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HolobiomicsLab

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1. ▌
   Graph Based Knowledge Representation · holobiomicslab

   Use when annotating metabolites in untargeted metabolomics experiments where both established biochemical pathways and experimental MS2 similarity patterns must be simultaneously leveraged.
   0 installs
2. ▌
   Graph Node Edge Attribute Assignment · holobiomicslab

   Use when you have statistically significant LC-MS features grouped into structural clusters (isotopologue groups, adduct groups, cross-assay links) and correlation cluster assignments from upstream MamsiStructSearch, and you need to create an interactive graph representation suitable for Cytoscape.
   0 installs
3. ▌
   Heterogeneous Graph Embedding Design · holobiomicslab

   Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time prediction across different chromatographic columns, methods, or conditions).
   0 installs
4. ▌
   Hit Metric Evaluation Fold Averaging · holobiomicslab

   Use when when you have a trained MS/MS spectral embedding model and need to measure compound identification accuracy on a held-out test set, but want to mitigate sensitivity to a single random train/test split. Use this skill if the original training set split is fixed (e.
   0 installs
5. ▌
   Hydrogen Rearrangement Rules Scoring · holobiomicslab

   Use when after MS-CleanR has filtered and clustered LC-MS features and formatted them for MS-FINDER input (m/z, retention time, MS/MS spectra).
   0 installs
6. ▌
   Interactive Plot Customization Bokeh · holobiomicslab

   Use when when you have loaded extracted ion chromatogram traces (via SqMassLoader from sqMass files) and need to render them as interactive web-based visualizations where users can pan, zoom, hover for metadata, mute individual traces, and optionally visualize peak boundaries from OpenSwath results.
   0 installs
7. ▌
   Interactive Visualization Inspection · holobiomicslab

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

   Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications and need to monitor internal standard retention time, m/z, and intensity variation across samples as part of automated or user-defined QC checks during instrument runs.
   0 installs
9. ▌
   Ion Mobility Dimension Interpolation · holobiomicslab

   Use when when processing raw IM-MS data (Agilent MassHunter .
   0 installs
10. ▌
    Ion To Molecule Relationship Mapping · holobiomicslab

    Use when after dereplication and cosine similarity clustering have been completed and you have merged molecular predictions with ion metadata (m/z, adduct type, intensity).
    0 installs
11. ▌
    Isotope Adduct Anchor Identification · holobiomicslab

    Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a cohort.
    0 installs
12. ▌
    Isotope Labeling Data Interpretation · holobiomicslab

    Use when you have LC-MS FAM measurements from an isotope-labeling experiment and need to correct them to obtain true MDV values.
    0 installs
13. ▌
    Jupyter Notebook Workflow Automation · holobiomicslab

    Use when when you have raw LC-MS/MS spectral data in .
    0 installs
14. ▌
    Kegg Pathway Prediction From Spectra · holobiomicslab

    Use when you have untargeted MS2 spectral data (in MS2MP-compatible format) and need to assign KEGG pathway annotations to unknown metabolites.
    0 installs
15. ▌
    Lc Hrms Metabolomics Data Processing · holobiomicslab

    Use when you have LC-HRMS raw data files (.mzML or .abf format) from metabolomics experiments and need to extract, align, and annotate features in a reproducible manner across multiple computational environments.
    0 installs
16. ▌
    Lc Ms Scan Acquisition Orchestration · holobiomicslab

    Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that strategy will acquire MS1 and MS2 scans over a defined retention-time window.
    0 installs
17. ▌
    M Z Alignment And Mass Grid Assembly · holobiomicslab

    Use when when processing multiple centroided mzML LC-MS files from the same study and you need to identify which mass tracks represent the same metabolite across samples.
    0 installs
18. ▌
    Mass Distribution Vector Calculation · holobiomicslab

    Use when you have raw LC-MS fractional abundances (FAM) data from isotope labeling experiments and need to obtain true mass distribution vectors (MDV) that represent only the isotopic labeling contribution.
    0 installs
19. ▌
    Mass Spectra Encoding Neural Network · holobiomicslab

    Use when you have a collection of MS/MS spectra (in mzML or MGF format) from a proteomics experiment and need to group or retrieve spectra derived from the same peptide without prior peptide identification.
    0 installs
20. ▌
    Mass Spectral Fingerprint Generation · holobiomicslab

    Use when you have unaligned MS2 spectra from one or more samples (in formats like .mgf, .mzML, or .mzXML) and need to compare them in a retention-time-agnostic manner.
    0 installs
21. ▌
    Mass Spectrometry Benchmark Analysis · holobiomicslab

    Use when you have implemented or modified a tandem mass spectrometry formula inference model and need to measure whether a specific architectural change (e.
    0 installs
22. ▌
    Mass Spectrometry Data Format Import · holobiomicslab

    Use when you have raw mass spectrometry data in one of the supported spectral formats (mzML, mzXML, msp, MGF, JSON, or metabolomics-USI) and need to load it into a Python environment for cleaning, processing, or similarity comparison.
    0 installs
23. ▌
    Mass Spectrometry Data Normalization · holobiomicslab

    Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed peak information into a transformer-based spectral embedding model that expects normalized, fixed-length tensor inputs.
    0 installs
24. ▌
    Mass Spectrometry Data Preprocessing · holobiomicslab

    Use when you have raw LCMS data in mzML or mzXML format from DDA, DIA, or fullscan analyses and need to extract metabolite features with unified m/z, retention time, and intensity values across multiple samples before performing MS2 annotation or in-source fragment analysis.
    0 installs
25. ▌
    Correlation Matrix Construction · holobiomicslab

    Use when after obtaining per-sample model predictions and metabolite signal intensities from a trained deep learning model (e.g., DeepMSProfiler) on LC-MS data from multiple disease groups, and you need to identify and visualize metabolite–disease associations as correlation strengths.
    0 installs
26. ▌
    Cross Software Feature Matching · holobiomicslab

    Use when you have collected feature lists in CSV format from two or more MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), processing software packages (e.g., vendor-specific vs. open-source), or instrument platforms (e.
    0 installs
27. ▌
    Document Structure Verification · holobiomicslab

    Use when when uploading or ingesting paired omics project documents into the Pairing Omics Data Platform, or when you need to verify that a JSON project file conforms to the expected schema structure before processing MS/MS mass spectra linkages, genome associations, or submission to external.
    0 installs
28. ▌
    Evaluation Data Object Handling · holobiomicslab

    Use when after completing an Environment simulation run with save_eval flag enabled, when you need to preserve the EvaluationData object containing scan provenance, chemical source definitions, and fragmentation events for later inspection, validation, or reanalysis without re-running the full.
    0 installs
29. ▌
    Exact Mass Accuracy Calculation · holobiomicslab

    Use when you have feature pairs identified by temporal correlation in direct-injection MS data and need to confirm their relationship is consistent with known adduct/fragment mass shifts.
    0 installs
30. ▌
    Feature Abundance Normalization · holobiomicslab

    Use when after peak picking (e.g., via MS-DIAL) and quality control filtering, when you have a raw feature abundance matrix with intensity values across multiple samples and need to make intensities comparable before statistical testing or multivariate analysis.
    0 installs
31. ▌
    Feature Annotation Augmentation · holobiomicslab

    Use when when a traditional peak extraction pipeline (e.g., XCMS) has generated a feature table from LC-MS data but fails to detect known or suspected compounds present in your sample. Specifically, when you have a suspect database (e.
    0 installs
32. ▌
    Feature Grouping By Mass Defect · holobiomicslab

    Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.
    0 installs
33. ▌
    Feature Quantification Analysis · holobiomicslab

    Use when when you have loaded search result files from one or more DIA-MS analysis tools and need to assess the quantitative performance of identified features.
    0 installs
34. ▌
    Feature Specificity Calculation · holobiomicslab

    Use when when you have a quantitative feature table from MZmine2/MZmine3 with peak area and m/z data aligned across multiple extract samples, and you need to identify which features are characteristic of individual samples (high specificity) versus ubiquitous across the extract set.
    0 installs
35. ▌
    Fragment Match Rate Computation · holobiomicslab

    Use when after denoising MS/MS spectra at multiple frequency thresholds and matching each thresholded spectrum against a -matching reference spectrum.
    0 installs
36. ▌
    Gap Filling Algorithm Selection · holobiomicslab

    Use when when processing untargeted LC-MS data with SLAW and observing incomplete feature detection across the sample cohort—i.e., features present in some samples but with missing values (zeros or NAs) in others due to signal dropout, retention time drift, or mass calibration drift.
    0 installs
37. ▌
    Gcf Mf Hierarchical Aggregation · holobiomicslab

    Use when when you have predicted BGC-spectrum IOKR scores or other pairwise linking scores, and need to rank genomic clusters (GCFs from BiG-SCAPE) against metabolomic clusters (MFs from MS/MS spectra grouping), particularly in NPLinker workflows where one GCF may contain multiple BGCs and one MF.
    0 installs
38. ▌
    Gcf Mf Link Scoring Computation · holobiomicslab

    Use when you have paired GCF and MF datasets with strain membership information and need to rank candidate GCF–MF links to identify which biosynthetic gene clusters likely produce detected metabolites.
    0 installs
39. ▌
    Gcf Spectra Association Ranking · holobiomicslab

    Use when when you have integrated genomic data (GCFs from AntiSMASH via BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to identify and rank which secondary metabolites detected in spectra are likely produced by which biosynthetic.
    0 installs
40. ▌
    Gnps Workflow Result Processing · holobiomicslab

    Use when when you have run a spectral networking job on GNPS (e.g. ProteoSAFe-METABOLOMICS-SNETS-V2) and need to reuse the network output files locally with MetaMiner or another tool that accepts spectral network input directories.
    0 installs
41. ▌
    Inchikey Smiles Standardization · holobiomicslab

    Use when when you have raw MS/MS spectra from repositories like GNPS that lack or have inconsistent chemical structure annotations (InChI/SMILES), and you need to produce a curated dataset with uniform 14-character InChIKey and SMILES/InChI annotations for downstream machine learning or similarity.
    0 installs
42. ▌
    Interactive Workflow Validation · holobiomicslab

    Use when after automated peak detection has identified candidate peaks from LC-MS mzML files, but before exporting the final metabolite library. Use this skill when you need to: (1) optimize noise and peak-detection parameters by visualizing their effect on a representative subset of peaks;
    0 installs
43. ▌
    Isotope Mass Offset Enumeration · holobiomicslab

    Use when you have a detected feature table (m/z, drift_time, retention_time, intensity) from LC-IMS-MS or similar multidimensional MS data and want to identify and annotate isotopic families (e.g., singly-charged C13 patterns).
    0 installs
44. ▌
    Jms Compliant Database Querying · holobiomicslab

    Use when you have grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments (via khipu), and you need to assign candidate metabolite identities at Level 4 annotation depth by matching against curated reference libraries.
    0 installs
45. ▌
    Kegg Identifier To Mass Mapping · holobiomicslab

    Use when you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites. This skill must be applied before the matching stage if you are working with a KEGG database (KeggDB or sample.keggDB) and require a precomputed adduct/fragment lookup table.
    0 installs
46. ▌
    Lc Ms Data Structure Validation · holobiomicslab

    Use when before launching TARDIS peak detection on a new LC–MS dataset or target compound list. Apply this skill when you have raw MS data files in vendor formats (e.g., .raw, .d) and/or a spreadsheet-based target list (.xlsx or .
    0 installs
47. ▌
    Lc Ms Feature M Z Rt Extraction · holobiomicslab

    Use when you have preprocessed LC-MS intensity data (e.
    0 installs
48. ▌
    Lc Ms Profile Data Segmentation · holobiomicslab

    Use when you have raw profile (not centroided) LC-MS data in .mzML format and need to prepare it for automated peak detection using a trained object detection network.
    0 installs
49. ▌
    Lc Ms Retention Time Adjustment · holobiomicslab

    Use when you have centroided .mzML LC–MS data with multiple sample runs and a preliminary compound target table with theoretical or measured retention times, but you suspect the expected RT values may not align with actual retention windows in your dataset.
    0 installs
50. ▌
    Lcms Feature Table Construction · holobiomicslab

    Use when you have centroided, single-polarity mzML files from DDA LC-MS experiments and need to generate a quantitative feature table with aligned m/z and retention time coordinates, isotopic annotations, and MS2 spectra for downstream statistical or annotation analysis.
    0 installs
51. ▌
    Lda Result Database Persistence · holobiomicslab

    Use when after running gensim LDA on a corpus of MS2 fragmentation features, when you need to store the LDA results (topics, document-topic assignments, term-topic distributions) in a PostgreSQL database so they can be queried and visualized by a Django web application or other downstream consumers.
    0 installs
52. ▌
    Lipid Ontology Category Mapping · holobiomicslab

    Use when you have a list of detected lipids (e.g., from LC-MS/MS lipidomics data) with associated statistical measures (p-values, fold-changes), and you need to test whether specific lipid ontology categories (e.
    0 installs
53. ▌
    Machine Learning Model Training · holobiomicslab

    Use when you have a labeled dataset of DIA raw files (.raw, .d, .wiff) with known quality annotations and have extracted the 15 iDIA-QC metrics (raw file characteristics from timsTOF, TripleTOF, or Orbitrap instruments).
    0 installs
54. ▌
    Mass Action Law Flux Prediction · holobiomicslab

    Use when when you have quantified intracellular metabolite abundances (LC-MS normalized values) from multiple samples and need to predict how differences in substrate availability translate into differences in metabolic flux for specific reactions in a constraint-based metabolic model.
    0 installs
55. ▌
    Mass Spectral Feature Alignment · holobiomicslab

    Use when when you have separate LC-MS peak tables for unlabeled (C12) and labeled (C13) isotope tracer experiments and need to identify which features correspond to the same metabolite across the two labeling conditions.
    0 installs
56. ▌
    Mass Spectrometry Data Querying · holobiomicslab

    Use when you have a directory of mzML mass spectrometry files and need to systematically identify and extract scans or peaks matching specific m/z values, retention time windows, intensity thresholds, or spectral fingerprints (e.g., product ion patterns, neutral loss signatures).
    0 installs
57. ▌
    Mass Spectrometry Scan Indexing · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs. MSn to enable level-specific filtering, (3) retrieve scan ranges or specific scan numbers for targeted spectral extraction, or (4) plan.
    0 installs
58. ▌
    Mass Spectrum Adduct Assignment · holobiomicslab

    Use when when analyzing tandem mass spectra with unknown precursor adduct identity, especially for positive-mode data containing non-protonated adducts ([M+Na]+, [M+K]+, [M+NH4]+).
    0 installs
59. ▌
    Mass Spectrum Database Matching · holobiomicslab

    Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your sample.
    0 installs
60. ▌
    Mass Spectrum Semantic Encoding · holobiomicslab

    Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format) and need to identify structurally related metabolites from a reference database by computing similarity in learned semantic space rather than direct spectral matching.
    0 installs
61. ▌
    Mass2motif Substructure Mapping · holobiomicslab

    Use when you have created a GNPS molecular network (classical or feature-based workflow) and run an MS2LDA experiment on the corresponding MGF spectra, and you want to annotate network nodes with shared Mass2Motifs and chemical class information to interpret the structural basis of network.
    0 installs
62. ▌
    Metabolite Cv Ratio Calculation · holobiomicslab

    Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment. Use it to remove features that are poorly reproducible or show inconsistent signal across samples relative to instrument/technical variation.
    0 installs
63. ▌
    Metabolite Metadata Integration · holobiomicslab

    Use when when you have separate quantification data (abundance matrix), sample metadata (phenotypes, treatment groups, experimental conditions), and spectral data (MS/MS fragmentation patterns or other spectral features) that must be combined for mass spectrometry-based metabolite analysis.
    0 installs
64. ▌
    Metabolite Set Activity Scoring · holobiomicslab

    Use when when you have log2-normalized, standardized peak intensity data (rows=peaks, columns=samples) with compound annotations (peak-to-metabolite mappings via KEGG/ChEBI IDs) and need to collapse individual peak signals into pathway-level summary scores for statistical comparison across.
    0 installs
65. ▌
    Metabolomics Data Preprocessing · holobiomicslab

    Use when you have raw LC/HRMS data files in mzXML, mzML, or netCDF format and need to identify individual and aggregated aligned peaks with their retention time and m/z values before applying spectral deconvolution or chemical annotation. This is the obligatory first step when using IDSL.
    0 installs
66. ▌
    Metabolomics Peak Table Loading · holobiomicslab

    Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with sample metadata for reproducibility filtering, mispicked-ion removal, or group-based feature exclusion.
    0 installs
67. ▌
    Molecular Descriptor Extraction · holobiomicslab

    Use when you have a collection of chemical structures in SMILES format and need to create paired structure–spectrum training data for a generative model, but do not have experimental MS/MS spectra available.
    0 installs
68. ▌
    Molecular Geometry File Parsing · holobiomicslab

    Use when when you have a molecular structure in XYZ or similar coordinate format and need to initialize QCxMS2 or related workflows for EI mass spectrum calculation.
    0 installs
69. ▌
    Ms Annotation Result Validation · holobiomicslab

    Use when after running annotateRC on LC–MS AIF features with fragment libraries (e.
    0 installs
70. ▌
    Ms Modification Site Evaluation · holobiomicslab

    Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the true structure of the unknown compound (oracle mode) or a reference modification site annotation.
    0 installs
71. ▌
    Ms Ms Spectral Library Matching · holobiomicslab

    Use when you have experimental MS/MS spectra from nontargeted metabolomics data and need to assign molecular identities or identify structurally related analogs.
    0 installs
72. ▌
    Ms Spectrum Similarity Grouping · holobiomicslab

    Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to a cluster group for downstream analysis such as peptide identification or spectral library construction.
    0 installs
73. ▌
    Ms2 Peak Detection And Counting · holobiomicslab

    Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when samples were acquired using different LC methods, mass spectrometer technologies, or exhibit poor feature overlap or large.
    0 installs
74. ▌
    Ms2 Spectra Parsing And Loading · holobiomicslab

    Use when when beginning a MEMO analysis workflow with raw or unaligned MS2 spectra files and needing to extract fragmentation data and precursor information before counting MS2 peaks and neutral losses to generate sample fingerprints.
    0 installs
75. ▌
    Ms2 Spectral Feature Extraction · holobiomicslab

    Use when you have LC-MS/MS metabolomics data in MGF format and need to prepare it for Latent Dirichlet Allocation (LDA) topic modeling.
    0 installs
76. ▌
    Ms2 Spectral Similarity Scoring · holobiomicslab

    Use when after temporal intensity profile correlation and exact mass difference refinement have identified candidate ion-species pairs in direct-injection plasma ionization MS data (e.g., DBDI-MS, DBDI-FT-ICR-MS).
    0 installs
77. ▌
    Ms2 Spectrum Feature Extraction · holobiomicslab

    Use when you have DDA (data-dependent acquisition) LC-MS/MS data with MS2 spectra and want to discover metabolic features that may be missed by MS1-only peak picking, or when you need an alternative feature extraction workflow that leverages fragmentation patterns to identify true metabolite.
    0 installs
78. ▌
    Ms2 Spectrum Format Preparation · holobiomicslab

    Use when you have raw or unstructured MS2 spectral data (from untargeted tandem mass spectrometry experiments) and plan to run MS2MP inference for KEGG pathway prediction.
    0 installs
79. ▌
    Ms2lda Motif To Network Mapping · holobiomicslab

    Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered substructural motifs to support structural elucidation and chemical family interpretation.
    0 installs
80. ▌
    Multi Cell Line Rps Calculation · holobiomicslab

    Use when when you have LC-MS normalized intracellular metabolite abundance measurements for multiple cell lines and need to estimate reaction activity driven by substrate availability rather than enzyme expression alone.
    0 installs
81. ▌
    Multi Dimensional Data Encoding · holobiomicslab

    Use when you have loaded LC-MS feature tables or peak detection output containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to detect anomalies such as retention time drift, m/z shifts, or intensity loss that.
    0 installs
82. ▌
    Multi Source Spectrum Retrieval · holobiomicslab

    Use when when you have a Universal Spectrum Identifier (USI) string or collection of USI strings and need to programmatically retrieve the corresponding mass spectrometry spectrum data from one of seven supported repositories (GNPS Molecular Networking, GNPS Spectral Libraries, ProteoXchange.
    0 installs
83. ▌
    Mzml File Parsing And Ingestion · holobiomicslab

    Use when you have raw profile LC-MS data in .mzML format and need to prepare it for targeted or untargeted peak detection.
    0 installs
84. ▌
    Nearest Neighbor Index Querying · holobiomicslab

    Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by precursor m/z).
    0 installs
85. ▌
    Neural Network Encoder Freezing · holobiomicslab

    Use when when you have a pre-trained encoder (e.g., TCN spectrum encoder in FIDDLE) that has learned useful representations on a source task (e.g., MS/MS spectrum encoding), and you want to train lightweight task-specific modules (e.
    0 installs
86. ▌
    Neutral Mass Derivation From Mz · holobiomicslab

    Use when after adduct configuration is complete and before querying formula databases. Use it whenever you have m/z peak lists from mass spectrometry data and need to identify the neutral mass underlying each observed ion, particularly when multiple adduct types are active in the same experiment.
    0 installs
87. ▌
    Nextflow Pipeline Orchestration · holobiomicslab

    Use when when you have raw LC-HRMS metabolomics data in .mzML or .
    0 installs
88. ▌
    Notification Payload Formatting · holobiomicslab

    Use when when a QC check fails during an LC-MS instrument run and you need to alert users in real time.
    0 installs
89. ▌
    Object Detection Model Training · holobiomicslab

    Use when you have annotated LC-MS ROI snippets with ground-truth peak/non-peak labels and boundary coordinates (peak start/end positions), and you need to build a model that can discriminate true peaks from false peaks while precisely localizing peak boundaries for area integration in future LC-MS.
    0 installs
90. ▌
    Object State Mutation Detection · holobiomicslab

    Use when when calling filter functions (e.g., filter_mispicked_ions(), filter_group(), filter_cv()) on R6-based metabolomics data objects in the mpactr package and you need to verify whether the original object's state is preserved.
    0 installs
91. ▌
    Order Agnostic Dispatch Routing · holobiomicslab

    Use when when your untargeted LC-MS pipeline must support multiple peak-picking backends and you need to let users specify which algorithm to use (via configuration file or parameter) without hard-coding algorithm dependencies.
    0 installs
92. ▌
    Peak Quality Metric Computation · holobiomicslab

    Use when you have completed XCMS preprocessing (getEIC() and fillPeaks()) on untargeted LC-MS metabolomics data and need to assign per-peak quality scores prior to manual curation, classifier training, or downstream statistical analysis.
    0 installs
93. ▌
    Peak Table Row Count Comparison · holobiomicslab

    Use when you need to validate the reference-semantics behavior of mpactr filter functions, particularly when using copy_object=FALSE. Use it to confirm that a filtering operation (e.
    0 installs
94. ▌
    Peak Table Row Count Validation · holobiomicslab

    Use when when using mpactr filter functions (e.g., filter_mispicked_ions, filter_group, filter_cv) with R6 reference semantics and uncertain whether the copy_object parameter controls deep copying or in-place modification.
    0 installs
95. ▌
    Peakmap Heatmap Rendering Mz Rt · holobiomicslab

    Use when when you have mass spectrometry data organized in a Pandas DataFrame with m/z values, retention time (RT), and intensity measurements, and you want to visualize the joint distribution and correlation of these three dimensions to identify peaks, assess separation, and detect patterns across.
    0 installs
96. ▌
    Peptide Level Spectrum Grouping · holobiomicslab

    Use when after embedding MS/MS spectra into a 32-dimensional vector space using GLEAMS, when you need to identify and group all spectra originating from the same peptide sequence.
    0 installs
97. ▌
    Per Sample Spectral Aggregation · holobiomicslab

    Use when you have raw MS2 spectra from a sample and need to collapse them into a single sample-level representation for comparison across multiple samples, particularly when samples have poor feature overlap, strong retention time shifts between LC methods, or were acquired on different mass.
    0 installs
98. ▌
    Psm Annotation And Ion Matching · holobiomicslab

    Use when when you have an MS2 scan with observed peak data (m/z, intensity, charge state), a known peptide sequence, and need to determine which observed ions correspond to B and Y fragment ions. Apply this skill particularly when working with natural abundance (1.
    0 installs
99. ▌
    Python R Data Structure Mapping · holobiomicslab

    Use when when you have mass spectrometry data in R's Spectra format but need to leverage Python libraries (matchms, spectrum_utils) for specialized operations like spectral similarity scoring, filtering, or normalization that lack native R implementations or perform better in Python.
    0 installs
100. ▌
     Python Sqlite Migration And Etl · holobiomicslab

     Use when you have MS/MS spectral library data currently stored in multiple file formats (JSON, CSV, or binary) and need to enable fast, filtered queries by metadata (e.g., precursor m/z, retention time, molecular class) without loading entire libraries into memory.
     0 installs