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HolobiomicsLab

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1. ▌
   Container Image Management 2 · holobiomicslab

   Use when your LC-HRMS metabolomics data (.mzML or .abf files) must be processed reproducibly across multiple machines (local workstations, HPCs, cloud) without manual tool installation, or when you need to enforce identical computational environments for peer review and long-term archival.
   0 installs
2. ▌
   Cross Omics Strain Mapping 2 · holobiomicslab

   Use when when you have paired genomics (AntiSMASH BGC annotations) and metabolomics (GNPS spectra and molecular families) data from the same microbial strains and need to identify which biosynthetic pathways produce which observed natural products.
   0 installs
3. ▌
   De Novo Peptide Sequencing 2 · holobiomicslab

   Use when you have annotated MS/MS spectra in MGF format and need to identify peptide sequences that may not exist in reference protein databases—such as in immunopeptidomics, metaproteomics, paleoproteomics, venomics, or monoclonal antibody assembly workflows.
   0 installs
4. ▌
   Dependency Version Parsing 2 · holobiomicslab

   Use when before launching a multi-tool computational workflow (e.g., QCxMS2 mass spectra calculations) that depends on external programs with version-sensitive APIs or features. Apply this skill when: (1) the workflow has explicit minimum version requirements for one or more dependencies;
   0 installs
5. ▌
   Eic File Format Generation 2 · holobiomicslab

   Use when after completing MS2 annotation in the JPA metabolomics workflow, when you have aligned feature data (feature matrix with m/z, retention time, intensity, and sample assignments) and need to extract and export EIC traces for individual features or feature subsets for external validation.
   0 installs
6. ▌
   Email Delivery Integration 2 · holobiomicslab

   Use when when a QC check fails during an active LC-MS run and configured email notification targets exist in the system. Use this skill to ensure that QC failures are communicated to stakeholders immediately, complementing Slack-based alerts for users who prefer or require email notification.
   0 installs
7. ▌
   Entropy Similarity Scoring 2 · holobiomicslab

   Use when you need to quantify the degree of match between two MS/MS spectra—either to validate that a denoised spectrum remains faithful to a reference ground-truth spectrum, or to rank candidate library matches for a query spectrum.
   0 installs
8. ▌
   Executable Path Resolution 2 · holobiomicslab

   Use when when preparing to run QCxMS2 or similar multi-tool orchestration software that depends on five or more external programs with strict version floors.
   0 installs
9. ▌
   Gnps Network File Handling 2 · holobiomicslab

   Use when you have a GNPS molecular network job and need to programmatically load the network structure, merge external annotations (chemical class, MS2LDA substructural motifs), and export a unified annotated network for visualization in Cytoscape or other graph analysis tools.
   0 installs
10. ▌
    Graph Attribute Annotation 2 · holobiomicslab

    Use when after dereplication and cosine similarity clustering have been completed on merged LC-MS/MS data, when you need to construct the final molecular network output with predicted molecules as nodes and their parent ions as a second node class, connected by edges that preserve the fragmentation.
    0 installs
11. ▌
    Graph Tensor Serialization 2 · holobiomicslab

    Use when after constructing feature tensors encoding atom adjacency matrices, bond types, and chemical properties from canonical SMILES—and before feeding graphs into a GNN training loop—to enable reproducible, portable, and memory-efficient storage of graph objects that will be loaded in batches.
    0 installs
12. ▌
    Hdf5 Feature Table Loading 2 · holobiomicslab

    Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for multi-dimensional alignment, CCS calibration, or isotope detection.
    0 installs
13. ▌
    Interactive Plot Embedding 2 · holobiomicslab

    Use when you have resolved USI (Unified Spectrum Identifier) spectrum data from a supported repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, or MS2LDA) and need to create a figure suitable for journal publication or supplementary materials that retains a link to the.
    0 installs
14. ▌
    JSON Directive Application 2 · holobiomicslab

    Use when when you have extracted intermediate JSON conforming to the Experiment Description Specification and need to restructure, filter, sort, or aggregate records (e.
    0 installs
15. ▌
    Lcms Feature Table Parsing 3 · holobiomicslab

    Use when you have raw nontargeted LCMS feature tables from one or more analytical methods in tabular format (with m/z, RT, and intensity columns) that need to be aligned or clustered, or when integrating multiple feature tables into a shared BMXP processing pipeline that requires standardized.
    0 installs
16. ▌
    Lipid Maps Database Lookup 2 · holobiomicslab

    Use when when you have a parsed lipid species table (output from LipidSearch or LIQUID) containing lipid names or identifiers, and you need to annotate each entry with its standardized LIPID MAPS category (e.g., Glycerophospholipids, Sphingolipids) and subcategory (e.
    0 installs
17. ▌
    M Z Based Feature Grouping 2 · holobiomicslab

    Use when after retention-time clustering has grouped features from multiple LC-MS samples, when you need to refine feature assignments by enforcing m/z consistency and eliminate duplicate or near-duplicate features with the same mass but potentially misaligned retention times.
    0 installs
18. ▌
    Mass Spectrum Scan Parsing 2 · holobiomicslab

    Use when you have raw mass spectrometry data files from a Thermo instrument (e.
    0 installs
19. ▌
    Masst Output Visualization 2 · holobiomicslab

    Use when you have completed one or more domain-specific MASST searches (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and have aggregated search outputs (matches.tsv, library.tsv, datasets.
    0 installs
20. ▌
    Module Import Verification 2 · holobiomicslab

    Use when after installing a Python package (especially one with optional dependencies) to confirm that: (1) core modules are accessible and importable;
    0 installs
21. ▌
    Ms2 Spectrum Consolidation 3 · holobiomicslab

    Use when after sample alignment and feature grouping steps in untargeted LC-MS workflows, when you have DDA-mode raw files with both MS1 and MS2 scans and need to link tandem mass spectra to quantified features for annotation and structural characterization.
    0 installs
22. ▌
    Mzpeak Format File Parsing 2 · holobiomicslab

    Use when you have an mzPeak file (uncompressed ZIP archive containing Parquet files) and need to extract and work with spectrum metadata (scan descriptions, precursors, selected ions), spectrum signal data (profile or centroid m/z and intensity arrays), or chromatogram data.
    0 installs
23. ▌
    Network File Format Export 2 · holobiomicslab

    Use when after completing dereplication and cosine similarity clustering in the MolNotator pipeline, when you have finalized molecular network data with molecule–ion relationships and need to visualize, analyze, or share the network in external software.
    0 installs
24. ▌
    Nmr Peak Quality Filtering 2 · holobiomicslab

    Use when you have a CSV or table-formatted input spectral peak list (chemical shifts, intensities, metadata) destined for NMRformer metabolite identification, and you observe or suspect that the list contains noisy peaks or peaks with chemical shifts that do not match known reference standards.
    0 installs
25. ▌
    Nmr Spectrum Normalization 2 · holobiomicslab

    Use when when preparing library compound spectra and observed mixture spectra for mcfNMR analysis, normalize both spectra to cumulative distribution functions (CDFs) scaled by total intensity.
    0 installs
26. ▌
    Nmr Spectrum Preprocessing 2 · holobiomicslab

    Use when you have raw or semi-processed 1D NMR spectra (¹H and/or ¹³C) from routine laboratory instruments and need to feed them into a CNN–transformer architecture for end-to-end structure elucidation.
    0 installs
27. ▌
    Pathway Annotation Mapping 2 · holobiomicslab

    Use when you have a metabolomics dataset with metabolite identifiers in mixed formats (e.g., common names, KEGG accessions, HMDB IDs) and need to assign each metabolite to its canonical pathway(s) before performing pathway-level classification, feature selection, or prognosis modeling.
    0 installs
28. ▌
    Peak Boundary Localization 2 · holobiomicslab

    Use when after you have (1) extracted regions of interest (ROIs) around candidate peaks in LC-MS data and (2) run those ROIs through a trained CNN-Transformer peak detection model that outputs both binary peak classifications and bounding box coordinates.
    0 installs
29. ▌
    Peak Data Integrity Checks 2 · holobiomicslab

    Use when implementing or modifying a writable MsBackend subclass (e.g., MsBackendMemory, MsBackendDataFrame) and need to replace peak data (m/z values, intensity values, or peaksData).
    0 installs
30. ▌
    Peak Similarity Assessment 2 · holobiomicslab

    Use when you have a set of picked peaks from INADEQUATE NMR spectra and need to group them into networks to identify which peaks co-originate from the same metabolite compound.
    0 installs
31. ▌
    Precursor Mass Calculation 2 · holobiomicslab

    Use when when you have a compound's SMILES string or molecular formula and need to determine the expected precursor ion m/z for comparison against observed spectra, particularly before applying formula-based denoising, entropy similarity scoring, or denoising search against reference libraries.
    0 installs
32. ▌
    Python Library Integration 2 · holobiomicslab

    Use when when you have Thermo Fisher RAW mass spectrometry files and need to extract mass-to-charge ratios, intensities, scan metadata, and peak lists within a Python script or notebook for downstream computational analysis, and you require programmatic control over extraction parameters rather.
    0 installs
33. ▌
    Python Package Integration 2 · holobiomicslab

    Use when when you have LC-MS/MS data in MZmine-generated MGF and CSV files (for positive and/or negative ionization modes) and need to apply a sequence of deduplication, annotation, and dereplication steps defined in a MolNotator YAML configuration file to predict actual molecules and build.
    0 installs
34. ▌
    Qc Failure Event Detection 3 · holobiomicslab

    Use when rapid QC-MS is actively monitoring LC-MS data acquisition and a QC check result (e.g., internal standard retention time drift, m/z deviation, or intensity threshold breach) returns a fail status.
    1 install
35. ▌
    Qc Summary Data Extraction 2 · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a feature table, use qc_summary() to extract the pass/fail status of each ion across all applied filters.
    0 installs
36. ▌
    Qvalue Threshold Filtering 2 · holobiomicslab

    Use when after loading search result files (e.g., from DIA-NN or OpenSwath) containing feature identification results with associated Q-value scores, apply this filter when you need to select a subset of high-confidence identifications before generating comparison plots or summary statistics across.
    0 installs
37. ▌
    R S4 Object Accessor Usage 2 · holobiomicslab

    Use when you have constructed or received a SummarizedExperiment object (or similar S4 class) containing MS feature tables, counts matrices, or sample-level metadata, and need to retrieve specific slots (e.
    1 install
38. ▌
    Raw File Header Extraction 2 · holobiomicslab

    Use when beginning an LC-MS data analysis pipeline and you need to rapidly inspect instrument metadata, acquisition parameters, or scan statistics from proprietary Thermo .raw files without the I/O overhead of loading full spectra.
    0 installs
39. ▌
    Retention Time Mz Indexing 2 · holobiomicslab

    Use when when you have parsed .mzML or Thermo .raw LC-MS data and need to support interactive or programmatic queries by retention time (RT) and mass-to-charge ratio (m/z) without re-scanning the entire file.
    0 installs
40. ▌
    Richness Index Computation 2 · holobiomicslab

    Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular species across experimental conditions—for example, to test whether inoculation or environmental perturbation alters the.
    0 installs
41. ▌
    S4 Class Method Inspection 2 · holobiomicslab

    Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on NumericList or similar container objects, rather than inefficient loops or apply functions.
    1 install
42. ▌
    Sample Membership Tracking 3 · holobiomicslab

    Use when when aligning detected features across multiple LC-IMS-MS/MS samples and you need to identify which input samples contributed to each consensus feature cluster, especially to filter out spurious or low-confidence alignments, validate clustering completeness, or perform sample-specific.
    0 installs
43. ▌
    Spatial Coordinate Mapping 2 · holobiomicslab

    Use when after LC-MS feature detection, alignment, quantification, and optional filtering/normalization are complete, and you have intensity values for molecular features that correspond to spatial positions (e.g., tissue coordinates, imaging pixel locations).
    0 installs
44. ▌
    Validation Report Generation 2 · holobiomicslab

    Use when when you have loaded a project JSON document from the Pairing Omics Data Platform and need to identify and document constraint violations (such as whitespace in URL fields) defined in the JSON schema.
    2 installs
45. ▌
    API Adapter Layer Design 2 · holobiomicslab

    Use when when you have multiple mass spectrometry data formats (mzML, mzXML, or others) that must be ingested into a single format-agnostic processing engine (e.g., mspack compression), and you need to avoid replicating the core logic for each format.
    0 installs
46. ▌
    Formula Annotation Ranking 2 · holobiomicslab

    Use when after generating candidate formula/adduct pairs from m/z database matching but before final metabolite annotation. Use it when you have observed isotopic patterns from feature detection (e.
    0 installs
47. ▌
    Jupyter Notebook Execution 3 · holobiomicslab

    Use when when you have three coordinated mass spectrometry data tables (quantification, metadata, spectral) ready for integrated preprocessing and statistical analysis, and you need to generate a standardized JSON artifact for downstream interactive exploration rather than static tabular outputs.
    0 installs
48. ▌
    Lipid Nomenclature Parsing 2 · holobiomicslab

    Use when you have received raw lipid identification output from LipidSearch or LIQUID in CSV or TSV format containing lipid species names or identifiers, and you need to extract their structural components and map them to standardized LIPID MAPS categories before building a quantitative data matrix.
    0 installs
49. ▌
    Metabolite Peak Annotation 2 · holobiomicslab

    Use when after peak detection has identified significant m/z and retention time features in untargeted or targeted mass spectrometry data (as a .raw, .d, or mzXML file).
    0 installs
50. ▌
    Metadata Structure Mapping 2 · holobiomicslab

    Use when you have mzML-format raw data files from mass spectrometry experiments and need to ingest them into MS-DIAL for untargeted metabolomics or lipidomics analysis.
    0 installs
51. ▌
    Mzpeak File Format Parsing 2 · holobiomicslab

    Use when when you have mass spectrometry data stored in mzPeak format (ZIP archive containing Parquet files) and need to read spectrum metadata, chromatogram metadata, and signal data (m/z and intensity arrays) for analysis. Use this skill if your input is an .
    0 installs
52. ▌
    R List Object Manipulation 2 · holobiomicslab

    Use when you have extracted metadata or spectral information from a Thermo Fisher Scientific .
    0 installs
53. ▌
    Spectral Bucket Assignment 2 · holobiomicslab

    Use when you have a collection of mass spectrometry spectral data (m/z and intensity pairs) that must be indexed for fast neighbor retrieval or similarity search, and you need to trade some precision in similarity matching for substantial gains in query speed and memory efficiency across large.
    0 installs
54. ▌
    Isobaric Ion Detection Msi 2 · holobiomicslab

    Use when you have loaded MSI data with an extracted peak list and need to annotate matrix-related signals, particularly when the dataset may contain isobaric ions or peaks with overlapping spatial distributions that could be misclassified during downstream annotation filtering.
    0 installs
55. ▌
    Mean Intensity Aggregation 2 · holobiomicslab

    Use when after importing imzML or vendor-specific MSI data into napari and visualizing the raw spectral dataset.
    0 installs
56. ▌
    Blank Contamination Filtering 2 · holobiomicslab

    Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.
    0 installs
57. ▌
    Chemical Metadata Integration 2 · holobiomicslab

    Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared structural features or chemical families across spectral clusters.
    0 installs
58. ▌
    Coeluting Compound Resolution 3 · holobiomicslab

    Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw chromatogram.
    0 installs
59. ▌
    Feature Hashing Vectorization 2 · holobiomicslab

    Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
    0 installs
60. ▌
    Formula Sampler Configuration 2 · holobiomicslab

    Use when you need to generate a set of candidate chemical formulas for LC-MS/MS simulation—specifically when you want to populate a virtual mass spectrometer with realistic chemical structures drawn from a reference database (HMDB) or a uniform m/z distribution, and you need to apply m/z filtering.
    0 installs
61. ▌
    Gc Ms Chromatogram Processing 3 · holobiomicslab

    Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against reference libraries such as PNNLMetV20191015.MSL.
    0 installs
62. ▌
    Large Scale Spectral Matching 2 · holobiomicslab

    Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all-pairs or many-to-many spectrum similarity to identify related compounds, build spectral libraries, or perform large-scale library searching.
    0 installs
63. ▌
    Mass Spectral Data Validation 3 · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
    0 installs
64. ▌
    Mass Spectral Peak Annotation 2 · holobiomicslab

    Use when you have centroided MS2 spectra (in mzML format from data-dependent acquisition) and a list of known or suspect PFAS diagnostic fragment masses, and you need to systematically flag which detected features contain fragments characteristic of PFAS compounds (e.
    0 installs
65. ▌
    Molecular Fingerprint Parsing 2 · holobiomicslab

    Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract the predicted molecular fingerprint representation and associated scoring metrics for compound identification or CANOPUS.
    0 installs
66. ▌
    Mzml Metabolomics Data Import 2 · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in mzML or ABF format that needs to be processed through a reproducible pipeline. Use this skill when: (1) you have public or proprietary .mzML LC-MS datasets (e.g. from MetaboLights, MassIVE, or PRIDE);
    0 installs
67. ▌
    Polarity Aware Data Filtering 2 · holobiomicslab

    Use when when performing targeted peak detection on LC-MS data where compounds have been assigned expected ionization polarities (positive or negative mode) in the target list, and you want to prevent false peak assignments from the opposite polarity and avoid manual pre-filtering of raw data by.
    0 installs
68. ▌
    Retention Time Mass Alignment 2 · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to identify which features in one dataset correspond to features in the other.
    0 installs
69. ▌
    Spectrum Vector Serialization 2 · holobiomicslab

    Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
    0 installs
70. ▌
    Tandem Ms Data Reorganization 3 · holobiomicslab

    Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment fields rather than in dedicated SMILES/InChIKey fields, or when positive and negative ionization mode spectra are commingled.
    0 installs
71. ▌
    Train Test Split Verification 2 · holobiomicslab

    Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to confirm that the change produces the documented training/test split counts.
    0 installs
72. ▌
    Adduct Mass Shift Calculation 2 · holobiomicslab

    Use when when you have a list of observed m/z values from LC/MS feature detection and need to identify candidate metabolites by testing whether those m/z values correspond to known database compounds in specific ionization forms.
    0 installs
73. ▌
    Anchor Feature Pair Selection 2 · holobiomicslab

    Use when after completing feature m/z grouping and pairwise alignment detection on two LC-MS datasets acquired under non-identical conditions.
    0 installs
74. ▌
    API Request Response Handling 2 · holobiomicslab

    Use when you have nuclear magnetic resonance (NMR) peak data (proton 1H and carbon-13 13C measurements) that you need to classify using a deployed deep learning model, and you have access to a TensorFlow Serving instance running the SMART 3 classification model.
    0 installs
75. ▌
    Array Of Objects Construction 2 · holobiomicslab

    Use when you have tabular experimental data (e.g., sample metadata, mass spectrometry parameters, NMR acquisition details) in JSON table format and need to produce a list of structured objects for submission to a data repository (e.g., Metabolomics Workbench) or downstream format conversion.
    0 installs
76. ▌
    Baseline Comparative Analysis 2 · holobiomicslab

    Use when your research proposes a new spectral embedding, matching algorithm, or retrieval method and you need to quantify its improvement over known baselines. Specifically, when you have a test dataset (e.
    0 installs
77. ▌
    Bioactivity Score Aggregation 2 · holobiomicslab

    Use when when you have both (1) a molecular network graph from GNPS with aligned MS/MS features (nodes and edges) and (2) a bioassay-guided fractionation activity matrix (fractions × bioactivity measurements), and you need to determine which molecular features are responsible for observed.
    0 installs
78. ▌
    Bioconda Package Installation 2 · holobiomicslab

    Use when you have identified a package available in the Bioconda channel (indicated by a conda version badge or Bioconda recipe URL) and need to verify that installation succeeds and that the package's critical modules are importable in the target Python environment, especially before integrating.
    0 installs
79. ▌
    Bleu Score Metric Computation 2 · holobiomicslab

    Use when you have a trained sequence-to-sequence model (such as GCMSFormer) that predicts mass spectra from overlapped peaks, and you need to evaluate model performance on a held-out test set.
    0 installs
80. ▌
    Ce Ms Data Import And Parsing 2 · holobiomicslab

    Use when you have raw CE-MS instrument output in mzML or netCDF format and need to extract specific ion traces (by m/z value), filter by effective mobility windows, or apply transformations to migration time data.
    0 installs
81. ▌
    Chemical Formula Tokenization 2 · holobiomicslab

    Use when you have collections of chemical formulae (e.g., from SIRIUS decomposition or subformula labeling) derived from MS/MS spectra and need to feed them into a transformer encoder.
    0 installs
82. ▌
    Chromatogram Artifact Removal 2 · holobiomicslab

    Use when raw NetCDF-format GCxGC-MS chromatograms exhibit steady or increasing baseline intensity caused by instrumental contamination, column bleeding, or thermal drift;
    0 installs
83. ▌
    Clustering Tool Orchestration 2 · holobiomicslab

    Use when you have raw tandem MS metabolomics data (in mzML or MGF format) and wish to compare the clustering performance of two or more MS clustering tools on the same dataset.
    0 installs
84. ▌
    Conditional Record Resolution 2 · holobiomicslab

    Use when converting JSON metadata and you need to populate a target field by selecting or iterating over records only when they satisfy a logical test condition (e.g., 'include this record only if a specific field has a particular value').
    0 installs
85. ▌
    Configuration File Generation 2 · holobiomicslab

    Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5 and need version-specific parameter defaults (e.g., column names and scaling factors that differ between versions).
    0 installs
86. ▌
    Consensus Taxonomy Generation 2 · holobiomicslab

    Use when when you have structural annotations from multiple sources (in silico predictions via SIRIUS/CANOPUS and GNPS spectral library matches) for the same molecular features and need a single authoritative taxonomy assignment.
    0 installs
87. ▌
    Corpus Preparation Validation 2 · holobiomicslab

    Use when when you have raw LC-MS-MS fragmentation spectra in MGF format and need to convert them into a corpus JSON file before running topic modeling.
    0 installs
88. ▌
    Covariance Matrix Computation 2 · holobiomicslab

    Use when after normalization (Step 7) is complete and you have a clean feature matrix ready for multivariate statistical analysis.
    0 installs
89. ▌
    Cross Sample Feature Matching 3 · holobiomicslab

    Use when you have detected feature tables from two or more LC-IMS-MS/MS samples and need to establish correspondence between features across samples to enable quantitative comparison, statistical analysis, or consensus feature calling.
    0 installs
90. ▌
    Dependency Version Management 2 · holobiomicslab

    Use when when you need to document or reproduce a Python-based research application (or any package-dependent workflow) and discover that the original publication or repository specifies dependencies without versions, or when you want to verify that a documented set of pinned versions can be.
    0 installs
91. ▌
    Development Environment Setup 2 · holobiomicslab

    Use when when you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution. Specifically when the package declares dev dependencies in setup.py or pyproject.toml and maintains a pytest test suite in a tests/ directory.
    0 installs
92. ▌
    Feature Gap Filling Recursion 2 · holobiomicslab

    Use when after sample alignment has established consensus m/z and retention time coordinates, and after grouping of isotopologues and adducts is complete.
    0 installs
93. ▌
    Feature Table Filtering Logic 2 · holobiomicslab

    Use when when you have a quantitative feature table (peak intensities across samples) and need to isolate molecular features that show differential abundance between defined sample groups within a specified fold-change range.
    0 installs
94. ▌
    Feature Table Matrix Assembly 2 · holobiomicslab

    Use when when you need to generate a realistic LC/GC-MS feature table (peak intensity matrix) with controlled, quantifiable condition effects (e.g., differential metabolite abundance across disease states) and batch effects (e.g., instrument drift, sample processing day).
    0 installs
95. ▌
    Feature Table Quality Control 2 · holobiomicslab

    Use when when you have a feature intensity matrix (samples × compounds) from untargeted LC–MS/MS or GC–MS analysis and accompanying sample-type metadata (blank, curve, QC, unknown classifications), and you need to remove features with high measurement variability, low QC detection rates, high blank.
    0 installs
96. ▌
    Feature Table Standardization 2 · holobiomicslab

    Use when you have feature tables from external metabolomics software (MS-DIAL, XCMS, vendor tools) in CSV format and need to integrate them into JPA for cross-sample alignment and metabolite annotation.
    0 installs
97. ▌
    Fixed Size Integration Method 3 · holobiomicslab

    Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.
    0 installs
98. ▌
    Fragment Ion Library Matching 2 · holobiomicslab

    Use when you have peak-picked experimental MS/MS data (m/z, retention time, intensity) from UHPLC-HRMS/MS instruments (Orbitrap or Q-TOF from Agilent, Bruker, SCIEX, or similar vendors) and need to annotate detected features with specific lipid identifications using in-silico fragmentation.
    0 installs
99. ▌
    Gc Ms Abundance Preprocessing 2 · holobiomicslab

    Use when after autoQ has extracted isotopologue peak area measurements from mz(X)ML files and you need to prepare the integrations data frame for visualization with metBarPlot or comparative analysis.
    0 installs
100. ▌
     Gcims Dataset Object Creation 3 · holobiomicslab

     Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS preprocessing pipeline.
     0 installs