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HolobiomicsLab

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1. ▌
   Molecular Network Attribute Enrichment 2 · holobiomicslab

   Use when you have a GNPS mass spectral molecular network (in .graphml or Cytoscape format) and wish to annotate its nodes and edges with chemical class assignments from the GNPS library and/or MS2LDA motif probabilities from an independent LDA experiment.
   0 installs
2. ▌
   Multi Score Complementarity Evaluation 2 · holobiomicslab

   Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine whether they capture complementary information that justifies combining them.
   0 installs
3. ▌
   Peak Filtering And Preprocessing Lc Ms 3 · holobiomicslab

   Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform library matching, molecular networking, or spectral similarity comparison.
   0 installs
4. ▌
   Retention Time Mass Proximity Matching 2 · holobiomicslab

   Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for features that are detected in some samples but fall below the detection threshold in others.
   0 installs
5. ▌
   Sample Type Stratified Feature Masking 2 · holobiomicslab

   Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that fail to show meaningful enrichment in actual study samples relative to blank contamination.
   0 installs
6. ▌
   Spectral Fingerprint Web Service Query 2 · holobiomicslab

   Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural classification (compound class and subclass) with confidence estimates.
   0 installs
7. ▌
   Workflow Pipeline Execution Validation 2 · holobiomicslab

   Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically informed annotation pipeline, or after pipeline execution to verify all outputs were generated correctly.
   0 installs
8. ▌
   Baseline Model Training And Evaluation 2 · holobiomicslab

   Use when when you need to establish comparable performance baselines for a novel spectrum prediction model and require fair comparison across multiple baseline architectures. Trigger this skill when: (1) you have a new spectrum prediction approach (e.g., ICEBERG, SCARF) to benchmark;
   0 installs
9. ▌
   Configuration File Validation Dynaconf 2 · holobiomicslab

   Use when when setting up NPLinker for natural products data mining and you have a TOML configuration file (nplinker.toml) that specifies root_dir, mode (local or podp), and paths to GNPS, AntiSMASH, and MIBiG directories.
   0 installs
10. ▌
    Dimensionality Reduction Visualization 2 · holobiomicslab

    Use when after generating large feasible flux distributions (e.g., 1 million sampled solutions per cell line) from constrained metabolic models, apply t-SNE when you need to assess whether distinct biological samples (e.
    0 installs
11. ▌
    Directory Structure Schema Enforcement 2 · holobiomicslab

    Use when you have raw or partially organized natural products data from multiple sources (GNPS molecular networking, AntiSMASH BGC predictions, BigScape clustering, MIBiG metadata) and need to prepare them for NPLinker integration.
    0 installs
12. ▌
    Drift Time To Ccs Correlation Modeling 3 · holobiomicslab

    Use when you have tunemix or other reference standards with known m/z, drift-time, charge state, and CCS values, and you need to establish a predictive calibration model for your ion-mobility mass spectrometry instrument.
    0 installs
13. ▌
    Dynamic Method Signature Introspection 2 · holobiomicslab

    Use when when building an automated converter discovery and job enumeration system where converter classes are dynamically loaded from package directories and you need to extract and validate their internal conversion method signatures without prior knowledge of which converters will be available.
    0 installs
14. ▌
    Isotopologue Quantification Extraction 2 · holobiomicslab

    Use when you have GC-CI-MS or LC-MS data in mzML format targeting a defined set of compounds with known monoisotopic mass, retention time, and chemical formula, and you need per-isotopologue (M+0, M+1, M+2, etc.) quantification metrics (area, maxo intensity, abundance).
    0 installs
15. ▌
    Mass Spectral Metadata Standardization 3 · holobiomicslab

    Use when you have acquired EI or MS/MS spectral libraries from multiple public sources (NIST, RIKEN, MoNA, SWGDRUG, GNPS) with inconsistent metadata field layouts, missing or misplaced SMILES entries, undocumented retention indices, or mixed polarity modes, and you need to merge them into a single.
    0 installs
16. ▌
    Mass Spectrometry Network Construction 2 · holobiomicslab

    Use when you have deconvolved GC-MS spectra (output from auto-deconvolution) and want to group similar spectra into clusters to discover spectral families, identify co-eluting compounds, or organize unknown metabolites by structural similarity.
    0 installs
17. ▌
    Metabolite Annotation Ensemble Ranking 3 · holobiomicslab

    Use when you have ESI/LC-MS test spectra requiring candidate metabolite ranking, pre-trained MLP (NEIMS) and GNN baseline models are available or can be trained, you seek quantified improvement over single-model average rank performance (baseline MLP shows ~339 average rank), and your evaluation.
    0 installs
18. ▌
    Metabolite Ranking By Annotation Score 2 · holobiomicslab

    Use when when you have generated a set of candidate metabolites for a given experimental MS/MS spectrum and need to determine which candidate is most likely to be the true metabolite.
    0 installs
19. ▌
    Metadata Batch Assignment Verification 2 · holobiomicslab

    Use when after data merging and before applying batch correction algorithms (ComBat, SVA, or normalization techniques) to a merged feature table from non-targeted LC-MS/MS metabolomics data.
    0 installs
20. ▌
    Metadata Extraction From Spectral Data 2 · holobiomicslab

    Use when you have raw mass spectrometry files in one of the supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to parse out metadata fields (e.
    0 installs
21. ▌
    Microbe Metabolite Module Construction 2 · holobiomicslab

    Use when when you have trained multi-layer perceptron neural network models on paired microbiome-metabolome data (from ≥10-fold cross-validation iterations) and need to identify functional modules—groups of microbes and metabolites with co-varying or synergistic relationships—for systems-level.
    0 installs
22. ▌
    Molecular Spectrum Prediction Baseline 2 · holobiomicslab

    Use when you have multiple mass spectrum prediction models to compare and need to establish a level playing field by implementing at least one well-characterized baseline (such as NEIMS) with both FFN and GNN encoder variants.
    0 installs
23. ▌
    Molecular Weight Prediction From Ei Ms 2 · holobiomicslab

    Use when you have EI-MS spectrum data (m/z and intensity pairs) from a sample and need a direct, model-based prediction of molecular weight.
    0 installs
24. ▌
    Ms1 Spectral Annotation Chemical Space 2 · holobiomicslab

    Use when you have (1) a peaklist from untargeted LC/HRMS analysis with m/z and intensity values (typically output from IDSL.IPA or similar peak-picking tools), (2) a need to assign molecular formulas to detected peaks, and (3) only MS1 spectral data available (MS/MS is not required).
    0 installs
25. ▌
    Python Package Dependency Installation 2 · holobiomicslab

    Use when you need to enable optional modules in Pyteomics that depend on external libraries not bundled with the core package—such as h5py and hdf5plugin for mzMLb format access, sqlalchemy for Unimod database queries, or psims for ProForma parsing.
    0 installs
26. ▌
    Pytorch Model Loading And Forward Pass 2 · holobiomicslab

    Use when when you have a pre-trained PyTorch model checkpoint (e.g., a MWFormer transformer) and structured input data (e.g., electron ionization mass spectrum m/z and intensity pairs) that must be converted to tensor format and passed through the model to produce a direct numerical output (e.
    0 installs
27. ▌
    Qc Metric Visualization Across Samples 2 · holobiomicslab

    Use when you have processed LC-MS peak detection output or feature tables containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to visually monitor whether internal standards are within acceptable QC.
    0 installs
28. ▌
    Retention Time Drift Time M Z Querying 3 · holobiomicslab

    Use when you have multidimensional MS data converted to MZA HDF5 format and need to retrieve specific spectra or chromatographic slices defined by one or more of: retention time (in minutes), ion mobility arrival time (in milliseconds for DT/SLIM or Vs/cm² for TimsTOF), or m/z value (as a float or.
    0 installs
29. ▌
    Snakemake Dag Generation And Execution 3 · holobiomicslab

    Use when you have multiple mzML or mzML.gz files from LC-IMS-MS/MS instruments and need to apply DEIMoS feature detection, alignment, and calibration operations in a reproducible, traceable manner.
    0 installs
30. ▌
    Spectra Data Extraction And Subsetting 2 · holobiomicslab

    Use when when you need to extract m/z and intensity peak values from a Spectra object backed by MsBackendMzR or similar on-disk backends; when analyzing subsets of spectra without loading all peaks into memory;
    0 installs
31. ▌
    Spectral Similarity Network Generation 2 · holobiomicslab

    Use when after feature detection and alignment across LC-MS/MS runs (via MZmine2 or Optimus) have produced a feature quantification table and MGF file with MS/MS spectra, and you need to discover molecular relationships and detect unknown compounds through spectral clustering and library matching.
    0 installs
32. ▌
    Spectrum Record Consistency Validation 2 · holobiomicslab

    Use when when you have a mass spectrometry data file (such as mzPeak) that has been read by two or more independent implementations (e.g., Rust, Python/pyarrow, R/arrow) and need to verify that all implementations produce identical spectrum metadata, data types, row counts, and numerical values.
    0 installs
33. ▌
    Unsupervised Pattern Discovery Spectra 3 · holobiomicslab

    Use when when you have preprocessed mass spectral data (normalized peak intensities or binned m/z representations) and need to discover latent spectral patterns to enhance neural network predictors without labeled spectral classes.
    0 installs
34. ▌
    Validated Link Proportional Comparison 2 · holobiomicslab

    Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and IOKR), and you need to determine whether combining scores improves discrimination of true links from false positives.
    0 installs
35. ▌
    Collision Cross Section Prediction 2 · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) and need to predict their collision cross sections for ion mobility mass spectrometry workflows, particularly when generating large-scale searchable CCS databases for compound identification and characterization.
    0 installs
36. ▌
    Saturation Threshold Configuration 2 · holobiomicslab

    Use when when executing peak integration on preprocessed GC-IMS data (after alignment and baseline correction) and you need to decide whether to include or exclude peaks that exhibit saturation artifacts from the RIP signal. Set a threshold (e.g., 0.
    0 installs
37. ▌
    Activity Score Robustness Assessment 3 · holobiomicslab

    Use when after computing PLAGE-derived activity scores for pathways or metabolite sets (Molecular Families, Mass2Motifs) from log2-standardized metabolomics intensity data.
    0 installs
38. ▌
    Apache Arrow Columnar Format Parsing 2 · holobiomicslab

    Use when you have mzPeak files stored as Parquet tables within a ZIP archive and need to load spectrum metadata, chromatogram metadata, signal data (profile or centroid), or peaks into memory for analysis in R, Python, or another Arrow-supported language.
    0 installs
39. ▌
    Custom Mzml Index Pattern Definition 2 · holobiomicslab

    Use when your mzML file contains custom or non-standard spectrum index identifiers that do not follow the default mzML indexing convention, and you need random-access retrieval of spectra by these identifiers.
    0 installs
40. ▌
    Isotopic Peak Intensity Distribution 2 · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their isotopic distribution pattern for MS instrument simulation, peak deconvolution, or validation of observed isotopic envelopes.
    0 installs
41. ▌
    JSON Schema Validation For Dashboard 2 · holobiomicslab

    Use when after running the msfeast_pipeline notebook to generate dashboard_data.json from quantification tables, metadata, and spectral data. Use this skill to verify that the exported JSON contains all required fields and structure before attempting to load the file into msFeaST_Dashboard_bundle.
    0 installs
42. ▌
    Mass Spectrometry Feature Collapsing 2 · holobiomicslab

    Use when after XCMS CentWave feature extraction when your feature table contains redundant entries — multiple features with highly similar m/z and retention time values that represent the same metabolite.
    0 installs
43. ▌
    Nearest Neighbor Candidate Retrieval 2 · holobiomicslab

    Use when when you have a large spectral library (thousands to millions of spectra represented as high-dimensional vectors) and need to search unknown query spectra against it, particularly under open modification search scenarios where all possible mass shifts must be considered.
    0 installs
44. ▌
    Extracellular Flux Constraint Integration 2 · holobiomicslab

    Use when you have constraint-based metabolic models of multiple cell lines, experimental measurements of extracellular metabolite concentrations at two timepoints (e.
    0 installs
45. ▌
    Fold Change Sign Determination Statistics 2 · holobiomicslab

    Use when you have paired measurements (e.g., gene expression counts, protein abundance, or sampled flux distributions) from two cell lines or conditions and need to assign a directional sign to each reaction or gene for downstream concordance analysis.
    0 installs
46. ▌
    Fragment Frequency Threshold Optimization 2 · holobiomicslab

    Use when you have replicate MS/MS spectra with labeled fragment recurrence frequencies and need to select an optimal frequency threshold (beyond the default 0.1) that maximizes spectral quality metrics while minimizing false positive noise.
    0 installs
47. ▌
    Fragment Ion Mass Matching With Tolerance 2 · holobiomicslab

    Use when denoising MS/MS spectra and you have: (1) a precursor ion with measured m/z and known molecular formula (from SMILES or direct formula input), (2) an adduct type ([M+H]+, [M+Na]+, etc.), (3) a list of fragment ions with observed m/z values, and (4) a need to distinguish chemically valid.
    0 installs
48. ▌
    Instrument Platform Compatibility Mapping 2 · holobiomicslab

    Use when when adopting a mass spectrometry data processing tool (e.g., LipidMatch) and needing to verify whether your specific instrument platform (vendor + model) and acquisition mode combination (targeted, ddMS2-topN, AIF, direct infusion, imaging) have been formally validated.
    0 installs
49. ▌
    Ionization Mode Peak Retention Comparison 2 · holobiomicslab

    Use when when you have loaded a raw mass spectrum (e.g. ESI_NEG_SRFA.
    0 installs
50. ▌
    Mass Spectrometry Substructure Assignment 2 · holobiomicslab

    Use when after Mass2Motif discovery via LDA on preprocessed MS/MS spectra, when you have a set of inferred motifs (fragments and neutral losses with LDA probabilities) and need to assign putative substructure identities rather than retain anonymous motif labels.
    0 installs
51. ▌
    Model Uncertainty Quantification Variance 2 · holobiomicslab

    Use when when you have predictions from multiple independently trained models (e.g., ROASMI_1–ROASMI_5) for the same set of compounds in a reversed-phase liquid chromatography system at eluent pH ~2.7, and you need to estimate prediction reliability without ground-truth labels.
    0 installs
52. ▌
    Molecular Structure Generation Evaluation 2 · holobiomicslab

    Use when you have access to pre-trained MSGO model weights (PFAS or lipid variants) and a set of 300+ real mass spectra (LC–QTOF or similar), and need to verify whether the model can generate correct molecular structures for unknown chemicals.
    0 installs
53. ▌
    Multivariate Ordination Analysis Nmds Pca 2 · holobiomicslab

    Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in overall molecular composition across experimental conditions or sample groups.
    0 installs
54. ▌
    Neural Network Model Inference Deployment 2 · holobiomicslab

    Use when you have a pre-trained neural network model (e.g., MSBERT weights in .
    0 installs
55. ▌
    Parallel Computing Workflow Orchestration 2 · holobiomicslab

    Use when when compiling EI or MS/MS spectral libraries from multiple gigabyte-scale sources (e.
    0 installs
56. ▌
    Pareto Front Multi Objective Optimization 2 · holobiomicslab

    Use when you have evaluated a parametric denoising strategy (e.g., frequency-based filtering) at multiple threshold values and computed two or more competing metrics (e.g., signal loss and noise reduction) for each threshold.
    0 installs
57. ▌
    Summary Visualization Artifact Generation 2 · holobiomicslab

    Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and visualize the aggregated match results in a format compatible with metadataMASST web interface or downstream analysis.
    0 installs
58. ▌
    Targeted Metabolomics Feature Elaboration 2 · holobiomicslab

    Use when you have targeted metabolomics data with peak area intensities organized in rows (samples) × columns (compounds), accompanying sample metadata indicating which samples are blanks, calibration curve points, or QC samples with known concentration values, and a compound legend assigning.
    0 installs
59. ▌
    Transformer Encoder Architecture Training 2 · holobiomicslab

    Use when you have paired tandem MS spectra and either (1) molecular fingerprints or structures as labels for supervised fingerprint prediction, or (2) both spectra and unpaired structure/SMILES libraries and want to train embeddings for database-free structure lookup.
    0 installs
60. ▌
    Version Control Feature Branch Management 2 · holobiomicslab

    Use when when you have modifications to propose for a shared codebase (e.g., bug fixes, new features, or documentation updates) and need to integrate them without disrupting the main development branch.
    0 installs
61. ▌
    CSV Delimiter Parsing And Configuration 2 · holobiomicslab

    Use when when uploading a new mass spectrometry data file to Punc'data in CSV or delimited-text format, before attempting to map columns to their semantic roles (m/z value, intensity, formula).
    0 installs
62. ▌
    Molecular Complexity Metric Computation 2 · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the structural diversity, elemental stoichiometry patterns, or complexity landscape of the organic mixture.
    0 installs
63. ▌
    Noise Perturbation Sensitivity Analysis 2 · holobiomicslab

    Use when when comparing pathway analysis methods on metabolomics peak data and you need evidence that one method is more robust than another to the noise and missing peaks that are prevalent in real metabolomics experiments.
    0 installs
64. ▌
    Targeted Peak Detection And Integration 2 · holobiomicslab

    Use when you have centroided LC–MS data in .mzML format, a validated table of target compounds with adjusted expected retention times (RT in minutes), and you need to extract peak areas and quality metrics across all sample runs.
    0 installs
65. ▌
    Deep Learning Model Inference On Test Sets 2 · holobiomicslab

    Use when you have a pretrained deep learning model, a reserved test set with ground-truth annotations, and need to evaluate prediction quality or generate embeddings for downstream analysis. Typical triggers: benchmarking a new model against classical baselines (e.
    0 installs
66. ▌
    Mass Spectrometry Precursor Identification 2 · holobiomicslab

    Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate LC-MS retention time linearity, assess method reproducibility, or establish retention time calibration curves.
    0 installs
67. ▌
    Missing Value Imputation By Data Recursion 2 · holobiomicslab

    Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to features falling below the detection limit in some samples but being present above-threshold in others.
    0 installs
68. ▌
    Retention Time Agnostic Spectral Alignment 2 · holobiomicslab

    Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts between acquisitions, or use of different LC-MS platforms (e.g., Orbitrap vs. Q-ToF).
    0 installs
69. ▌
    Sodium Adduct Detection And Classification 3 · holobiomicslab

    Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in the range of ~20–25 Da (characteristic of Na adducts).
    0 installs
70. ▌
    Spectral Feature Clustering And Comparison 2 · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.
    0 installs
71. ▌
    Annotation Coverage Statistics Computation 2 · holobiomicslab

    Use when you have run MSMetaEnhancer's annotate_spectra() method on a .
    0 installs
72. ▌
    Cnn Transformer Hybrid Architecture Design 3 · holobiomicslab

    Use when when you need to detect and classify peaks in LC-MS regions of interest (ROIs) and simultaneously localize their boundaries for area integration.
    0 installs
73. ▌
    Cross Platform Software Capability Mapping 2 · holobiomicslab

    Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization features are already implemented in competing or complementary tools (e.
    0 installs
74. ▌
    Deep Learning Model Training And Inference 2 · holobiomicslab

    Use when you have paired tandem MS/MS spectra with known molecular fingerprints, chemical formulae, or SMILES annotations, and you want to learn a generalizable model that can predict molecular properties or annotate unknown spectra by ranking candidates.
    0 installs
75. ▌
    Isotopic Signature Clustering And Grouping 3 · holobiomicslab

    Use when you have a feature table (m/z, drift_time, retention_time, intensity) from LC-IMS-MS or similar multi-dimensional MS acquisition and need to (1) link isotopic variants to their monoisotopic parent features, (2) disambiguate true chemical features from noise or instrumental artifacts, or.
    0 installs
76. ▌
    Latent Dirichlet Allocation Model Training 2 · holobiomicslab

    Use when when you have preprocessed MS/MS spectral data (filtered, noise-reduced, with neutral losses extracted) and need to discover recurring fragmentation patterns across a spectral dataset.
    0 installs
77. ▌
    Mass Spectrometry Plot Type Specialization 2 · holobiomicslab

    Use when you have a Pandas DataFrame containing mass spectrometry data (e.
    0 installs
78. ▌
    Metabolic Regulation Classification Scheme 2 · holobiomicslab

    Use when when you have computed Reaction Activity Scores (RAS) from transcriptomics and GPR rules, Reaction Presence Scores (RPS) from RAS normalized flux predictions, and Flux Fold-change Distributions (FFD) from metabolomic data and mass-action constraints across multiple sample pairs, and you.
    0 installs
79. ▌
    Metabolite Prediction Correlation Analysis 2 · holobiomicslab

    Use when after training a neural network or regression model to predict metabolomic profiles from microbiome data.
    0 installs
80. ▌
    Metabolomics Quality Metric Interpretation 2 · holobiomicslab

    Use when after batch correction of metabolomics data using pooled study quality control (SQC) samples and calculation of compound/internal standard ratios, when you need to decide which compounds are reliable for reporting and which internal standard minimizes technical variation (RSDQC) for each.
    0 installs
81. ▌
    Metadata Field Based Sample Stratification 2 · holobiomicslab

    Use when you have a feature table and accompanying CSV metadata that includes a 'Sample Type' field (or equivalent) with entries such as 'BLANK', 'QC', 'STD', or 'Unknown'.
    0 installs
82. ▌
    Multi Modal Spectroscopic Data Integration 2 · holobiomicslab

    Use when you have acquired complementary spectroscopic measurements (NMR, HSQC, COSY, IR) for the same molecular sample and need to combine them for structure elucidation.
    0 installs
83. ▌
    Multidimensional Spectral Array Extraction 3 · holobiomicslab

    Use when you have multidimensional MS data (with LC and/or ion mobility dimensions) converted to MZA HDF5 format and need to retrieve raw spectral intensity and m/z values for specific scans, retention times, drift times, or mass ranges.
    0 installs
84. ▌
    Non Targeted Preprocessing Tool Comparison 2 · holobiomicslab

    Use when you have LC-HRMS mzML data processed by at least one non-targeted pre-processing tool (XCMS, MZmine 2, MZmine 3, MS-DIAL, OpenMS, El-MAVEN, or similar), you have access to curated retention time boundaries and molecular formulas for a set of known target compounds (ideally 30+ molecules.
    0 installs
85. ▌
    Published Metabolic Profile Implementation 3 · holobiomicslab

    Use when you have Nightingale Health 1H-NMR metabolomics measurements for a new cohort and wish to compute one or more established metabolic risk scores (mortality, MetaboAge, cardiovascular event, type-2 diabetes, COVID-19 severity) without recalibration.
    0 installs
86. ▌
    Python Package Installation And Management 2 · holobiomicslab

    Use when when you need to validate that a Python package (or update to it) is accessible to end users through official distribution channels, or when you are preparing a release and need to confirm that installation from PyPI and/or Bioconda does not introduce import failures or missing.
    0 installs
87. ▌
    Sensitivity Threshold Stability Assessment 2 · holobiomicslab

    Use when you have labeled MS/MS spectra from replicate measurements and need to determine a frequency threshold for denoising that balances competing objectives: retaining true fragment signals while removing noise.
    0 installs
88. ▌
    Spectral Library Merging And Deduplication 3 · holobiomicslab

    Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf, NIST binary) and ionization modes (positive/negative MS/MS or EI) that need to be combined into a single.
    0 installs
89. ▌
    Structural Cluster Annotation Metabolomics 2 · holobiomicslab

    Use when after identifying statistically significant LC-MS features (e.g., via MB-VIP with p < 0.01 and permutation testing), when you need to consolidate multiple ionization and isotopic forms of the same metabolite into structural groups for annotation and pathway mapping.
    0 installs
90. ▌
    Vendor Proprietary Format Interoperability 3 · holobiomicslab

    Use when you have mass spectrometry raw data in a proprietary vendor format (Thermo .raw, Agilent .d with or without ion mobility, Bruker ion mobility .d, or mzML) and need to enable reproducible, language-agnostic access to multidimensional spectra (e.
    0 installs
91. ▌
    Ft Icr Spectrum Recalibration Validation 2 · holobiomicslab

    Use when after applying mass calibration functions (LedFord, linear, or quadratic equations) to an FT-ICR transient or magnitude-mode dataset, before running SearchMolecularFormulas. Specifically, validate recalibration when: (1) comparing recalibrated spectra against reference calibration files (e.
    0 installs
92. ▌
    Molecular Formula Parsing And Validation 2 · holobiomicslab

    Use when you have received a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table containing molecular formulas and mass values) and need to convert those formula strings into quantified elemental compositions before computing molecular descriptors, diversity indices, or transformation.
    0 installs
93. ▌
    Cross Database Structural Homology Matching 2 · holobiomicslab

    Use when when you have antiSMASH-predicted BGCs and wish to link them to metabolomic data via structure prediction, but only BGCs with sufficient structural homology to characterized reference clusters will yield reliable predictions.
    0 installs
94. ▌
    Interactive Network Visualization Rendering 2 · holobiomicslab

    Use when after structural clustering (isotopologue grouping, adduct detection, cross-assay linking) and correlation clustering of LC-MS features, when you need to inspect and communicate the topology of structural relationships—particularly when the number of features or link types is too dense for.
    0 installs
95. ▌
    Isotopic Signature Validation And Filtering 3 · holobiomicslab

    Use when after isotope detection has enumerated C13 isotopologue patterns across m/z, drift time, and retention time dimensions, and you need to reduce false positives by retaining only well-populated isotopic signature clusters before annotation or export.
    0 installs
96. ▌
    Metabolite Feature Matching Across Datasets 2 · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature tables (e.
    0 installs
97. ▌
    Metabolite Structure Annotation Integration 3 · holobiomicslab

    Use when you have a set of candidate transformed structures generated by biotransformation rules (e.
    0 installs
98. ▌
    Orbitrap Spectrum Extraction From Raw Files 2 · holobiomicslab

    Use when you have a Thermo Fisher Orbitrap .raw file and need to retrieve a specific scan's spectral data (m/z and intensity arrays), validate instrument parameters (resolving power, AGC injection time), or assess signal-to-noise characteristics of fragment ions for a known precursor peptide (e.
    0 installs
99. ▌
    Repository Cloning And Structure Navigation 2 · holobiomicslab

    Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.
    0 installs
100. ▌
     Spectral Overview Representation Generation 3 · holobiomicslab

     Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D projection suitable for dashboard visualization or high-level pattern discovery without losing similarity structure.
     0 installs