat, etc.) has fully initialized and the web service is listening on the mapped port and URL path.
    0 installs
38. ▌
    Suspect Screening Exposomics Workflow · holobiomicslab bundle

    Use when you have untargeted HRMS data and want to screen for a defined suspect list of environmental / exposure-relevant compounds — detect features, match them to suspect-list entries by exact mass/RT/MS2, elucidate structures of hits by in-silico fragmentation, and assign identification confidence levels (Schymanski), producing a confidence-annotated suspect-hit table.
    0 installs
39. ▌
    Targeted Lcms Quantification Workflow · holobiomicslab bundle

    Use when you have targeted LC-MS data for a defined panel of analytes and want absolute or relative concentrations — extract and integrate the target transitions/ion chromatograms, build calibration curves from standards with internal-standard normalization, apply them to samples, and QC the batch (response drift, QC-sample RSD) to a reportable quantification table.
    0 installs
40. ▌
    Untargeted Lcmsms Annotation Workflow · holobiomicslab bundle

    Use when you have untargeted LC-MS/MS data (mzML) and want an annotated feature table — preprocessing, blank/QC filtering, feature-based molecular networking, spectral library matching, SIRIUS de novo annotation, optional taxonomy-aware re-weighting, and a fused master table. This is the canonical metabopipe-style annotation pipeline.
    0 installs
41. ▌
    Edger Dgeobject Construction · holobiomicslab

    Use when you have transcript-level abundance estimates and count matrices from tximport (derived from Salmon, Sailfish, or kallisto output) and need to prepare them for differential expression analysis in edgeR.
    2 installs
42. ▌
    Gene Set Enrichment Analysis · holobiomicslab

    Use when when you have a ranked list of gene-level statistics (e.
    0 installs
43. ▌
    Isoform Structure Annotation · holobiomicslab

    Use when when you have a GTF genome annotation and need to catalog all transcript isoforms and local alternative splicing event variants (exon skipping, intron retention, alternative splice sites, mutually exclusive exons, alternative first/last exons) before quantifying their inclusion levels.
    0 installs
44. ▌
    Rnaseq Count Matrix Analysis · holobiomicslab

    Use when you have a count matrix (genes × samples) from HTSeq, featureCounts, or transcript abundance quantification (Salmon, kallisto), a sample metadata table with experimental design, and you need to test for differential expression while controlling false discovery rate via independent.
    0 installs
45. ▌
    Umap Embedding Visualization · holobiomicslab

    Use when after completing PCA and k-nearest neighbor graph construction on preprocessed, log-normalized, highly-variable-gene-filtered single-cell RNA-seq data (stored in an AnnData object), compute UMAP embeddings when you need a 2-D visualization for cluster inspection, cell-type annotation, or.
    2 installs
46. ▌
    Ion Trace Extraction And Filtering · holobiomicslab

    Use when you have CE-MS raw data (mzML or netCDF format) containing a known target analyte with a precise m/z value, and you need to isolate its signal within a defined effective mobility window (e.
    0 installs
47. ▌
    Mass To Charge Tolerance Filtering · holobiomicslab

    Use when extracting migration times of specific analyte or reference markers (e.g., Paracetamol EOF marker) from CE-MS files using peak-picking workflows.
    0 installs
48. ▌
    Peak Picking Avoidance Ms Analysis · holobiomicslab

    Use when analyzing raw 2D MS data (m/z vs. retention time maps) where conventional peak picking introduces unacceptable error rates, particularly in untargeted metabolomics or chemometrics studies requiring sensitive marker identification at trace levels (e.g., parts per billion).
    0 installs
49. ▌
    Retention Time Prediction Modeling · holobiomicslab

    Use when you have a set of small-molecule compounds (e.g., from MS/MS library matching or database annotation) that require retention time validation or ranking to resolve ambiguous identifications.
    2 installs
50. ▌
    Retrieval Metric Hit K Calculation · holobiomicslab

    Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct compound appears in the top-1, top-5, or top-10 retrieved candidates.
    0 installs
51. ▌
    Chromatographic Peak Detection Msw · holobiomicslab

    Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time dimensions. Use this skill when you must isolate individual ion signals before applying calibration corrections (e.
    0 installs
52. ▌
    Condition Effect Matrix Generation · holobiomicslab

    Use when you need to create a synthetic feature table with known, ground-truth condition effects for method validation when: (1) testing normalization or batch-correction algorithms that must not confound condition signal with batch noise;
    0 installs
53. ▌
    Ground Truth Intensity Calculation · holobiomicslab

    Use when when generating synthetic LC/GC-MS .mzML files with companion ground-truth peak tables for method validation, you need to calculate the absolute maximum intensity that each simulated peak would exhibit in the raw mass spectrometry matrix.
    1 install
54. ▌
    Linear Algebra Peak Reconstruction · holobiomicslab

    Use when after a Transformer model (e.g. GCMSFormer) has predicted the pure mass spectral matrix S for all components in overlapped peaks.
    0 installs
55. ▌
    Mass Spectral Component Extraction · holobiomicslab

    Use when raw GC-MS data (netCDF or mzML format) contains overlapping chromatographic peaks with co-eluting ions that cannot be resolved by retention time alone.
    0 installs
56. ▌
    Mass Spectrometry Feature Grouping · holobiomicslab

    Use when after raw data processing and feature extraction (e.g., via XCMS, OpenMS, or enviPick) when you have detected features across multiple LC-MS or GC-MS analyses and need to identify which features represent the same chemical across samples.
    0 installs
57. ▌
    Mass Spectrometry Library Matching · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (with ≥10 peaks, precursor m/z, and at least 5 fragment ions) and need to identify it by comparing against a curated spectral library with annotated InChIKeys or chemical structures.
    2 installs
58. ▌
    Metabolomics Software Benchmarking · holobiomicslab

    Use when you have completed peak picking with two or more competing tools (e.g., IDSL.IPA, MZmine 2, xcms, MS-DIAL) on the same LC/HRMS dataset(s) and need to quantify which performs better. Use this skill when tool selection claims require validation (e.g., 'IDSL.
    0 installs
59. ▌
    Modulation Parameter Configuration · holobiomicslab

    Use when you have a raw GCxGC-MS chromatogram in NetCDF format (.cdf file) and need to import it into R as a 2D-TIC object for preprocessing (smoothing, baseline correction, peak alignment) or multivariate analysis.
    0 installs
60. ▌
    Noise Suppression Spectral Imaging · holobiomicslab

    Use when your input is a raw two-dimensional MS map (m/z vs retention time) derived from chromatography–mass spectrometry data with poor signal-to-noise characteristics, and you need to discriminate individual analytes and identify marker features reliably.
    0 installs
61. ▌
    Pure Component Spectrum Extraction · holobiomicslab

    Use when analyzing GC-MS data containing overlapped peaks where two or more components co-elute within the same retention time window, making direct spectral assignment impossible.
    0 installs
62. ▌
    Quality Control Sample Aggregation · 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.
    0 installs
63. ▌
    R Object Inspection And Validation · holobiomicslab

    Use when after performing assignment operations (assign_ri, assign_smiles) or combining multiple library objects (e.
    0 installs
64. ▌
    Sample Capacity Constraint Setting · holobiomicslab

    Use when when designing injection sequences for LC/GC-MS multi-omics experiments where you need to distribute samples across multiple plates and must account for mandatory QC sample positions (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, and custom QC).
    1 install
65. ▌
    Spectral Adduct Ionmode Validation · holobiomicslab

    Use when when processing raw or aggregated mass spectra datasets (from .mgf, .msp, .json, or .
    0 installs
66. ▌
    Adduct Based Feature Consolidation · holobiomicslab

    Use when after accurate mass searching has assigned multiple detected m/z features to the same metabolite via positive and negative adduct libraries, and before sample-level feature merging.
    0 installs
67. ▌
    Adduct Fragment Table Construction · holobiomicslab

    Use when when initializing an mWISE annotation pipeline with a new or custom KEGG database, or when you need to reconstruct the Cpd.Add matching table with modified adduct/fragment specifications (e.g., subset to instrument-specific adducts or adjust frequency thresholds).
    0 installs
68. ▌
    Algorithm Performance Benchmarking · holobiomicslab

    Use when you have refactored or reimplemented a core computational method (e.g., entropy similarity calculation) and need to verify that the new implementation produces mathematically equivalent results to the original before deploying it to production.
    0 installs
69. ▌
    Aligned Feature Table Manipulation · holobiomicslab

    Use when after multi-sample alignment has been completed in JPA (Part 5), when you have an aligned feature table containing consolidated features across samples and need to extract ion chromatograms, perform CAMERA annotation, or validate feature assignments prior to MS2 annotation.
    0 installs
70. ▌
    Attention Mechanism Implementation · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) datasets with peak intensity features organized as spatial graphs (nodes = pixels/voxels, edges = spatial adjacency), and you need to discover latent peak patterns for automatic peak picking or marker ion identification without manual feature.
    0 installs
71. ▌
    Background Ion Contaminant Removal · holobiomicslab

    Use when you have a feature table from LC-MS data alongside blank (solvent-only) sample runs, and you want to remove features whose intensity in study samples is not substantially higher than their intensity in blanks.
    0 installs
72. ▌
    Batch Normalization Implementation · holobiomicslab

    Use when apply batch normalization after dense hidden layers (but not the final embedding layer) in a deep neural network trained on MS/MS spectral data, particularly when the network processes high-dimensional binned spectra (9948-dimensional vectors) and you need to stabilize gradient flow across.
    0 installs
73. ▌
    Categorical Ion Status Aggregation · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object when you need to understand the distribution of ions across filter status categories (passed vs. failed filters) and want to visualize or report the count and percentage composition of each status group.
    0 installs
74. ▌
    Ccs Calibration Polynomial Fitting · holobiomicslab

    Use when you have acquired tunemix or reference standard data in ion mobility spectrometry with known m/z, drift time, and CCS values, and you need to establish a drift-time-to-CCS mapping for a specific instrument, ionization mode (positive or negative), and buffer gas.
    0 installs
75. ▌
    Chromatographic Data Visualization · holobiomicslab

    Use when after peak detection has been completed and a feature table has been generated in MetCohort.
    0 installs
76. ▌
    Chromatographic Feature Extraction · holobiomicslab

    Use when you have centroided mzML files from LC- or GC-HRMS instruments (acquired in data-dependent mode with ddMS2) and need to systematically identify chromatographic peaks, measure their mass and retention time coordinates, and quantify their intensities before applying PFAS-specific.
    2 installs
77. ▌
    Chromatographic Feature Refinement · holobiomicslab

    Use when after performing retention-time-based grouping on LC-MS data (e.g., with a 10–20 second window) and observing that many feature groups contain features with similar retention times but dissimilar abundance patterns across samples or different extracted ion chromatogram peak shapes.
    2 installs
78. ▌
    Cnn Inference On Metabolomics Data · holobiomicslab

    Use when you have LC-MS feature tables (with m/z and retention time columns) paired with raw .mzXML or .mzML files, and you need to automatically validate which detected features correspond to genuine chromatographic peaks versus false positives or noise.
    0 installs
79. ▌
    Compound Identification From Ms Ms · holobiomicslab

    Use when you have LC-MS/MS data in mgf format and a custom spectral database prepared with CFM-id (or an in-built database), and you need to identify unknown compounds by comparing their experimental fragmentation patterns against predicted or reference spectra with quantified match scores.
    0 installs
80. ▌
    Compound Identification Validation · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (in .
    2 installs
81. ▌
    Conditional Dispatch Routing Logic · holobiomicslab

    Use when a mass spectrometry analysis pipeline must accept data from multiple sources with different identifier schemes (GNPS Task ID, Universal Spectrum Identifiers, or Feature-Based Molecular Networking task IDs), and you need to transparently route each to the correct loader without requiring.
    1 install
82. ▌
    Controlled Vocabulary Term Mapping · holobiomicslab

    Use when you have collected or inherited sample-information metadata from multiple sources (e.
    0 installs
83. ▌
    Corpus Bag Of Words Representation · holobiomicslab

    Use when when you have raw LC-MS/MS data in MGF format and need to prepare it for unsupervised topic modeling of metabolomics fragmentation patterns.
    2 installs
84. ▌
    Data Interchange Format Conversion · holobiomicslab

    Use when you have deconvoluted or processed MS/MS spectra from SWATH-MS data that need to be (1) ingested into tools requiring open formats (e.g., spectral library matching, metabolite identification pipelines), (2) archived in public repositories, or (3) shared across different analysis platforms.
    0 installs
85. ▌
    Dataset Size Threshold Enforcement · holobiomicslab

    Use when when you have partitioned public MS/MS files from MassIVE using the ReDU File Selector into one or more filtered groups (G1–G6) and need to verify that each group's file count complies with computational constraints before submitting to GNPS molecular networking (3000 file limit) or.
    0 installs
86. ▌
    Deep Learning Model Initialization · holobiomicslab

    Use when you have downloaded the LC-MS spectral peak dataset (DOI 10.25345/C5FD2F) and need to train a DNN model from scratch rather than using a pre-trained checkpoint.
    0 installs
87. ▌
    Difference Count Table Integration · holobiomicslab

    Use when when analyzing tandem MS/MS spectra with SIMILE V2 and you want to leverage both fragment ion mass differences and neutral loss patterns to improve spectral similarity scoring.
    0 installs
88. ▌
    Dropout Regularization Application · holobiomicslab

    Use when when training a deep neural network on mass spectrometry spectral data where overfitting is a risk (especially with data augmentation applied), and when you need both regularization during training AND uncertainty quantification at inference time via multiple forward passes with dropout.
    0 installs
89. ▌
    Feature Abundance Pattern Matching · holobiomicslab

    Use when after initial retention-time-based feature grouping when you have groups of multiple features at similar m/z and retention time but need to determine which features actually arise from the same compound.
    2 installs
90. ▌
    Feature Clustering Intensity Based · holobiomicslab

    Use when after matching mass-to-charge ratios to a KEGG database and obtaining multiple candidate metabolites per feature, but before filtering quasi-molecular adducts.
    0 installs
91. ▌
    Feature Pairing Confidence Scoring · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) and need to establish reliable correspondence between features across datasets.
    2 installs
92. ▌
    Feature Quality Assessment Metrics · holobiomicslab

    Use when after nontargeted peak detection and segmentation has generated a feature table from raw LC-MS data (mzML or vendor format), apply quality assessment when you need to rank or filter features by confidence before annotation, adduct grouping, or MS/MS matching.
    0 installs
93. ▌
    Feature Table Row Count Validation · holobiomicslab

    Use when after peak quality filtering has been applied to a composite map peak detection output using SNR (>2), goodness-of-fit (peakshape > 0.5), minimum peak height (default 1e5), and prominence (≥20% of peak_height) thresholds.
    0 installs
94. ▌
    File Format Parsing And Validation · holobiomicslab

    Use when you have peak/feature tables from one or more of MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest them into LipidMatch for lipid identification. The input files are in tabular format (CSV, TSV, or Excel) and their upstream tool origin may be unknown or mixed.
    0 installs
95. ▌
    File Grouping By Sample Attributes · holobiomicslab

    Use when you have a validated ReDU sample-information metadata table (gnps_metadata.tsv) loaded from a MassIVE accession, and you need to partition public MS/MS files into multiple analysis cohorts by one or more sample attributes.
    0 installs
96. ▌
    Formula Accuracy Metric Evaluation · holobiomicslab

    Use when when training or validating a deep learning model for molecular formula prediction from tandem MS/MS spectra, use this metric to track whether the model's predicted formula (including hydrogen atoms) exactly matches the annotated ground-truth formula.
    2 installs
97. ▌
    Formula Based Network Construction · holobiomicslab

    Use when you have a formula-assigned dataset from FT-ICR MS (or other compound-annotated mass spectrometry) and you want to characterize molecular transformations and their co-occurrence patterns—particularly in studies of DOM reactivity, fermentation, or oxidative treatment of organic mixtures.
    1 install
98. ▌
    Formula Network Extraction From Mz · holobiomicslab

    Use when you have an observed m/z value from spatially-resolved mass spectrometry imaging and need to assign one or more plausible molecular formulae with confidence metrics.
    0 installs
99. ▌
    Fragment Level Spectrum Prediction · holobiomicslab

    Use when when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict its tandem mass spectrum for structural elucidation or mass spectrometry validation.
    0 installs
100. ▌
     Fragmentation Spectrum Ion Pairing · holobiomicslab

     Use when you have two MS/MS spectra (precursor m/z and fragment ion lists) and need to identify the non-overlapping set of fragment ion alignments. Use this skill when: (1) you want to move beyond monotonic alignment to capture complex ion relationships;
     0 installs