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HolobiomicsLab

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1. ▌
   Contact Distance Binning Logarithmic · holobiomicslab

   Use when you have a precomputed expected contact frequency table (TSV format with columns: dist_bp, contact_frequency, n_valid) derived from cooler files and need to compress distance-dependent contact probabilities into log-spaced bins.
   2 installs
2. ▌
   Cosine Similarity Metric Application · holobiomicslab

   Use when you are performing dimensionality reduction on a sparse single-cell count matrix (in CSR format) and need to compute pairwise cell similarities before spectral decomposition.
   2 installs
3. ▌
   Cross Modality Embedding Integration · holobiomicslab

   Use when you have paired scATAC-seq peak matrices and scRNA-seq gene expression matrices from the same cells (multiome data) and need to perform joint clustering, visualization, or correlation analysis across both chromatin accessibility and gene expression in a single coordinate system.
   0 installs
4. ▌
   Dependency Resolution And Validation · holobiomicslab

   Use when before running HiC-Pro or similar multi-stage pipelines on a new system or environment, especially when dependency installation is not automated (e.g., not in a conda environment or container).
   0 installs
5. ▌
   Dna Methylation File Format Handling · holobiomicslab

   Use when you have CpG methylation call files (from Bismark or MethylDackel) and need to load them into R for differential methylation analysis, but anticipate memory constraints or want to avoid loading the entire dataset into memory.
   2 installs
6. ▌
   Methylation Object Merging And Union · holobiomicslab

   Use when you have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level comparative analysis across two or more samples.
   0 installs
7. ▌
   Motif Enrichment Statistical Testing · holobiomicslab

   Use when after identifying a set of differentially accessible peaks (via tl.diff_test or equivalent), when you need to infer which transcription factors may regulate the observed chromatin state changes.
   2 installs
8. ▌
   Peak Calling Pseudo Bulk Aggregation · holobiomicslab

   Use when after clustering single-cell ATAC-seq data (e.g., via Leiden clustering on spectral embeddings), use this skill to identify peaks within each cluster. Triggering conditions: (1) you have sparse, per-cell insertion counts organized in a tile matrix;
   0 installs
9. ▌
   Python Dependency Version Resolution · holobiomicslab

   Use when when setting up a new conda environment for a Python-based bioinformatics pipeline and you need to confirm that all declared dependencies (e.g., pysam >=0.15.4, bx-python >=0.8.8, numpy >=1.18.1, scipy >=1.4.
   0 installs
10. ▌
    Adduct Mass Calculation From Smiles · holobiomicslab

    Use when when you have a metabolite SMILES structure and need to predict which adduct ions will appear in a mass spectrum acquired with a chemical derivatizing matrix.
    0 installs
11. ▌
    API Response Parsing And Validation · holobiomicslab

    Use when after submitting a POST request to the /api/smart3/search endpoint with peak data as a JSON payload, you receive an HTTP response and need to extract classification predictions and confidence scores.
    0 installs
12. ▌
    Bgc Mf Link Scoring Standardisation · holobiomicslab

    Use when you have computed raw strain correlation scores and IOKR scores for the same set of GCF–MF (gene cluster family–molecular feature) pairs, and you want to compare or combine them fairly without one score dominating due to scale differences.
    0 installs
13. ▌
    Biochemical Transformation Matching · holobiomicslab

    Use when you have a filtered FT-ICR MS peak list (m/z values and assigned molecular formulas per sample) and wish to reconstruct biochemical transformation networks ab initio to characterize how microbial or environmental metabolic pathways differ across conditions.
    0 installs
14. ▌
    Byte Level Serialization Validation · holobiomicslab

    Use when when you have implemented a binary file format encoder (such as igzip header construction) and need to verify that the binary output is correct before deploying it to read or write real files.
    0 installs
15. ▌
    Chemical Structure Feature Encoding · holobiomicslab

    Use when when you have a set of molecules with known chemical structures and need to prepare them for classification or prediction tasks.
    0 installs
16. ▌
    Code Quality Metrics Interpretation · holobiomicslab

    Use when after a GitHub Actions CI workflow has executed static analysis (e.g., via Sonarcloud) and generated a quality report.
    2 installs
17. ▌
    Collision Cross Section Calculation · holobiomicslab

    Use when you have raw or processed arrival-time data from a traveling-wave ion mobility mass spectrometry (TWIM-MS) platform and need to convert it into standardized collision cross section (CCS) values for comparative analysis across samples or datasets.
    2 installs
18. ▌
    Cross Reference Publication Linking · holobiomicslab

    Use when when cataloging a suite of related bioinformatics tools or web applications (particularly in domains like metabolomics, microbiology, or systems biology) and you need to establish the authoritative peer-reviewed or preprint publication for each tool, verify publication URLs are live, and.
    0 installs
19. ▌
    Cytoscape Edge Node File Formatting · holobiomicslab

    Use when after computing pairwise mass-difference transformations between FT-ICR MS peaks and matching them to a reference biochemical transformation key, you have putative edge data (source peak, target peak, transformation type, mass error) and node data (peaks with m/z, molecular formula.
    0 installs
20. ▌
    Dataframe Plotting Interface Design · holobiomicslab

    Use when when building a scientific visualization library that must support multiple plotting backends and needs to avoid backend-specific code duplication. Specifically: (1) your domain (e.
    0 installs
21. ▌
    Feasible Flux Distribution Sampling · holobiomicslab

    Use when after integrating transcriptomics-derived (RAS), metabolomics-derived (RPS), and extracellular flux constraints into cell-relative metabolic models, sample the feasible flux region when you need to: (1) visualize and compare the metabolic phenotype distributions across biological samples.
    0 installs
22. ▌
    Functional Trait Diversity Analysis · holobiomicslab

    Use when when you have abundance-normalized FT-ICR MS peak data with assigned molecular formulas and need to distinguish between richness (total number of distinct metabolites) and functional diversity (diversity in metabolic potential).
    0 installs
23. ▌
    Growth Yield Computation From Omics · holobiomicslab

    Use when you have constraint-based metabolic models with integrated transcriptomics (gene expression), intracellular metabolomics (substrate concentrations), and extracellular flux measurements (glucose uptake, lactate production, etc.), and you need to test whether differential expression of.
    0 installs
24. ▌
    Ion Mobility Feature Classification · holobiomicslab

    Use when you have raw or processed TWIM-MS data (arrival time and m/z pairs) from multiple lipid, protein, or metabolite classes and need to classify features by biomolecular type before—or instead of—performing feature identification.
    0 installs
25. ▌
    Java Application Build Verification · holobiomicslab

    Use when when you need to confirm that a Java project's GitHub Actions workflow (e.g., 'dev_build_release.yml') has completed successfully and generated usable build artifacts;
    0 installs
26. ▌
    JSON Data Serialization And Parsing · holobiomicslab

    Use when you have discovered Mass2Motifs via LDA and need to (1) load a pre-computed motifset JSON file (e.g., motifset_optimized.
    2 installs
27. ▌
    Mass Spectrometry Adduct Annotation · holobiomicslab

    Use when you have preprocessed MS/MS spectra with measured precursor m/z values but the ionization adduct type is unknown or ambiguous—particularly in metabolomics workflows where multiple adducts co-occur or in de novo formula annotation without access to curated spectral databases.
    0 installs
28. ▌
    Metabolite Abundance Stratification · holobiomicslab

    Use when you have a peak-abundance matrix from FT-ICR MS (peaks as rows, samples as columns with raw peak intensities) and need to compute abundance-based diversity indices or functional diversity metrics that are sensitive to relative vs. absolute peak heights.
    0 installs
29. ▌
    Metabolite Generation Logic Mapping · holobiomicslab

    Use when when you have access to the MAGMa source code and need to understand or audit how in silico metabolite candidates are enumerated from parent structures.
    1 install
30. ▌
    Motif Database Lookup And Retrieval · holobiomicslab

    Use when after completing the MS2LDA LDA modeling step when you have a JSON-serialized inferred motifset (Mass2Motifs with fragment and neutral-loss patterns) and need to annotate those motifs by comparing them against a curated MotifDB reference database to identify known structural subpatterns.
    0 installs
31. ▌
    Multi Dimensional Feature Alignment · holobiomicslab

    Use when you have two or more feature tables in HDF5 format with detected peaks characterized across multiple dimensions (mz, drift_time, retention_time, intensity) and need to harmonize feature coordinates across samples to account for instrument variation, enabling downstream cross-sample.
    0 installs
32. ▌
    Multi Service Dependency Management · holobiomicslab

    Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed and initialized in a coordinated sequence, with explicit dependency declarations and network communication paths between.
    0 installs
33. ▌
    Mzml To Mzpeak Binary Serialization · holobiomicslab

    Use when you have one or more mzML files (XML-based mass spectrometry data) and need to convert them into mzPeak format for downstream analysis, archival, or integration with tools that consume Parquet-based spectra.
    0 installs
34. ▌
    Natural Product Database Validation · holobiomicslab

    Use when after curating and integrating structure-organism pairs from multiple source databases, and before publishing or using the dataset for computational research. Apply this skill when you have aggregated organism counts binned by structural diversity (e.
    0 installs
35. ▌
    Peak Data Extraction And Formatting · holobiomicslab

    Use when when you have initialized an MsBackend subclass (e.
    1 install
36. ▌
    Poisson Noise Injection For Imaging · holobiomicslab

    Use when augmenting mass spectrometry ion images for contrastive learning, particularly when the model must generalize across different detector conditions or signal-to-noise ratios.
    0 installs
37. ▌
    Reaction Activity Score Computation · holobiomicslab

    Use when you have RNA-seq read count data and a metabolic model with GPR rules, and you need to assess how differential gene expression translates into differential metabolic reaction capacity across multiple biological conditions or cell lines.
    0 installs
38. ▌
    Response Status Code Interpretation · holobiomicslab

    Use when when you need to confirm that a documented web service endpoint is deployed and accessible before using it for analysis, or when troubleshooting tool availability in a bioinformatics pipeline. Apply this skill after obtaining a service URL (e.
    2 installs
39. ▌
    Sinusoidal Embedding Implementation · holobiomicslab

    Use when building a transformer-based neural network for chemical formula ranking or classification from mass spectrometry spectra, and you need to encode categorical chemical formulas (e.
    2 installs
40. ▌
    Spectral Library Parallel Ingestion · holobiomicslab

    Use when you have multiple MSP or spectral library files (e.g., one per batch of analytical standards, or organized in a directory structure) that need to be read and merged into a single library object for downstream enrichment (SMILES assignment, RI annotation, write operations).
    0 installs
41. ▌
    Toml Configuration File Preparation · holobiomicslab

    Use when you have exported lipid identifications from MS-DIAL (version 4 or 5) and need to run LipoCLEAN quality filtering on that output.
    2 installs
42. ▌
    Volume Mount And Persistence Design · holobiomicslab

    Use when you are composing multiple containerized services that have data dependencies—e.g., a web application that launches calculation jobs, a calculation engine that consumes a pre-built lookup database, and a data-processing service that generates that lookup.
    0 installs
43. ▌
    Aligned Feature Matrix Construction · holobiomicslab

    Use when when you have extracted feature tables from multiple breath samples (mzML/mzXML files) using feature extraction, and you need to identify which features are the same across samples to enable downstream statistical or comparative analysis.
    0 installs
44. ▌
    Analyte Degradation Risk Assessment · holobiomicslab

    Use when you have measured metabolites or lipids from biobanked or processed blood samples (EDTA plasma or serum) and know the pre-analytical conditions (time delay before/after centrifugation in hours, processing temperature in °C, sample matrix).
    1 install
45. ▌
    Approximate Nearest Neighbor Search · holobiomicslab

    Use when when you have pre-computed spectrum embeddings (e.g., Word2vec vectors) and need to rapidly retrieve the most similar spectra from a large in-silico or experimental library (thousands to millions of spectra).
    0 installs
46. ▌
    Arrival Time Based Class Assignment · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to label each experimental feature by biomolecular class before feature identification or peak detection steps are complete.
    0 installs
47. ▌
    Asynchronous Workflow Orchestration · holobiomicslab

    Use when when you have a Streamlit-based scientific application (e.g. OpenMS workflows) that must support both online Docker deployments with multiple worker processes and offline local deployments, and you need to prevent long-running analyses from blocking the web UI thread.
    0 installs
48. ▌
    Batch Effect Correction Application · holobiomicslab

    Use when you have a SummarizedExperiment object containing metabolomics assay data (compound areas, internal standard areas) organized by batch and sample type (including pooled SQC samples), and you need to correct systematic variation across batches before calculating Relative Standard Deviation.
    2 installs
49. ▌
    Batch File Processing Orchestration · holobiomicslab

    Use when when you have multiple CDF imaging files (e.g., from mass spectrometry imaging scans of biological samples) that need to be read into a single Matlab workspace with consistent structure and metadata (spectral intensity, m/z arrays, spatial coordinates).
    0 installs
50. ▌
    Bipartite Graph Layout Optimization · holobiomicslab

    Use when after constructing a bipartite network graph with metabolites and proteins as nodes weighted by association strength and disease class, when you need to render the network visually for interpretation and publication.
    0 installs
51. ▌
    Blockwise Data Parsing And Indexing · holobiomicslab

    Use when when you need random access into a large text or XML file that you want to keep compressed, where the file has natural logical divisions (chapters, spectra, records) that can be written independently.
    2 installs
52. ▌
    Breath Volatile Peak Classification · holobiomicslab

    Use when after feature extraction and alignment when you have a numerical feature table (CSV or dataframe) with intensity values across retention time or m/z dimensions, and you need to identify and rank peaks by signal quality and prominence rather than relying on all extracted features equally.
    0 installs
53. ▌
    Candidate Peak Filtering Annotation · holobiomicslab

    Use when you have a peak list extracted from MSI data that includes candidate peaks with potential m/z overlap or spatial co-localization patterns across tissue images.
    0 installs
54. ▌
    Cascade Search Strategy Fdr Control · holobiomicslab

    Use when when searching high-resolution mass spectra against spectral libraries and you need to identify both unmodified and post-translationally modified peptides while maintaining strict control over false positive identifications.
    0 installs
55. ▌
    Ccs Value Assignment From Standards · holobiomicslab

    Use when you have TWIM-MS experimental data with arrival/drift times and m/z values, and you possess calibrant reference standards with known CCS values.
    0 installs
56. ▌
    Chemical Classification Aggregation · holobiomicslab

    Use when you have a collection of standardized molecular structures (SMILES or MOL format) that have been submitted to ClassyFire and you need to collect and organize their classification results into a single CSV or JSON table for downstream analysis, validation, or retention time modeling.
    0 installs
57. ▌
    Chemical Formula Annotation Mapping · holobiomicslab

    Use when you have processed MSI peak data (in rMSIproc format) and need to distinguish matrix-related ions from analyte signals. Specifically: (1) you have a peak matrix with m/z values and spatial intensity maps; (2) you have a reference matrix identity (e.g., 'Ag1' for silver);
    0 installs
58. ▌
    Chromatographic Baseline Estimation · holobiomicslab

    Use when you have extracted ion chromatogram (EIC) candidate data from untargeted LC/HRMS files (mzXML, mzML, or netCDF format) and need to identify genuine peaks within each EIC.
    2 installs
59. ▌
    Chromatographic Peak Classification · holobiomicslab

    Use when you have (1) a benchmark dataset of reference peaks with validated m/z, retention time boundaries, and isotopologue assignments, and (2) NPP output feature tables (unaligned and aligned) from tools like XCMS, MZmine 2, or MS-DIAL that you wish to evaluate.
    0 installs
60. ▌
    Compiled Module Import Verification · holobiomicslab

    Use when after compiling nanobind-based C++ bindings into a Python extension module (e.g., pyOpenMS), or when integrating a newly built native module into a Python environment. Apply this skill to confirm that the generated .so/.pyd/.
    0 installs
61. ▌
    Contrastive Learning Encoder Design · holobiomicslab

    Use when when you have mass spectrometry ion image data and need to learn meaningful low-dimensional representations through self-supervised contrastive learning.
    0 installs
62. ▌
    Cross Instrument Data Harmonization · holobiomicslab

    Use when you have mass spectrometry spectral data from multiple instrument types (e.g., direct infusion MS, ambient ionization MS, laser desorption/ionization MS) and need to perform unified species discrimination or database scoring across all samples regardless of their source instrument.
    0 installs
63. ▌
    Cross Platform Dependency Detection · holobiomicslab

    Use when when developing a standalone scientific application that relies on external binaries or libraries and must run on a specific operating system (e.g., Microsoft Windows 64-bit). Use this skill to verify Gnuplot 5.4.
    0 installs
64. ▌
    Cross Validation Strategy Selection · holobiomicslab

    Use when when preparing to train supervised binary classification models (logistic regression, random forest, XGBoost) on metabolomics datasets in MeTEor, you must first decide between stratified k-fold cross-validation (suitable for larger, balanced cohorts) and leave-one-out cross-validation.
    0 installs
65. ▌
    CSV XLSX File Conversion And Export · holobiomicslab

    Use when when you have validated mass spectrometry transition data (precursor m/z, product m/z, intensity, retention time, and compound identifiers) formatted in one tabular format (CSV or XLSX) and need to convert it to the other format for ingestion into EISA-EXPOSOME or long-term archival.
    0 installs
66. ▌
    Cumulative Distribution Calculation · holobiomicslab

    Use when you have numeric distribution data (e.g., gene expression, abundance, or measurement values) in CSV format and need to compare cumulative empirical distributions either within a single cohort or across multiple sample groups (e.g., control vs. treatment, disease subtype vs. healthy).
    2 installs
67. ▌
    Data Column Recognition And Mapping · holobiomicslab

    Use when when uploading a delimited CSV or similar tabular file to Punc'data containing high-resolution mass spectrometry results, and the column headers are present but their semantic roles (e.
    0 installs
68. ▌
    Data Handoff Pipeline Orchestration · holobiomicslab

    Use when you have raw MS files (with associated metadata: filename, upload path, file format) staged in an uploader repository and need to route them to a proteomics processor for analysis while preserving audit trails and ensuring format compatibility before processing begins.
    2 installs
69. ▌
    Duplicate Spectrum Detection Splash · holobiomicslab

    Use when when processing large collections of mass spectra from multiple Open Mass Spectra Libraries (OMSLs) or databases that may contain redundant spectral records with identical m/z–intensity peak patterns but potentially different metadata annotations.
    0 installs
70. ▌
    Effect Size Calculation Metabolites · holobiomicslab

    Use when after applying statistical tests (e.g., Student's t-test) to identify differentially abundant metabolites between two or more sample groups in a MultiAssayExperiment object.
    0 installs
71. ▌
    Embedding Vector Similarity Ranking · holobiomicslab

    Use when you have a query mass spectrum and need to retrieve the most chemically similar reference spectra from a large experimental or predicted library (thousands to millions of entries).
    0 installs
72. ▌
    Enrichment Statistic Interpretation · holobiomicslab

    Use when after performing two-group or multi-group differential analysis on a lipidomics dataset and obtaining log fold-change (logFC) values for individual lipid molecules, use this skill to determine whether specific lipid classes, chain lengths, or unsaturation patterns are systematically up- or.
    2 installs
73. ▌
    Feature Abundance Table Preparation · holobiomicslab

    Use when you have raw omics data (microbiome OTU/ASV tables, metabolomic or transcriptomic abundance matrices) that needs to be reformatted or validated before correlation analysis.
    0 installs
74. ▌
    Feature Frequency Filtering Imaging · holobiomicslab

    Use when after peak alignment across all spectra in an imaging dataset, use this skill when you have detected many peaks but need to reduce false positives and sparse features.
    1 install
75. ▌
    Feature Relationship Edge Weighting · holobiomicslab

    Use when after structural clusters have been identified by MamsiStructSearch (via isotopologue, adduct, and cross-assay link detection), and you need to construct a NetworkX graph where edges encode the biochemical relationship type and strength between features for downstream curation.
    2 installs
76. ▌
    Feature Table Export And Validation · holobiomicslab

    Use when after executing an MZmine batch processing workflow on raw metabolomics data (mzML/mzXML format), when you need to convert the in-memory feature detection and alignment results into a shareable, schema-compliant tabular format suitable for downstream statistical analysis, figure.
    0 installs
77. ▌
    Feature Table Subsetting And Export · holobiomicslab

    Use when you have a raw metabolite abundance matrix with substantial missing data (NAs or zero-valued entries) and need to remove poorly-measured features before downstream analysis. Apply this skill when the proportion of missing values per metabolite exceeds a predefined threshold (e.
    0 installs
78. ▌
    Gcf Assignment From Distance Matrix · holobiomicslab

    Use when when you have pre-computed BGC feature vectors (from domain architecture or other representations) and need to group them into functionally coherent GCFs for comparative analysis.
    0 installs
79. ▌
    Genotype Phenotype Data Preparation · holobiomicslab

    Use when when you have raw genotype and phenotype data files (e.g., from a GWAS dataset or genetic study) and need to apply PaIRKAT or similar pathway-level association tests.
    0 installs
80. ▌
    Graph Neural Network Implementation · holobiomicslab

    Use when when your input includes molecular structures (SMILES, conformers) and you need to predict a continuous property (e.g., CCS, binding affinity, solubility) that depends on molecular connectivity and spatial relationships.
    0 installs
81. ▌
    Graph Neural Network Model Training · holobiomicslab

    Use when when you have a molecular dataset (e.g., SMRT retention-time pairs) that you want to model as node-and-edge graphs, a PyTorch + PyG architecture already instantiated, and need to perform supervised training with checkpoint persistence and per-epoch metric logging.
    2 installs
82. ▌
    Gui Widget Filtering Implementation · holobiomicslab

    Use when a GUI widget (e.g., isotopes display, compound list, or metabolite selector) should honor user preferences to show only a subset of available items, and the filtering logic must read from application preferences and apply it during widget rendering or refresh cycles.
    0 installs
83. ▌
    Hierarchical Normalisation Strategy · holobiomicslab

    Use when when you have multiple batches of metabolomics data with embedded intra-batch (short) and inter-batch (batch) replicate samples, visible run-order signal drift in individual metabolites within batches, and batch effects visible in PCA or run plots.
    2 installs
84. ▌
    High Performance Metric Computation · holobiomicslab

    Use when you have implemented or are evaluating an algorithmic or system optimization (e.g., MASST+) that claims to reduce execution time, and you need to quantify and statistically validate the speedup against a baseline system (e.g., MASST).
    0 installs
85. ▌
    Igraph Object Creation Manipulation · holobiomicslab

    Use when after computing pairwise correlations across features (10,000+ in high-dimensional omics datasets) and applying correlation thresholding to retain only significant edges, you need to construct an igraph object that preserves edge weights, supports node annotation, and enables module.
    0 installs
86. ▌
    Interactive Plot Backend Evaluation · holobiomicslab

    Use when you have mass spectrometry data (chromatograms, spectra, peak maps, mobilograms) that you want to visualize interactively using pyOpenMS-viz, and you need to select between bokeh and plotly backends based on execution time and feature parity.
    2 installs
87. ▌
    Jupyter Notebook Development Python · holobiomicslab

    Use when when building reproducible Python-based computational workflows that must serve both beginner and expert users; when the analysis requires interactive parameter tuning, file upload capability, or real-time result visualization;
    0 installs
88. ▌
    Jupyter Notebook Workflow Execution · holobiomicslab

    Use when you have a curated training dataset of molecular structures with known CCS values, a target set of ≤10,000 molecules requiring CCS predictions, and need to apply a pre-configured Sklearn-based machine learning model within a reproducible, browser-accessible environment.
    0 installs
89. ▌
    Jvm Heap Memory Tuning Verification · holobiomicslab

    Use when when deploying the ipbhalle/metfragweb Docker container and you need to confirm that custom JVM heap sizes (specified via JAVA_OPTS=-Xmx?g -Xms?g) have taken effect, or when troubleshooting memory-related runtime issues in the running container.
    2 installs
90. ▌
    Label Propagation Network Algorithm · holobiomicslab

    Use when you have a ranked list of seed genes or metabolites (e.g., from metabolomic enrichment analysis with MSEA scores, or exome-derived candidate genes) and you want to propagate their signals across a gene–protein interaction network (e.
    0 installs
91. ▌
    Lipid Database Query And Annotation · holobiomicslab

    Use when you have parsed MRM transition data (m/z values, retention times, transition parameters) from mass spectrometry experiments and need to map each detected transition to a known lipid identity.
    0 installs
92. ▌
    Lipid Nomenclature Pattern Matching · holobiomicslab

    Use when when loading a lipidomics dataset into lipidr and the parsing step generates warnings about unparsed molecules due to unsupported naming patterns.
    0 installs
93. ▌
    M Z Retention Time Feature Matching · holobiomicslab

    Use when after extracting a feature table from XCMS, MS-Dial, or similar tools, when you possess a reference compound database with known m/z, retention time, and metadata, and you need to assign high-confidence (AnnoLevel 1) compound identities.
    0 installs
94. ▌
    Mass Accuracy Tolerance Application · holobiomicslab

    Use when when you have generated in silico annotations (from GNPS ISDB, SIRIUS, or timaR) and need to distinguish true matches from false positives by enforcing a mass accuracy constraint. Apply this skill before computing novelty metrics (e.
    0 installs
95. ▌
    Mass Spectrometry Adduct Assignment · holobiomicslab

    Use when when processing in-silico or experimental MS spectra records from databases with incomplete metadata, specifically when the adduct field is null or absent but the ionmode field (positive/negative polarity) is present.
    0 installs
96. ▌
    Mass Spectrometry Format Conversion · holobiomicslab

    Use when when you have mass spectrometry spectra in one of the six supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to convert them to a different format for compatibility with downstream tools, or when importing raw spectra into matchms for the first time and need to.
    0 installs
97. ▌
    Mass Spectrometry Peak Data Loading · holobiomicslab

    Use when when you have raw or parsed MS spectra data (m/z values, intensity values, and spectral metadata) and need to integrate it into a Spectra object for downstream processing.
    0 installs
98. ▌
    Mass Spectrometry Raw File Handling · holobiomicslab

    Use when you have raw MS data files from Thermo Orbitrap or other vendor instruments that must be uploaded into a centralized platform for automated processing. Use it at the start of a multi-stage omics workflow where data collection, management, processing, and visualization are integrated;
    2 installs
99. ▌
    Mass Spectrometry Tune Data Loading · holobiomicslab

    Use when you have positive- or negative-mode tune reference compound data stored in HDF5 format (e.g., example_tune_pos.h5) and need to extract the tune mass spectrum for CCS calibration. This skill is the entry point before applying deimos.calibration.
    0 installs
100. ▌
     Matplotlib Static Figure Generation · holobiomicslab

     Use when you have mass spectrometry data in a pandas DataFrame with retention time (rt) and intensity columns, and need to produce a static figure for publication, presentation, or archival.
     1 install