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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Docker Container Execution · holobiomicslab

   Use when you have GNPS-style MGF spectral files as input and need to run Mass2SMILES MS/MS-to-structure inference without installing TensorFlow, CUDA, or Python dependencies locally.
   2 installs
2. ▌
   Dual Branch Feature Fusion · holobiomicslab

   Use when when you have molecular input data available in two or more distinct formats (e.g., RDKit-extracted fingerprints AND torch_geometric Graph objects representing molecular topology) and your prediction target (e.
   0 installs
3. ▌
   Eic File Format Generation · 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
4. ▌
   Email Delivery Integration · 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
5. ▌
   Entropy Similarity Scoring · 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
6. ▌
   Executable Path Resolution · 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
7. ▌
   External Registry Querying · holobiomicslab

   Use when your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations. The platform needs to auto-populate these fields to enable browsing and cross-linking with public genomic databases. Trigger this skill when you have genome IDs (e.
   0 installs
8. ▌
   Feature Annotation Mapping · holobiomicslab

   Use when you have a trained decision tree model on ChemEcho sparse feature vectors and need to convert a specific decision path (root to leaf) into a deployable query.
   0 installs
9. ▌
   Fragment Ion Mass Matching · holobiomicslab

   Use when you have a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
   0 installs
10. ▌
    Gnps Network File Handling · 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
11. ▌
    Gradient Flow Verification · holobiomicslab

    Use when after implementing a composite loss function that combines multiple loss terms (e.g., InfoNCE contrastive loss and MSE reconstruction loss) in a PyTorch module, and before running full-scale training on MS/MS spectra data.
    0 installs
12. ▌
    Graph Attribute Annotation · 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
13. ▌
    Hmdb Metabolite Extraction · holobiomicslab

    Use when you have downloaded raw HMDB data (hmdb_metabolites.zip or pickle file) and need to generate a representative set of chemical objects for simulating LC-MS/MS acquisition strategies.
    1 install
14. ▌
    Interactive Plot Embedding · 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
15. ▌
    Ionization Mode Annotation · holobiomicslab

    Use when when converting MS/MS spectra from .msp format library files (e.g., MassBank) into a custom fragment library for metabolite annotation, and the source spectra are tagged with ionization mode information (positive or negative).
    0 installs
16. ▌
    Large Scale Data Retrieval · holobiomicslab

    Use when you have a query mass spectrum (or a metabolite reference spectrum from public data) and need to search it against a large-scale spectral repository (≥billions of spectra, e.g., GNPS library) where execution time and resource efficiency are critical.
    0 installs
17. ▌
    Lc Ms Spectral Data Import · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for interactive exploration using the specXplore dashboard.
    0 installs
18. ▌
    Lcms Feature Table Parsing · 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.
    2 installs
19. ▌
    Lipid Maps Database Lookup · 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
20. ▌
    Lipid Nomenclature Mapping · holobiomicslab

    Use when you need to generate a comprehensive, non-redundant inventory of lipid species that span a defined lipid class (e.g., phosphatidylcholine, triacylglycerol) and a range of fatty acid compositions (e.g., C14:0 to C22:6).
    0 installs
21. ▌
    Lipid Spectral Data Export · holobiomicslab

    Use when after generating a complete lipid spectral library with adduct-specific fragmentation patterns and retention time metadata, when you need to deploy the library for targeted or data-dependent acquisition on specific mass spectrometry instruments—either Excalibur-controlled orbitrap.
    0 installs
22. ▌
    M Z Based Feature Grouping · 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
23. ▌
    Mass Spectrum Scan Parsing · holobiomicslab

    Use when you have raw mass spectrometry data files from a Thermo instrument (e.
    0 installs
24. ▌
    Masst Output Visualization · 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
25. ▌
    Memomatrix Object Handling · holobiomicslab

    Use when you have generated one or more MemoMatrix objects (MS2 fingerprint matrices from separate sample sets) and need to combine them for cross-cohort alignment, validate structural consistency after merging, or prepare merged matrices for downstream filtering and visualization.
    2 installs
26. ▌
    Model Artifact Persistence · holobiomicslab

    Use when after a deep neural network model has completed training on LC-MS spectral peak classification data and you need to preserve the learned weights and architecture for downstream inference, validation on held-out test sets, or sharing with collaborators.
    0 installs
27. ▌
    Ms2 Spectrum Consolidation · 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
28. ▌
    Mzml Feature Table Parsing · holobiomicslab

    Use when you have raw LCMS data in mzML format and a feature table (CSV) from a peak detection pipeline (e.g., MZmine) and need to prepare these inputs for NeatMS preprocessing, batch creation, or peak classification. This skill is the mandatory entry point for any NeatMS workflow.
    0 installs
29. ▌
    Network File Format Export · 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
30. ▌
    Pathway Annotation Mapping · 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
31. ▌
    Peak Boundary Localization · 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
32. ▌
    Peak Data Integrity Checks · 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
33. ▌
    Precursor Mass Calculation · 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
34. ▌
    Python Library Integration · 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.
    2 installs
35. ▌
    Python Package Integration · 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
36. ▌
    Pytorch Module Development · holobiomicslab

    Use when when constructing a composite loss function for contrastive learning on structured data (e.
    0 installs
37. ▌
    Qc Summary Data Extraction · 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
38. ▌
    Qiime2 Artifact Inspection · holobiomicslab

    Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly produced, before using it as input to downstream analyses.
    0 installs
39. ▌
    Qvalue Threshold Filtering · 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
40. ▌
    Raw File Header Extraction · 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
41. ▌
    Retention Time Mz Indexing · 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
42. ▌
    Sample Membership Tracking · 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. ▌
    Schema Constraint Checking · holobiomicslab

    Use when a user uploads a JSON project file to the platform and you need to verify it matches the required format defined in app/public/schema.json before accepting it into the database.
    0 installs
44. ▌
    Spatial Coordinate Mapping · 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
45. ▌
    Spectra Mgf Format Loading · holobiomicslab

    Use when when you have downloaded a GNPS molecular networking archive (GNPS1 or GNPS2 workflow output) and need to reconstruct spectral records for integration with genomic data (BGCs, antiSMASH results) or for computing molecular family links and spectral similarity scores.
    0 installs
46. ▌
    Spectral Alignment Scoring · holobiomicslab

    Use when you have paired MS/MS spectra (known compound and its structural analog) with assigned precursor m/z, charge, and SMILES; you want to quantify which parts of the molecular structure could have undergone modification by scoring peak alignment quality.
    0 installs
47. ▌
    Spectral Format Conversion · holobiomicslab

    Use when when raw spectral data exists in one mass spectrometry file format but downstream analysis requires a different format; when integrating spectra from multiple sources or instruments that produce heterogeneous file formats;
    0 installs
48. ▌
    Spectral Output Formatting · holobiomicslab

    Use when after generating tandem mass spectrum predictions from a neural model (ICEBERG, SCARF, or baseline), and before attempting retrieval ranking, metric computation, or validation against experimental spectra.
    0 installs
49. ▌
    Spectral Window Extraction · holobiomicslab

    Use when you have loaded multidimensional MS data (from MZA HDF5 files or other formats) and need to examine a specific m/z region—for example, to visualize a known lipid or metabolite mass range, perform peak detection within a narrow window, or reduce computational overhead by working on a subset.
    0 installs
50. ▌
    Spectrum Alignment Scoring · holobiomicslab

    Use when after generating probability predictions for potential modification sites (via ModiFinder.
    0 installs
51. ▌
    Spectrum Metadata Handling · holobiomicslab

    Use when when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries, MassBank, MetaboLights, Metabolomics Workbench, MS2LDA, or ProteoXchange) and need to extract its raw spectral data.
    0 installs
52. ▌
    Spectrum Subset Extraction · holobiomicslab

    Use when after duplicate filtering of MZmine-exported MGF and CSV files, when you have combined spectra from multiple samples in a single MGF and need to segregate them by sample identifier before fragment annotation or adduct assignment.
    2 installs
53. ▌
    Taxonomy Database Querying · holobiomicslab

    Use when a paired omics project record contains a genome identifier (e.g., from GenBank or NCBI) but lacks the corresponding organism scientific name.
    0 installs
54. ▌
    User Interface Integration · holobiomicslab

    Use when when you have a multi-step computational workflow (e.g., peak detection, filtering, manual review) implemented in R and need to expose it to end-users who lack R expertise.
    0 installs
55. ▌
    Bond Connectivity Prediction · holobiomicslab

    Use when you have predicted or partially assembled molecular fragments (as token sequences or substructure embeddings) and need to determine which atoms are bonded to which—that is, when the formula (atom inventory) is known or predicted but the connectivity graph is uncertain.
    0 installs
56. ▌
    Cohort Performance Reporting · holobiomicslab

    Use when you have NMR metabolite measurements from peripheral blood samples (plasma/serum) paired with processing delay metadata (pre-centrifugation and post-centrifugation times) and need to benchmark metabolic parameter stability across delay windows.
    2 installs
57. ▌
    Column Name Variant Matching · holobiomicslab

    Use when when processing mwTab metabolomics data files with variable column naming conventions (e.
    0 installs
58. ▌
    Hybrid Model Fusion Strategy · holobiomicslab

    Use when you have 1H NMR spectral data from complex mixtures and need to identify component compounds, but a single architecture (CNN or Transformer alone) fails to capture both fine local patterns in peak structures and long-range dependencies across the full spectral range.
    0 installs
59. ▌
    Isotopic Impurity Accounting · holobiomicslab

    Use when when analyzing LC-MS data from stable isotope labeling experiments where measured isotopologue abundances are contaminated by naturally occurring isotopes and tracer isotopic impurity, and you have access to unlabeled sample reference measurements to empirically model these confounding.
    0 installs
60. ▌
    Metabolite Database Matching · holobiomicslab

    Use when after peak networks have been identified and clustered from INADEQUATE spectra (typically via the clustering and finding modules), use this skill when you need to assign chemical identities to unknown peak networks by comparing them against reference spectral signatures in a simulated.
    0 installs
61. ▌
    Metabolite Spectral Matching · holobiomicslab

    Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference spectra in GNPS or a local indexed repository.
    0 installs
62. ▌
    Molecular Formula Prediction · holobiomicslab

    Use when you have 1D ¹H or ¹³C NMR spectra from an unknown organic compound and need to predict its molecular formula (e.g., C₆H₁₂O₂). The compound must contain ≤19 heavy (non-hydrogen) atoms. Use this as the first stage of a structure elucidation pipeline before predicting molecular connectivity.
    0 installs
63. ▌
    R Package Function Execution · holobiomicslab

    Use when you have raw Bruker NMR spectral data files (1D 1H format) stored in a directory structure and need to prepare them for automated metabolite identification and quantification in ASICS.
    0 installs
64. ▌
    Repository Cloning And Setup · holobiomicslab

    Use when when you need to deploy a containerized scientific tool (e.g., CloMet) for the first time on a local machine or CI/CD environment, and the project provides a Dockerfile and GitHub repository.
    0 installs
65. ▌
    Spectral Feature Engineering · holobiomicslab

    Use when you have molecular structures (SMILES or graph representations) and need to predict or analyze infrared spectral properties using message passing neural networks.
    0 installs
66. ▌
    Spectral File Format Parsing · holobiomicslab

    Use when you receive raw spectral data files (jcamp, RAW, or mzML) from NMR, IR, or MS instruments and need to extract peak tables, metadata, and spectral parameters before generating visualizations, performing peak annotation, or converting to standardized output formats.
    0 installs
67. ▌
    Stocsy Metabolite Assignment · holobiomicslab

    Use when use STOCSY when you have preprocessed 1H NMR spectral data with an unidentified peak of interest (driver signal at a specific δ ppm value) and need to determine its metabolite identity by finding correlated signals across the spectrum.
    0 installs
68. ▌
    Structured Report Generation · holobiomicslab

    Use when after applying jsonschema validation to a parsed mwTab file against MS or NMR schema definitions, when you have collected validation errors, warnings, and metadata column matching results and need to communicate findings to data curators or submitters in a structured, machine-readable.
    0 installs
69. ▌
    Hic Map Format Validation · holobiomicslab

    Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.
    0 installs
70. ▌
    Juicer CLI Tool Execution · holobiomicslab

    Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating domains, or annotate other structural features without re-running the full alignment and contact matrix construction.
    0 installs
71. ▌
    Macs3 Subcommand Chaining · holobiomicslab

    Use when when you have aligned ChIP-Seq reads (BED or BEDPE format) and a corresponding control sample, and you need explicit control over peak-calling parameters—including fragment-length prediction, local bias windows (d, slocal=1kb, llocal=10kb), background scaling, and score-cutoff.
    0 installs
72. ▌
    Badge Endpoint Retrieval · holobiomicslab

    Use when when you need to verify the current operational status of a software project across multiple dimensions (CI/CD, code quality, test coverage, containerization, archival) and those status indicators are exposed as badge endpoints in the project's README.
    0 installs
73. ▌
    Build Badge Verification · holobiomicslab

    Use when you need to validate that a repository's automated build and publish pipeline is functioning correctly on a release or target branch, particularly when assessing the reliability of release artifacts or the health of a CI/CD workflow.
    0 installs
74. ▌
    Code Repository Analysis · holobiomicslab

    Use when you have a published research article describing a new FT-ICR MS analysis tool and need to verify which analytical and visualization features are actually implemented (not just claimed).
    2 installs
75. ▌
    Interoperability Testing · holobiomicslab

    Use when when a new file format specification exists as a living document (e.
    1 install
76. ▌
    JSON Response Validation · holobiomicslab

    Use when after sending HTTP requests to API endpoints (such as /classify or /model/metadata on an NP-Classifier server) to verify that the response is parseable JSON and contains the expected output fields and metadata before attempting to extract or process the data programmatically.
    0 installs
77. ▌
    Lipid Candidate Matching · holobiomicslab

    Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
    2 installs
78. ▌
    Metabolic Model Curation · holobiomicslab

    Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
    2 installs
79. ▌
    Peak Pairwise Comparison · holobiomicslab

    Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover biochemical transformations without prior knowledge of reaction networks.
    0 installs
80. ▌
    Similarity Matrix Export · holobiomicslab

    Use when after computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular fingerprint-based, or metadata-related assessments), use this skill to persist the resulting similarity matrix to a named output file.
    0 installs
81. ▌
    Smiles String Formatting · holobiomicslab

    Use when you have a set of chemical structures (as SMILES strings or convertible to SMILES) and need to submit them programmatically to the NP Classifier /classify endpoint for batch or automated classification.
    2 installs
82. ▌
    Tabular Data Tag Parsing · holobiomicslab

    Use when you have raw tabular experimental data (CSV or Excel) with column headers annotated using MESSES tag syntax (#<table_name>.id for record identifiers, #.
    0 installs
83. ▌
    API Adapter Layer Design · 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.
    1 install
84. ▌
    Batch Vector Preparation · holobiomicslab

    Use when you have a metabolomics dataset with samples collected across multiple batches (e.g., different MS runs, sample preparation rounds, or instrument configurations) and need to apply batch-aware correction methods such as CordBat.
    0 installs
85. ▌
    CI Workflow Reproduction · holobiomicslab

    Use when you have access to a GitHub repository with a Maven-based CI workflow (e.g., defined in .
    0 installs
86. ▌
    Code Artifact Inspection · holobiomicslab

    Use when use when the workflow requires code_artifact_inspection.
    0 installs
87. ▌
    Dynamic Method Discovery · holobiomicslab

    Use when you need to enumerate all supported metadata conversions in a plugin-based architecture without hard-coding converter names or method signatures.
    0 installs
88. ▌
    Feature Table Subsetting · holobiomicslab

    Use when after loading an MS-DIAL feature table when you need to separate features into two disjoint groups: one meeting a quantitative threshold (e.g., m/z decimal values outside [4, 8], coefficient of variation below a cutoff, or mass defects within acceptable bounds) and one not meeting it.
    0 installs
89. ▌
    Gc CI Ms Data Processing · holobiomicslab

    Use when you have vendor-format GC-CI-MS raw data from a stable isotope labeling experiment, a list of targeted compounds with known monoisotopic m/z, retention time, and molecular formula, and you need to extract per-isotopologue area and intensity values across multiple samples with consistent.
    0 installs
90. ▌
    Header Key Value Mapping · holobiomicslab

    Use when when you have JSON table records (arrays of field-indexed objects) and need to restructure them into dictionaries where specific table columns are mapped to new key names, and you want to control which columns appear in the output and under what names.
    2 installs
91. ▌
    Job Artifact Persistence · holobiomicslab

    Use when when deploying OpenMS workflows in online mode via RQ (Redis Queue) in a Docker container where the Streamlit frontend may restart or rerun without losing track of submitted jobs.
    0 installs
92. ▌
    Lipid Similarity Scoring · holobiomicslab

    Use when you have two or more lipid structures (represented as molecular graphs or parsed lipid names) and need to quantify their structural dissimilarity for dendrogram construction, lipidome clustering, or identification of structurally similar lipids.
    2 installs
93. ▌
    Mass Accuracy Validation · holobiomicslab

    Use when after implementing or modifying an mzML parser module that converts mzML files into MS-DIAL's internal data model, and before integrating the parser into the production analysis pipeline.
    0 installs
94. ▌
    Mass Spectrum Simulation · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution patterns to compare against experimental MS data, validate peak assignments, or generate synthetic spectra for method development.
    0 installs
95. ▌
    Msi Spectral Data Import · holobiomicslab

    Use when use this skill at the start of any MSI analysis workflow when you have raw imzML files or vendor-specific MSI data that need to be loaded into napari-MSI-Explorer for visualization, mean intensity calculation, ROI analysis, or annotation.
    2 installs
96. ▌
    Omics Data Visualization · holobiomicslab

    Use when you have tabular omics data (expression matrices, p-values, fold changes, functional annotations, or clinical outcomes) in CSV format and need to generate publication-ready visualizations that reveal distributional patterns, statistical significance thresholds, group comparisons, or.
    0 installs
97. ▌
    Open Modification Search · holobiomicslab

    Use when your query spectra contain peptides with unknown modifications (e.g., oxidation, phosphorylation, acetylation, or non-enzymatic modifications not specified in the search parameters), and you have a reference spectral library in mzML or mzXML format.
    0 installs
98. ▌
    Pathway Function Mapping · holobiomicslab

    Use when when you have reconstructed metabolic networks for two or more organisms from KEGG and need to compare them both topologically and functionally.
    2 installs
99. ▌
    Peak List Column Mapping · holobiomicslab

    Use when when uploading a new peak list or complex sample data file with delimiter-separated columns to Punc'data, especially when column headers are ambiguous or use non-standard naming conventions.
    0 installs
100. ▌
     Poisson Noise Generation · holobiomicslab

     Use when when preparing augmented variants of ion images (single-channel 2D arrays or multi-channel spectral images) for contrastive learning in mass spectrometry imaging tasks.
     0 installs