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HolobiomicsLab

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1. ▌
   Per Read Mapping Agreement Assessment · holobiomicslab

   Use when comparing mapping outputs from two different salmon versions or implementations (e.g., C++ 1.12.0 vs. Rust 2.0) to determine if observed differences in total mapped read counts are due to true algorithmic bugs, parameter defaults, or index format changes.
   0 installs
2. ▌
   Rna Seq Read Mapping Parameter Tuning · holobiomicslab

   Use when when comparing two implementations of the same RNA-seq mapping algorithm on identical reference indices and read sets, if per-read mapping agreement is <99.8% or the overall mapping rate differs by >0.
   2 installs
3. ▌
   Transcript Quantification Integration · holobiomicslab

   Use when you have transcript quantification output (TPM or raw counts) from a pseudo-aligner (Salmon or kallisto) and an ioe/ioi event definition file from SUPPA2's generateEvents step, and you need to calculate PSI values—the relative inclusion level of alternative splicing events—across multiple.
   0 installs
4. ▌
   Mass Spectrometry File Inventory Management · holobiomicslab

   Use when you have uploaded MS/MS data to MassIVE with validated sample-information metadata and need to subset public files by sample attributes (organism, tissue type, extraction method, ionization source, pre-MS separation) to create reproducible, manageable cohorts for molecular networking.
   0 installs
5. ▌
   Ondiskmsnexp Object Manipulation And Export · holobiomicslab

   Use when you have raw CE-MS data and need to (1) transform migration time values to effective mobility using two calibration markers (e.
   2 installs
6. ▌
   Reaction Pathway Assignment And Propagation · holobiomicslab

   Use when you have detected and clustered unknown MS features from untargeted xenobiotic metabolomics data, computed fragmentation pattern similarity scores between features and reference spectra, and now need to systematically assign individual features to specific biotransformation reactions (e.
   0 installs
7. ▌
   Recursive Propagation Algorithm Development · holobiomicslab

   Use when when you have constructed a two-layer metabolite annotation network (knowledge-driven and data-driven) and need to propagate initial seed annotations (e.
   0 installs
8. ▌
   Xenobiotic Metabolite Annotation From Ms Ms · holobiomicslab

   Use when you have aligned MS/MS feature tables (e.g., from MSDial ver. 4.80) representing unknown metabolites suspected to be Phase I/II transformation products of xenobiotics, and you need to assign both chemical identity and biotransformation pathway context to each feature.
   0 installs
9. ▌
   Baseline Method Comparison And Benchmarking · holobiomicslab

   Use when you have developed or adapted an analytical method (e.g., NPFimg for GC–MS marker identification) and need to demonstrate its reliability or improved performance over a widely-used reference method (e.g., XCMS). Apply this skill when you have access to both the same raw input data (e.
   0 installs
10. ▌
    Chemical Metadata Retrieval And Aggregation · holobiomicslab

    Use when after raw GC-MS CSV input has been parsed into separate matrices (Component.RT, Base.Peak.MZ, Compound.Name, Match.Factor, Component.Area) and you need to enrich sample-level identifications with authoritative chemical properties.
    0 installs
11. ▌
    Chemical Type Classification And Annotation · holobiomicslab

    Use when after identifying query chemicals from GC-MS data (via Match.
    0 installs
12. ▌
    Data Structure Design For Spectral Searches · holobiomicslab

    Use when you have raw GC-MS output in CSV format with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.
    2 installs
13. ▌
    Mass Spectrometry Column Polarity Filtering · holobiomicslab

    Use when you have a combined EI library (from multiple sources such as NIST, RIKEN, MoNA) and access to NIST RI database files (ri.dat and USER.
    0 installs
14. ▌
    Mass Spectrometry Scoring Method Validation · holobiomicslab

    Use when you have high-resolution LC-MS data processed through both XCMS feature detection and RAMClustR clustering, and you need to verify the reliability of molecular weight assignments before downstream annotation or statistical analysis.
    0 installs
15. ▌
    Metadata Field Extraction And Restructuring · holobiomicslab

    Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g., Comment field) rather than in the dedicated SMILES field expected by mspcompiler's downstream processing steps.
    1 install
16. ▌
    Spectral Peak Word Embedding Representation · holobiomicslab

    Use when when you have MS/MS spectra (LC-MS or equivalent positive ionization mode data) that you intend to embed using Word2Vec or similar distributional semantic models, or when you need to prepare spectral data for training similarity models that learn peak co-occurrence patterns rather than.
    0 installs
17. ▌
    Adduct Form Prediction And Mass Calculation · holobiomicslab

    Use when you have a characterized lipid species (with defined class and fatty acid composition) and need to predict which adduct forms will ionize under your experimental ionization mode (positive or negative ESI), and you require accurate precursor m/z values for DDA method configuration or.
    0 installs
18. ▌
    Adduct Formation Prediction For Metabolites · holobiomicslab

    Use when when you have unidentified LC/MS features (m/z, retention time, intensity) and need to disambiguate which metabolites they represent by accounting for the fact that observed m/z values may correspond to different adduct forms (e.
    3 installs
19. ▌
    Annotation Benchmark Performance Evaluation · holobiomicslab

    Use when after running an end-to-end annotation workflow (matching, clustering, filtering, and prioritization) on untargeted LC-MS peak tables, when you have access to a curated reference dataset (df.Ref) containing validated peak assignments for the same biological sample.
    0 installs
20. ▌
    Batch Effect Assessment Via Quality Metrics · holobiomicslab

    Use when when you have processed metabolomics LC-MS/MS data organized by batch and sample type (including pooled QC replicates), and you need to quantify whether batch-to-batch and matrix effects are acceptable for downstream reporting.
    2 installs
21. ▌
    Box Cox Transformation Parameter Estimation · holobiomicslab

    Use when you have raw LC-MS feature-intensity tables (rows: samples, columns: metabolite features, values: raw intensities) with non-normal, skewed distributions and need to normalize them prior to statistical analysis.
    0 installs
22. ▌
    Calibration Coefficient Accuracy Assessment · holobiomicslab

    Use when after applying deimos.calibration.tunemix() to positive-mode or negative-mode tune mix reference data (containing known CCS values across m/z range 118–1522), assess whether the single-field calibration model's r-squared coefficient meets the expected precision (typically ≥0.
    2 installs
23. ▌
    Chromatogram Plot Generation Retention Time · holobiomicslab

    Use when you have mass spectrometry data loaded as a Pandas DataFrame with retention time and intensity columns, and you need to visualize the overall or mass-trace-specific signal intensity distribution across the chromatographic separation.
    2 installs
24. ▌
    Chromatographic Peak Detection And Grouping · holobiomicslab

    Use when when you have processed LC-MS data through XCMS alignment but suspect misaligned features due to retention-time drift over long acquisition periods (>1 week) or large sample batches (hundreds of samples), or when peak-filling produces unexpectedly high coefficient-of-variation (CV > 0.
    0 installs
25. ▌
    Classification Model Performance Evaluation · holobiomicslab

    Use when after fitting and optimizing a MB-PLS model on training data, apply this skill to the held-out test set (typically 10% of the original sample) to obtain unbiased performance estimates.
    0 installs
26. ▌
    Confidence Score Thresholding In Proteomics · holobiomicslab

    Use when when loading search results from Data-Independent Acquisition (DIA) mass spectrometry workflows (e.g., output from OpenSwath or similar feature detection tools) and you need to restrict the analyte pool to those meeting a strict false-discovery rate (FDR) threshold.
    0 installs
27. ▌
    Constraint Based Flux Sampling And Analysis · holobiomicslab

    Use when when you have constraint-based metabolic models for multiple samples or cell lines, and you want to determine whether integrating multiple omics constraint types (nutrient availability, extracellular metabolite ratios, gene expression) produces distinct and biologically meaningful.
    1 install
28. ▌
    Cross Database Structural Homology Matching · 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
29. ▌
    Cross Dataset Score Distribution Comparison · holobiomicslab

    Use when when you have applied multiple scoring functions (e.g., strain correlation and IOKR) to rank genomic-metabolomic (GCF-MF or BGC-spectrum) links and need to verify that: (1) standardisation produces zero mean and unit variance across all links;
    2 installs
30. ▌
    Cross Language Data Format Interoperability · holobiomicslab

    Use when you have mass spectrometry data (LC–MS/MS, ion mobility, DIA) converted to MZA format and need to read or analyze it in multiple programming languages (Python and R), or share datasets with collaborators using different environments without requiring proprietary vendor libraries or format.
    0 installs
31. ▌
    Data Driven Similarity Layer Implementation · holobiomicslab

    Use when you have untargeted metabolomics mass spectrometry data (MS2 spectra with m/z values and intensities) and an existing knowledge-driven metabolite network, and you need to enhance annotation accuracy and coverage by leveraging experimental similarity patterns rather than relying solely on.
    0 installs
32. ▌
    Dda Fragmentation Strategy Parameterization · holobiomicslab

    Use when you have a virtual chemical mixture (MS1 peaks) and need to prototype a new DDA acquisition strategy before testing on real instrumentation. Use this skill when you want to compare how different parameter combinations (e.g., TopN=3 vs TopN=5, isolation_width=0.5 Da vs 1.
    0 installs
33. ▌
    Entropy Based Spectral Distance Computation · holobiomicslab

    Use when when comparing two preprocessed MS/MS spectra for compound identification and you need higher accuracy than dot product similarity provides.
    0 installs
34. ▌
    Feature Sub Group Refinement And Validation · holobiomicslab

    Use when after initial retention-time-based feature grouping (e.
    0 installs
35. ▌
    Feature Table Annotation Table Construction · holobiomicslab

    Use when after feature extraction from XCMS or MS-Dial when you have a feature intensity table (samples × features), a feature info table with m/z and retention time measurements, and access to a reference compound database with known m/z, retention time, and compound metadata.
    0 installs
36. ▌
    Feature Table Integration And Normalization · holobiomicslab

    Use when when you have MS1 feature tables from heterogeneous sources—e.g., XCMS peak detection output mixed with vendor software (MS-DIAL, MZmine2) results—and need to merge them into a single, format-normalized table for ISFrag analysis.
    0 installs
37. ▌
    Filter Status Data Structure Interpretation · holobiomicslab

    Use when after applying a sequence of mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an LC-MS/MS peak table in Progenesis or MS-DIAL format, call qc_summary() to obtain a structured report of per-ion filtering outcomes and use this skill to understand.
    0 installs
38. ▌
    Gaussian Process Uncertainty Quantification · holobiomicslab

    Use when after collecting observed separation efficiency scores at sampled gradient conditions and you need to propose the next gradient to evaluate.
    0 installs
39. ▌
    Graph Neural Network Encoding For Molecules · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a reference library of compounds.
    0 installs
40. ▌
    Interactive Network Visualization Rendering · 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.
    2 installs
41. ▌
    Ionization Polarity Selection And Filtering · holobiomicslab

    Use when loading raw mass spectrometry data (MGF, mzML, or msp format) into MS2LDA and you need to isolate spectra from a single ionization polarity.
    0 installs
42. ▌
    Isotopic Signature Validation And Filtering · 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
43. ▌
    Latent Dirichlet Allocation Topic Inference · holobiomicslab

    Use when you have a preprocessed corpus of mass spectrometry spectra converted to bag-of-fragments format (with neutral losses extracted and noise filtered), and you seek to discover recurring fragmentation patterns or substructures that characterize multiple spectra without prior knowledge of the.
    0 installs
44. ▌
    Mass Accuracy Collision Energy Optimization · holobiomicslab

    Use when you have defined a set of lipid targets (species, adducts, chain compositions) for PRM or MRM analysis and need to generate precursor-to-fragment transition rules that will maximize signal intensity and specificity on your mass spectrometer (Thermo QExactive HF, Agilent QTOF, or.
    0 installs
45. ▌
    Mass Defect Filtering For Chemical Validity · holobiomicslab

    Use when after loading an MS-DIAL peak list (feature table with m/z, retention time, intensity, and sample assignments) when you need to remove non-organic or chemically implausible features.
    0 installs
46. ▌
    Mass Spectrometry Method Cycle Verification · holobiomicslab

    Use when when you have a Thermo Fisher Scientific Orbitrap .raw file and need to confirm that a targeted acquisition method (e.g., PRM targeting a specific precursor m/z) is achieving uniform cycle timing.
    0 installs
47. ▌
    Mass Spectrometry Scan Extraction By Target · holobiomicslab

    Use when you have raw LC-MS/MS chromatogram files in mzML/mzXML format (converted from Thermo, Waters, or Bruker instruments) acquired in DDA or targeted MS/MS mode, and you need to isolate specific MS1 precursors and their corresponding MS2 fragments based on known m/z values and optional.
    0 installs
48. ▌
    Metabolite Annotation Confidence Assignment · holobiomicslab

    Use when you have a feature intensity table with feature metadata (m/z, retention time) extracted from XCMS or MS-Dial, and you want to cross-reference each feature against a known-compound database to assign standardized confidence levels.
    2 installs
49. ▌
    Metabolite Annotation Taxonomic Integration · holobiomicslab

    Use when you have paired metabolomics data (MS/MS spectra and feature quantification) linked to organismal or tissue taxonomy, and you want to reduce false positive annotations and improve annotation rank by filtering candidate metabolites to those chemically plausible within the given taxon.
    0 installs
50. ▌
    Metabolite Candidate Ranking Interpretation · holobiomicslab

    Use when after running annotateRC() on LC-MS AIF features, when you need to validate whether a feature's rank-1 annotation is reliable or when you suspect that structurally similar metabolites (e.
    0 installs
51. ▌
    Metabolite Feature Filtering By Missingness · holobiomicslab

    Use when you have a raw metabolite abundance matrix (e.g., from MSPrep or another LC-MS/MS pipeline) with many features and samples, and you observe that a substantial fraction of metabolites are missing (NA or zero-valued) across replicates.
    0 installs
52. ▌
    Metabolite Feature Matching Across Datasets · holobiomicslab

    Use when you have two independent LC-MS untargeted metabolomic feature tables (e.
    0 installs
53. ▌
    Metabolite Identity Ground Truth Validation · holobiomicslab

    Use when after constructing candidate feature pair alignments and retention-time spline mappings in a multi-dataset LC-MS metabolomics integration workflow, when you have access to independent ground-truth annotations (e.
    0 installs
54. ▌
    Metabolite Structure Annotation Integration · holobiomicslab

    Use when you have a set of candidate transformed structures generated by biotransformation rules (e.
    0 installs
55. ▌
    Metabolomics Feature Integration Assessment · holobiomicslab

    Use when after XCMS peak picking and fillPeaks() when you have xcmsEIC and filled xcmsSet objects and need to systematically flag low-quality or unreliable peak integrations prior to statistical modeling or machine learning classification.
    0 installs
56. ▌
    Missing Value Imputation Strategy Selection · holobiomicslab

    Use when after mark_nas() has replaced non-NA missing-value codes (e.g., 0, 1) with R's NA in the exprs matrix of a MetaboSet object, and you need to decide whether to apply random forest imputation, simple imputation strategies, or defer imputation.
    0 installs
57. ▌
    Molecular Formula Isotopic Profile Matching · holobiomicslab

    Use when you have detected peaks from untargeted LC/HRMS analysis (via IDSL.IPA or equivalent peak picker) with m/z and retention time values, and you need to assign molecular formulas to those peaks.
    0 installs
58. ▌
    Motif Pseudo Spectra Optimization Filtering · holobiomicslab

    Use when after LDA has converged and inferred Mass2Motifs from preprocessed mass spectrometry spectral data, when the raw motif-fragment distributions contain noise or low-confidence associations that obscure the dominant fragmentation patterns.
    0 installs
59. ▌
    Ms2 Fingerprint Blank Contamination Removal · holobiomicslab

    Use when after aligning MS2 fingerprints across samples (generating a sample-by-feature occurrence matrix) and before applying visualization techniques (MDS/PCoA, TMAP, Heatmap) or statistical comparisons.
    2 installs
60. ▌
    Neighbor Wise Constraint Propagation In Dtw · holobiomicslab

    Use when when XCMS or other DTW-based aligners have produced misaligned LC-MS feature groups across hundreds of samples or long acquisition periods (>1 week), particularly when individual m/z bins or compounds show inconsistent retention-time drift patterns across neighboring samples.
    0 installs
61. ▌
    Neural Network Regularization Configuration · holobiomicslab

    Use when implementing or modifying a Siamese model (such as SiameseModel in ms2deepscore) if you need to make regularization hyperparameters user-configurable rather than hard-coded, or when training on spectral datasets where overfitting risk is high due to limited training examples or high model.
    2 installs
62. ▌
    Neutral Loss Extraction From Precursor Mass · holobiomicslab

    Use when after loading and noise-filtering raw MS/MS spectra (in .mgf, .mzML, or .msp format) and before applying LDA for Mass2Motif inference.
    0 installs
63. ▌
    Open Format Mass Spectrometry File Handling · holobiomicslab

    Use when you have raw mass spectrometry data in vendor-proprietary formats (e.g., .raw, .d, .ms) that you need to upload to MassIVE for public sharing or submit to GNPS for spectral library matching and chemical annotation.
    0 installs
64. ▌
    Orbitrap Spectrum Extraction From Raw Files · 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
65. ▌
    Peak Annotation Refinement Structure Driven · holobiomicslab

    Use when you have two related compounds (a known reference and its structural analog with unknown modification site), baseline peak annotations from cosine alignment, and newly available structural information (SMILES or molecular structure) for the modified compound.
    0 installs
66. ▌
    Pfas Characteristic Fragment Identification · holobiomicslab

    Use when you have centroided data-dependent acquisition (ddMS2) mzML spectra from LC- or GC-HRMS and need to prioritize putative PFAS features.
    0 installs
67. ▌
    Principal Component Analysis Interpretation · holobiomicslab

    Use when when you have normalized MS1 ion intensity features from multiple samples and need to assess overall data quality, detect systematic batch effects or instrumental drift, or identify which samples deviate significantly from the cohort norm in an omics-agnostic manner (metabolomics.
    2 installs
68. ▌
    Python Object Serialization Deserialization · holobiomicslab

    Use when when you have completed spectral data preprocessing in Jupyter notebooks and generated a specXplore session data object saved to disk, use this skill to restore that object into a live specXplore dashboard session instance for interactive LC-MS/MS spectral data exploration, without.
    2 installs
69. ▌
    Annotation Accuracy And Coverage Metrics Computation · holobiomicslab

    Use when after executing an end-to-end structure annotation pipeline (such as BAM) on a validation dataset with known reference annotations.
    0 installs
70. ▌
    Differential Expression Analysis Algorithm Selection · holobiomicslab

    Use when after preprocessing and normalizing count matrices from transcriptomics or other omics data, when you need to identify differentially expressed features between experimental groups and must choose between edgeR (for flexible formula/contrast designs), DESeq2 (for designs with explicit.
    0 installs
71. ▌
    Euclidean Distance Computation For Spatial Alignment · holobiomicslab

    Use when when you have preprocessed ST and SM AnnData objects with spatial coordinates and need to establish one-to-one spot correspondence between the two modalities prior to joint analysis.
    2 installs
72. ▌
    Feature Table Construction For Multivariate Analysis · holobiomicslab

    Use when when you have high-resolution mass-spectrometry (HRMS) breath data in mzML or mzXML format from multiple subjects or conditions and need to prepare a sample-by-feature intensity matrix for downstream statistical comparison, biomarker discovery, or classification tasks.
    0 installs
73. ▌
    Mass Spectrometry Mass Accuracy And Precision Tuning · holobiomicslab

    Use when when extracting and validating chromatographic peaks for target molecules from centroided mzML files, particularly when working with multiple isotopologues and adducts where mass tolerance directly affects whether predicted isotopologues are correctly grouped and detected as part of the.
    0 installs
74. ▌
    Mass Spectrometry Peak Identification And Extraction · holobiomicslab

    Use when when you have raw mass spectrometry data from direct-infusion (DI-MS) or ambient surface analysis probe (ASAP-MS) instruments and need to identify which m/z peaks are biologically or chemically informative for sample classification, rather than processing the entire spectrum including.
    0 installs
75. ▌
    Missing Value Imputation And Completeness Assessment · holobiomicslab

    Use when after loading raw omics expression data (protein, peptide, metabolite abundances) with inherent missing values.
    0 installs
76. ▌
    Mobility Dimension Interpolation For Peak Resolution · holobiomicslab

    Use when working with raw multiplexed IM-MS data (UIMF or Agilent MassHunter .
    2 installs
77. ▌
    Sequential And Random Access File Interface Patterns · holobiomicslab

    Use when when you need to support custom data storage backends (e.g., SQLite, HDF5, or proprietary databases) for mzML-equivalent spectra, but the pymzML parser expects only standard file formats (mzML, mzML.gz, indexed gzip).
    0 installs
78. ▌
    Software Dependency Management And Environment Setup · holobiomicslab

    Use when you are preparing to run the MetaboDirect pipeline for the first time on a new machine, or you need to reproduce a published benchmark or analysis on a different OS (Windows, Linux, MacOS) and want to guarantee that all six pipeline steps (data pre-processing, diagnostics, exploration.
    0 installs
79. ▌
    Transcript Abundance Normalization Across Cell Lines · holobiomicslab

    Use when you have computed raw RAS values for multiple cell lines or samples by resolving Gene-Protein-Reaction (GPR) logical rules against RNA-seq FPKM abundances, and you need to make reaction activity scores comparable across cell lines by removing sample-level abundance differences so that.
    0 installs
80. ▌
    Deseq2 Object Initialization From Transcript Data · holobiomicslab

    Use when you have transcript-level abundance, count, and length estimates (from salmon, Sailfish, or kallisto via tximport) and want to perform gene-level differential expression analysis in DESeq2 using the 'original counts and offset' method, which accounts for changes in effective gene length.
    0 installs
81. ▌
    Independent Filtering Multiple Testing Correction · holobiomicslab

    Use when analyzing RNA-seq count data from a DESeq2 workflow where you have fitted negative binomial generalized linear models and need to extract final results. Use it specifically when you want to identify genes with adjusted p-value below a predetermined significance threshold (e.g., α=0.
    0 installs
82. ▌
    Ms2 Spectrum Collection From Data Dependent Acquisition · holobiomicslab

    Use when you have DDA LC-MS/MS raw data (mzML format) with detected chromatographic peaks at a target m/z value and retention time window, and you need to build a high-confidence MS2 consensus spectrum for that peak to match against reference spectra (e.g., Metlin, GNPS).
    0 installs
83. ▌
    Sample Batch Balancing Across Classification Dimensions · holobiomicslab

    Use when designing multi-batch LC/GC-MS experiments where samples belong to multiple groups or conditions and you need to ensure that each injection plate receives a balanced representation of all groups.
    0 installs
84. ▌
    Biotransformation Candidate Integration With Networking · holobiomicslab

    Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to identify molecular families and annotate features with predicted structures by leveraging spectral similarity and network.
    0 installs
85. ▌
    Biotransformation Prediction Across Microbiota Contexts · holobiomicslab

    Use when you have one or more small-molecule chemical structures (as SMILES, MOL, or SDF) and need to systematically explore their fate across mammalian biotransformation, human gut microbial degradation, or environmental (soil/aquatic) microbial degradation.
    2 installs
86. ▌
    Chromatographic Peak Detection Retention Time Alignment · holobiomicslab

    Use when you have multiple high-resolution mzML files from LC-MS/MS experiments (e.
    1 install
87. ▌
    Empirical Compound Construction From Feature Clustering · holobiomicslab

    Use when after feature detection and quality control have produced a feature table in TSV format from Asari or equivalent preprocessing.
    0 installs
88. ▌
    Gene Cluster Family Formation And Similarity Clustering · holobiomicslab

    Use when you have antiSMASH v5.0.0 BGC predictions from a set of microbial genomes and you need to integrate those predictions with GNPS metabolomic data (MS2 spectra and molecular families).
    2 installs
89. ▌
    Hyperparameter Tuning Learning Rate Optimizer Selection · holobiomicslab

    Use when when training a fresh NeatMS CNN model from scratch on LCMS peak classification and you need to determine which optimizer (Adam vs. SGD) and learning rate will produce an AUC ROC > 0.9 without overfitting.
    0 installs
90. ▌
    Ion Tree Structure Optimization And Trunk Establishment · holobiomicslab

    Use when after you have partitioned a feature network into connected subnetworks (each containing ion features linked by isotope or adduct mass differences).
    0 installs
91. ▌
    Peak Evaluation Metrics Cselectivity Snr Gaussian Fit · holobiomicslab

    Use when after scipy.signal.find_peaks has identified candidate peaks on a composite mass track segment, evaluate each peak to decide whether to retain it in the final feature table.
    0 installs
92. ▌
    False Positive Negative Detection In Pattern Matching · holobiomicslab

    Use when when reconstructing or validating the ColumnFinder component in mwtab, you need to assess whether the combined NameMatcher.dict_match and ValueMatcher.series_match operations are correctly populating database-ID columns. Apply this skill after defining NameMatcher patterns (e.
    0 installs
93. ▌
    Knn Nearest Neighbor Matching For Spot Correspondence · holobiomicslab

    Use when when integrating two spatial omics modalities (ST and SM) measured on the same tissue sample but at different spatial resolutions or spot coordinates.
    0 installs
94. ▌
    Raw Spectral Data Input Handling Without Peak Picking · holobiomicslab

    Use when when you have raw mass spectrometry imaging data (full m/z profiles with intensity arrays) and want to classify spatial regions (e.
    2 installs
95. ▌
    Similarity Network Construction From Domain Adjacency · holobiomicslab

    Use when you have a collection of tokenized BGCs (each gene represented as a combination of Pfam domains and subPfams) and need to identify and remove redundant or highly similar clusters before downstream analysis such as sub-cluster detection or natural product annotation.
    0 installs
96. ▌
    Spearman Correlation Background Distribution Analysis · holobiomicslab

    Use when after cross-validated neural network or regression models have generated predicted metabolite abundances and you need to distinguish genuinely predictable metabolites from those with spuriously high correlations.
    0 installs
97. ▌
    Spectrum Random Access Retrieval Via Bracket Notation · holobiomicslab

    Use when when you need to retrieve specific spectra from mzML files by custom identifier (integer or string) rather than sequential iteration, especially when the mzML file uses non-standard index formatting that requires a regex pattern to parse spectrum IDs and file offsets.
    0 installs
98. ▌
    Volcano Plot Construction From Fold Change And Pvalue · holobiomicslab

    Use when you have omu_summary output containing log2FoldChange and adjusted p-values (e.g., BH-corrected) for a pairwise contrast (e.g., Strep vs Mock treatment), and you want to visualize metabolite significance and magnitude simultaneously while stratifying points by hierarchical class (e.
    0 installs
99. ▌
    Differential Expression Empirical Bayes Moderation · holobiomicslab

    Use when after fitting a linear model with lmFit on voom-transformed or log2-normalized RNA-seq or microarray expression matrices, apply eBayes moderation to moderate gene-wise variance estimates before extracting top differentially expressed genes.
    2 installs
100. ▌
     Nested Data Structure Construction For Chemical Metadata · holobiomicslab

     Use when you have loaded raw Agilent Unknowns Analysis CSV output with required columns (Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
     2 installs