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HolobiomicsLab

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1. ▌
   Structured Data Quality Assessment 2 · holobiomicslab

   Use when when you have deposited a collection of JSON project documents in a platform or repository and need to verify that all conform to a published JSON Schema specification before publication, distribution, or integration with downstream systems.
   0 installs
2. ▌
   System Call Invocation Via System2 2 · holobiomicslab

   Use when you need to query or extract data from Thermo Fisher Scientific .raw files or other proprietary binary formats accessible only through a compiled external executable (e.g., RawFileReader .NET assembly). The executable returns text or structured output (e.
   0 installs
3. ▌
   Tandem Mass Spectrum Normalization 2 · holobiomicslab

   Use when preparing tandem MS/MS datasets for cross-dataset similarity analysis or spectral matching, particularly when datasets originate from different instruments, acquisition dates, or sample preparation protocols that may introduce systematic variations in peak intensities.
   0 installs
4. ▌
   Tensor Preprocessing Normalization 2 · holobiomicslab

   Use when when you have raw MS/MS spectral data in the form of intensity arrays indexed by m/z values and need to feed them into the Spec2Mol encoder neural network. Apply this skill before encoder inference to ensure spectral inputs conform to the encoder's expected dimensionality and value ranges.
   0 installs
5. ▌
   Transfer Learning Encoder Freezing 2 · holobiomicslab

   Use when you have a pretrained spectrum encoder (e.g., TCN on mass spectrometry data) that has learned useful representations, and you need to train new components (e.g., a rescoring module) for a related but distinct task (e.
   0 installs
6. ▌
   Transformer Architecture Inference 2 · holobiomicslab

   Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained MultiModalSpectralTransformer checkpoint is available, and you need to predict molecular structures from these spectra without.
   0 installs
7. ▌
   Untargeted Metabolomics Annotation 2 · holobiomicslab

   Use when you have authentic metabolite standards analyzed by LC-MS in both positive and negative ESI modes (converted to .
   0 installs
8. ▌
   Validated Link Enrichment Analysis 2 · holobiomicslab

   Use when when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated links for the same strain(s), and need to assess whether combining or filtering by percentile thresholds improves.
   0 installs
9. ▌
   Generic Hdf5 Library API Usage 2 · holobiomicslab

   Use when when you have converted multidimensional MS data to MZA HDF5 format and need to programmatically read spectra, metadata, and ion mobility or mass-to-charge arrays in Python or R without vendor-specific dependencies.
   0 installs
10. ▌
    Bruker Mass Spectrum Data Import 2 · holobiomicslab

    Use when you have received a Bruker Solarix FT-ICR raw data directory (.d format, containing CompassXtract output or native ser/fid transients) and need to import it into a Python-based analysis workflow for FT-MS signal processing, calibration, or molecular formula search.
    0 installs
11. ▌
    Cpu Gpu Performance Benchmarking 2 · holobiomicslab

    Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate whether GPU acceleration is justified.
    0 installs
12. ▌
    Docker Container Volume Mounting 2 · holobiomicslab

    Use when when you have vendor raw mass spectrometry files on the host machine that need to be processed by a containerized tool (e.g., AirdPro), and the container must read input from and write output to specific host paths. Typical trigger: you have a .
    0 installs
13. ▌
    Mass Error Threshold Calibration 2 · holobiomicslab

    Use when you have isolated TIC peak regions and need to extract ion chromatograms (EICs) for XCMS parameter estimation via the EICparams function. Use it specifically when your mass analyzer's measurement accuracy is known (e.
    0 installs
14. ▌
    Ms Instrument Data Preprocessing 2 · holobiomicslab

    Use when you have raw mass spectrometry data files from a mass spectrometer instrument and need to feed them into a peptide feature detection pipeline (e.g., IsoFusion) that accepts only MS1 format input.
    0 installs
15. ▌
    Peak Quality Threshold Filtering 3 · holobiomicslab

    Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
    0 installs
16. ▌
    Visual Studio Project Management 2 · holobiomicslab

    Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench using .NET Framework 4.7.2, .NET Core 3.1, and .NET 6) and need to set up the build environment in Visual Studio, restore dependencies, select a specific build configuration (e.
    0 installs
17. ▌
    Spot Level Intensity Aggregation 2 · holobiomicslab

    Use when after loading spatial metabolomics data (from CSV, imzML, or merged positive/negative ion modes) into an AnnData object, and before filtering or alignment steps.
    0 installs
18. ▌
    Chemical Match Score Interpretation 2 · holobiomicslab

    Use when when you have query chemicals identified by GC-MS (with Match.Factor values) and need to verify structural similarity against a reference chemical library to confirm compound identity or detect structural analogs (e.g., isomers or homologs).
    0 installs
19. ▌
    Dataset Preprocessing And Filtering 2 · holobiomicslab

    Use when when you have a raw GNPS or other spectral library dataset with inconsistent or incomplete instrument annotations, and you need to verify or reproduce reported dataset split counts (e.g., training/test compound ratios). Apply this skill when an instrument allowlist fix (e.
    0 installs
20. ▌
    De Novo Structure Candidate Ranking 2 · holobiomicslab

    Use when when you have high-resolution LC-MS/MS data for an unknown metabolite or small molecule, have computed or measured the molecular ion mass and fragmentation spectrum, and require de-novo structure generation because the compound is absent from spectral libraries or structure databases.
    0 installs
21. ▌
    Eic Similarity Correlation Analysis 3 · holobiomicslab

    Use when after abundance-correlation-based feature group refinement when you observe that larger feature groups (particularly those with 3+ features in the same m/z–retention-time window) may contain features with different peak shapes or retention-time shifts in their EICs, or when abundance.
    0 installs
22. ▌
    Fixed Architecture Layer Validation 2 · holobiomicslab

    Use when after loading a specXplore session data object file from the hard drive and instantiating a dashboard session layer with it, validate that the architecture layer has initialized without errors and that the interactive dashboard is responsive to user input.
    0 installs
23. ▌
    Formula Ranking Accuracy Evaluation 2 · holobiomicslab

    Use when use this skill after training or fine-tuning a chemical formula transformer model on annotated tandem MS/MS spectra, when you need to measure whether the model's ranked formula candidates match ground truth.
    0 installs
24. ▌
    Hrms Feature Annotation Integration 2 · holobiomicslab

    Use when you have LC- or GC-HRMS data in mzML format and a feature list (CSV/TSL/Excel) from external feature detection software (e.
    0 installs
25. ▌
    Intensity Normalization And Scaling 2 · holobiomicslab

    Use when when working with raw or filtered MsmsSpectrum objects where peak intensities span a wide dynamic range and need to be normalized for downstream spectrum comparison, database matching, or publication-quality visualization.
    0 installs
26. ▌
    Intensity Threshold Noise Filtering 2 · holobiomicslab

    Use when you have loaded a raw or partially processed MsmsSpectrum object and need to reduce spectral noise before annotation, matching, or visualization. Use it especially when spectra contain many weak peaks (e.
    0 installs
27. ▌
    Lc Hrms Data Preprocessing Pipeline 2 · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform peak detection, feature alignment, and metabolite annotation in a reproducible, containerized environment.
    0 installs
28. ▌
    Mass Accuracy Tolerance Calibration 2 · holobiomicslab

    Use when you have experimental fragment m/z values from HRMS/MS instruments (Q-Exactive orbitrap, Q-TOF) in CSV or mzML-derived peaklist format, and need to match them against a library of 500,000+ in-silico fragmented lipid species.
    0 installs
29. ▌
    Mass Spectrometry Fragment Matching 2 · holobiomicslab

    Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table formats) and need to assign lipid identities using untargeted or targeted tandem MS data.
    0 installs
30. ▌
    Mgf Metadata Completion From Smiles 2 · holobiomicslab

    Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL import or polarity-based separation workflows.
    0 installs
31. ▌
    Similarity Threshold Interpretation 2 · holobiomicslab

    Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide which matches are sufficiently confident to include in per-motif annotation output.
    0 installs
32. ▌
    Singularity Container Backend Setup 2 · holobiomicslab

    Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers Singularity for security and portability. You have .mzML or .
    0 installs
33. ▌
    Sparse Distance Matrix Construction 2 · holobiomicslab

    Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on low-dimensional spectrum vectors (via feature hashing), and you need to compute only the relevant pairwise distances between.
    0 installs
34. ▌
    Spectral Match Result Consolidation 2 · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single coherent view.
    0 installs
35. ▌
    Workflow Architecture Documentation 2 · holobiomicslab

    Use when you need to understand how a complex MS/MS spectral search system routes query spectra through multiple parallel processing pipelines with different objectives (e.g., reliable exact matching vs. fast approximate matching).
    0 installs
36. ▌
    Acquisition Method Overlap Analysis 3 · holobiomicslab

    Use when you have acquired the same sample(s) using multiple LC-MS, LC-IMS-MS, or direct infusion methods (e.
    0 installs
37. ▌
    API Response Parsing And Validation 2 · 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
38. ▌
    Bgc Mf Link Scoring Standardisation 2 · 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
39. ▌
    Bgc Spectrum Iokr Score Computation 2 · holobiomicslab

    Use when when you have a collection of microbial genomes with predicted BGCs (via antiSMASH), a set of MS/MS spectra (e.g. from GNPS), and you want to score potential BGC-spectrum associations based on the presence of conserved molecular substructures inferred from the BGC's closest MIBiG homolog.
    0 installs
40. ▌
    Chemical Structure Feature Encoding 2 · 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
41. ▌
    Code Quality Metrics Interpretation 2 · holobiomicslab

    Use when after a GitHub Actions CI workflow has executed static analysis (e.g., via Sonarcloud) and generated a quality report.
    0 installs
42. ▌
    Comparative Omics Report Generation 3 · holobiomicslab

    Use when when you have feature lists (in CSV format) from two or more different MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), different processing software (e.
    0 installs
43. ▌
    Cross Validation Workflow Execution 2 · holobiomicslab

    Use when you have paired microbiome (16S rRNA/metagenomic) and metabolome (LC-MS/MS or similar) count data and need to evaluate how well a predictive model (e.g., neural network, Elastic Net) generalizes across samples.
    0 installs
44. ▌
    Dom Chemodiversity Characterization 2 · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (molecular formulas already assigned to individual mass features) and seek to understand the chemodiversity landscape and transformation relationships within DOM.
    0 installs
45. ▌
    Feasible Flux Distribution Sampling 2 · 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
46. ▌
    Feature Table Consensus Aggregation 3 · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples and need to establish a unified feature catalog in which each row represents a distinct molecular entity observed across one or more samples, with harmonized m/z, drift time, and retention time coordinates.
    0 installs
47. ▌
    Feature Table Export And Formatting 3 · holobiomicslab

    Use when after completing feature detection, alignment, and optional filtering (blank subtraction, QC reproducibility, feature occurrence thresholds) in MZmine2 or Optimus, and you need to prepare the feature table and MS/MS spectra for GNPS-based molecular networking, bioassay integration, or.
    0 installs
48. ▌
    File Path Resolution And Validation 2 · holobiomicslab

    Use when when initializing a SmartPeak session from a sequence file, you need to load and validate the workflow.csv and sequence.csv files that are co-located in the session directory.
    0 installs
49. ▌
    Fractional Abundance Transformation 2 · holobiomicslab

    Use when you have raw LC-MS fractional abundances of isotopologues (FAM) from a stable isotope labeling experiment (e.
    0 installs
50. ▌
    Fragmentation Database Construction 2 · holobiomicslab

    Use when when you have completed ORCA single-point energy calculations on interpolated reaction pathway geometries and need to convert quantum mechanical fragment energies and molecular properties into a structured fragmentation channel database suitable for automated EI mass spectrum simulation.
    0 installs
51. ▌
    Functional Trait Diversity Analysis 2 · 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
52. ▌
    Gpu Accelerated Spectrum Clustering 2 · holobiomicslab

    Use when you have a large collection of tandem mass spectra (≥100k spectra) in MGF format and need to group spectra by similarity (precursor m/z, charge, and fragment ion patterns) for spectral library construction, peptide identification, or quality control.
    0 installs
53. ▌
    Gpu Acceleration Cuda Configuration 2 · holobiomicslab

    Use when when clustering or encoding large MS/MS spectra datasets (>1 million spectra) where CPU-only runtime exceeds practical thresholds (hours to days).
    0 installs
54. ▌
    Growth Yield Computation From Omics 2 · 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
55. ▌
    High Dimensional Signal Enhancement 3 · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry imaging (MSI) data with limited spatial resolution, high noise, or incomplete molecular coverage, and you want to enhance signal fidelity to support multiscale tissue–single-cell mapping or brain biochemical profiling.
    0 installs
56. ▌
    Hmdb Metabolite Query And Retrieval 3 · holobiomicslab

    Use when you have identified one or more proton NMR spectral regions-of-interest (ROIs)—defined by lower and upper chemical-shift bounds in ppm—from complex biological samples (serum, saliva, urine, tissue, CSF) and need to generate a ranked list of plausible metabolite identities.
    0 installs
57. ▌
    Ion Mobility Calibration Validation 3 · holobiomicslab

    Use when when you have positive- or negative-mode ion mobility spectrometry data with tunemix reference standards (known m/z, drift times, and CCS values) and need to verify that the calibration model accurately captures the relationship between drift time, reference m/z, and collision cross.
    0 installs
58. ▌
    Ion Species Confirmation Validation 2 · holobiomicslab

    Use when after you have identified candidate ion-species pairs through pointwise correlation analysis of XIC temporal profiles and exact mass difference refinement, and you have MS2 fragment spectra available for those candidates.
    0 installs
59. ▌
    Library Spectrum Database Searching 2 · holobiomicslab

    Use when you have an unknown electron ionization (EI) mass spectrum and need to identify the compound by comparing it against a reference library (msp file format).
    0 installs
60. ▌
    Lipid Chain Composition Enumeration 2 · holobiomicslab

    Use when constructing a de novo or expanded lipid spectral library that must cover all theoretically possible chain compositions and double-bond positional isomers for one or more lipid classes.
    0 installs
61. ▌
    Mass Spectrometry Outlier Detection 3 · holobiomicslab

    Use when you have multi-sample MS1 data (LC-MS, LC-IMS-MS, or direct infusion across any omics domain) and need to detect samples with abnormal global ion intensity patterns or unusual per-ion metric behavior (intensity distribution, signal-to-noise, retention time stability) that may indicate.
    0 installs
62. ▌
    Mass Spectrum Structure Elucidation 3 · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision-induced dissociation, CID) and a known chemical formula (or narrow set of candidate formulas), and you need to identify the most likely structure(s) by ranking against a large candidate library such as PubChem.
    0 installs
63. ▌
    Metabolic Pathway Database Querying 2 · holobiomicslab

    Use when you have a ranked list of metabolite identifiers (PubChemCIDs, KEGG IDs, or chemical names) from differential abundance or ANOVA testing and need to determine which metabolic pathways are overrepresented or enriched among the most significant features.
    0 installs
64. ▌
    Metabolite Abundance Stratification 2 · 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
65. ▌
    Metabolite Generation Logic Mapping 2 · 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.
    0 installs
66. ▌
    Metabolite Taxonomy Database Lookup 3 · holobiomicslab

    Use when when you have MS/MS-annotated features from a natural extract (via SIRIUS, CANOPUS, or ISDB) and need to compute the Literature Component or Class Component of a priority rank—i.
    0 installs
67. ▌
    Metabolomic Feature Table Filtering 3 · holobiomicslab

    Use when after feature detection (e.g., Asari processing of mzML files to feature tables) but before normalization, batch correction, or annotation.
    0 installs
68. ▌
    Ms2 Spectral Similarity Computation 2 · holobiomicslab

    Use when you have two or more LC-MS/MS datasets (in mzML, mzXML, or MGF format) and need to quantify their overall spectral content similarity—typical scenarios include data quality control, species identification, molecular phylogenetics, or proteome comparison across samples, cell lines, or.
    0 installs
69. ▌
    Multi Criterion Scoring Integration 2 · holobiomicslab

    Use when you have an LC-HRMS feature table (m/z, retention time, isotope ratios, fragmentation patterns) and a suspect compound database with reference properties (m/z, expected RT windows, theoretical isotope ratios, characteristic neutral losses), and you need to rank which features most likely.
    0 installs
70. ▌
    Multi Service Dependency Management 2 · 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.
    2 installs
71. ▌
    Multidimensional Ms Data Conversion 3 · holobiomicslab

    Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments, and you need to: (1) store multidimensional spectra in a vendor-neutral, platform-agnostic format;
    0 installs
72. ▌
    Nextflow Pipeline Configuration Hpc 2 · holobiomicslab

    Use when your analysis target is an HPC environment (e.g., Slurm-managed cluster, university research computing center) where Singularity is available but Docker is restricted or unavailable; your workflow is already packaged in Docker but needs portability to HPC;
    0 installs
73. ▌
    Publication Image Asset Preparation 2 · holobiomicslab

    Use when you have resolved a USI string pointing to a spectrum in a supported repository (GNPS, MassBank, MassIVE, MetaboLights, Metabolomics Workbench, ProteoXchange, or MS2LDA) and need to embed a publication-ready visualization or machine-readable reference that preserves the spectrum's.
    0 installs
74. ▌
    Rank Performance Metric Computation 3 · holobiomicslab

    Use when when you have predictions from one or more metabolite annotation models (MLP baseline, GNN, or ESP ensemble) and need to quantify ranking performance on ESI/LC-MS test spectra.
    0 installs
75. ▌
    Retention Time Alignment Correction 2 · holobiomicslab

    Use when when processing a batch of centroided mzML or mzXML LC-MS raw data files where chromatographic retention times drift between sample acquisitions (common in large-scale metabolomics studies).
    0 installs
76. ▌
    Set Activity Prioritization Ranking 2 · holobiomicslab

    Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
    0 installs
77. ▌
    Spectral Match Score Interpretation 2 · holobiomicslab

    Use when when you have GC-MS output with Match.Factor values or structural similarity scores from categorate() and need to decide which identified compounds are reliable enough to carry forward. Specifically: (1) after running GC-MS and receiving a Match.Factor column;
    0 installs
78. ▌
    Spectral Scan Generation And Export 2 · holobiomicslab

    Use when you have real LC-MS/MS data (mzML) from a complex sample (e.g., beer, metabolomics extract) and need to prototype or validate a new data-dependent acquisition (DDA) strategy—such as Top-N fragmentation—before deploying it on physical instrumentation.
    0 installs
79. ▌
    Spectrum Pair Retrieval And Ranking 2 · holobiomicslab

    Use when you have a test set of annotated MS/MS spectra with known structural similarity (via molecular fingerprints or InChIKey), and you want to assess how well a spectral similarity measure (learned or classical) retrieves structurally related compound pairs across a full range of thresholds.
    0 installs
80. ▌
    Substructure Annotation Integration 3 · holobiomicslab

    Use when you have (1) a GNPS molecular network (classical or feature-based) with cluster/feature identifiers, (2) MS2LDA output containing Mass2Motif assignments with probability and overlap scores for those same clusters/features, and (3) a goal to annotate network nodes with substructural and.
    0 installs
81. ▌
    Targeted Transition List Generation 2 · holobiomicslab

    Use when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow (PRM or MRM) in Skyline.
    0 installs
82. ▌
    Tracer Impurity Correction Modeling 2 · holobiomicslab

    Use when when processing LC-MS data from isotope labeling experiments where the tracer (13C, 2H, 15N, 18O, or 34S) has known isotopic impurity and you observe discrepancies between measured isotopologue abundances (FAM) and expected labeling patterns.
    0 installs
83. ▌
    Workflow Reproducibility Validation 2 · holobiomicslab

    Use when after implementing or deploying a containerized Nextflow workflow that processes LC-HRMS metabolomics .
    0 installs
84. ▌
    Lipid Mass Spectral Matching 2 · holobiomicslab

    Use when you have peak-picked LC-HRMS/MS or direct infusion MS/MS data (m/z, retention time, intensity) from Q-Exactive, Agilent, Bruker, or SCIEX instruments and need to annotate experimental fragment patterns to known lipid structures.
    0 installs
85. ▌
    Lipid Class Stratified Analysis 3 · holobiomicslab

    Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
    0 installs
86. ▌
    Multi Charge State Ccs Handling 2 · holobiomicslab

    Use when your TWIM-MS dataset contains ions with multiple charge states (e.g., +1, +2, +3 for the same molecular species) and you need CCS values that correctly account for the relationship between drift time, m/z, and charge state.
    0 installs
87. ▌
    Histogram Bin Width Configuration 2 · holobiomicslab

    Use when you have uploaded a numeric column (e.g., H/C ratio, O/C ratio, or other derived properties from high-resolution mass spectrometry) and you are generating a histogram in Punc'data's Canvas tab.
    0 installs
88. ▌
    Pathway Rank Stability Assessment 3 · holobiomicslab

    Use when when you have completed a PALS pathway analysis on a clean metabolomics peak intensity matrix and pathway annotation set, and you need to verify that the ranked pathway discoveries are not artifacts of favorable data quality.
    0 installs
89. ▌
    Polarity Based Compound Filtering 2 · holobiomicslab

    Use when you have a multi-polarity compound target list (e.g., a .xlsx file with a polarity or ionization mode column indicating positive or negative ESI mode) and you are about to perform targeted peak detection in a single LC–MS acquisition mode (e.g., positive-ion mode only).
    0 installs
90. ▌
    Spectrum Grouping And Aggregation 2 · holobiomicslab

    Use when you have loaded raw PSM search results from a proteomics search engine (e.g., MaxQuant, MSGFPlus, Sage) and need to prepare them for multi-rank rescoring in MS²Rescore.
    0 installs
91. ▌
    Third Party Processor Integration 2 · holobiomicslab

    Use when when you have raw MS files (e.g., .raw, vendor-specific formats) stored in a centralized repository and need to invoke a third-party proteomics analysis tool—such as a mass spectrometry feature detector or quantification engine—without manually managing file transfers or output.
    0 installs
92. ▌
    Unit Test Design For File Parsing 2 · holobiomicslab

    Use when when implementing or extending file format parsers in a spectral data pipeline, you need unit tests to ensure that format-specific parsers correctly instantiate spectrum objects with expected m/z arrays, intensity arrays, and metadata attributes before releasing to users or integrating.
    0 installs
93. ▌
    Cross Domain Metadata Integration 2 · holobiomicslab

    Use when when you have conducted batch MS/MS searches across one or more domain-specific MASST tools and need to combine their hit scores, metadata annotations, and taxonomic lineages into a single coherent result set for comparative analysis or publication.
    0 installs
94. ▌
    File Format Detection And Routing 2 · holobiomicslab

    Use when when you receive a mass spectrometry imaging dataset in unknown or mixed vendor formats and need to apply format-specific preprocessing before generating ion images.
    0 installs
95. ▌
    Mass Spectrometry Peak Validation 2 · holobiomicslab

    Use when after peak alignment across all spectra in an MSImagingExperiment using peakAlign(), when you need to reduce the feature set to high-confidence peaks by removing spurious or low-frequency detections.
    0 installs
96. ▌
    Msi Array Data Structure Handling 2 · holobiomicslab

    Use when you have imported raw imzML or Analyze 7.5 imaging data and need to represent it as a preprocessed spectral array before applying statistical methods (PCA, clustering, classification).
    0 installs
97. ▌
    Chemical Class Assignment Classyfire 2 · holobiomicslab

    Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes molecules by chemical taxonomy.
    0 installs
98. ▌
    Conditional Routing Logic Extraction 3 · holobiomicslab

    Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing pipelines.
    0 installs
99. ▌
    Cross Assay Feature Linkage Analysis 3 · holobiomicslab

    Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.
    0 installs
100. ▌
     De Novo Mass Spectrum Interpretation 2 · holobiomicslab

     Use when you have MS/MS spectra (centroided m/z and intensity pairs) and corresponding MS1 precursor masses but lack reference spectra or a priori formula information.
     0 installs