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HolobiomicsLab

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1. ▌
   Isobaric Ion Misclassification Documentation · holobiomicslab

   Use when after matrix annotation has been performed on mass spectrometry imaging (MSI) data when you need to identify and document ions whose m/z values overlap with or are isobaric to other peaks, creating risk of false positive or false negative matrix assignments.
   0 installs
2. ▌
   Linear Regression Design Matrix Construction · holobiomicslab

   Use when after log-transformation and missing-value imputation of featuredata (via LogTransform and MissingValues functions), when you have normalized metabolomics intensity data and need to identify metabolites associated with specific biological or experimental factors encoded as covariates in a.
   0 installs
3. ▌
   Mass Spectra Tokenization Unified Vocabulary · holobiomicslab

   Use when when you have paired mass spectra and molecular structure data and need to train a unified model for structure elucidation. Use this skill at the data preparation stage before pretraining, when you want both modalities to share representational capacity rather than operate in isolation.
   2 installs
4. ▌
   Mass Spectrometry Intensity Drift Correction · holobiomicslab

   Use when mS quantification data exhibits intensity drift—a systematic decline or variation in detector response across the run sequence. Intensity drift is particularly common in long measurement sessions and compromises the accuracy of feature-by-sample intensity matrices.
   0 installs
5. ▌
   Metabolite Database Identifier Normalization · holobiomicslab

   Use when you have metabolomics metadata in mwTab or tabular format with column headers and values that may contain database identifiers (e.g., HMDB IDs, PubChem CIDs, KEGG compound IDs) in heterogeneous or non-canonical formats (mixed case, optional prefixes, variable naming conventions).
   2 installs
6. ▌
   Metabolomic Network Edge Type Prioritization · holobiomicslab

   Use when when your metabolomic network contains multiple edge types (Biochemical, Structural, Mass Spectral, Correlation) between the same node pairs and you want to export a unique-edge network in which each node pair is connected by exactly one edge—the one with highest priority according to the.
   2 installs
7. ▌
   Metabolomics Feature Detection And Alignment · holobiomicslab

   Use when you have raw metabolomics mass spectrometry data in mzML or mzXML format and need to extract, align, and normalize metabolic features across multiple samples or conditions.
   0 installs
8. ▌
   Missing Data Handling In Metabolite Datasets · holobiomicslab

   Use when when importing metabolomics datasets with multiple studies into amanida_read for quantitative or qualitative meta-analysis, and some studies report missing values for p-values, fold-changes, sample sizes, or other effect size metrics.
   0 installs
9. ▌
   Multi Factorial Experimental Design Handling · holobiomicslab

   Use when your lipidomics dataset includes multiple experimental factors (e.
   0 installs
10. ▌
    Multicontrast Statistical Testing Lipidomics · holobiomicslab

    Use when after removing outlier samples and confirming data quality through PCA or TIC plots, apply this skill when you need to quantify statistical significance of lipid abundance differences across defined sample groups (e.g., disease vs. control, treatment vs. untreated, cancer stages).
    0 installs
11. ▌
    Multivariate Metabolomic Statistical Testing · holobiomicslab

    Use when after WGCNA-derived metabolic modules have been identified and named in a normalized, imputed MultiAssayExperiment object, and you need to test whether specific modules show statistically significant association with a binary or categorical sample grouping (e.
    2 installs
12. ▌
    Neural Network Early Stopping Implementation · holobiomicslab

    Use when when training a multilayer perceptron neural network on paired microbiome-metabolome datasets where you have a held-out validation fold (20% of each cross-validation fold) and wish to prevent overfitting without manual epoch selection.
    0 installs
13. ▌
    Peak Table Imputation Missing Value Handling · holobiomicslab

    Use when after peak clustering in a GCIMS preprocessing pipeline, when the peak table matrix contains NA values corresponding to peaks detected in some samples but not others, and you have computed cluster statistics that characterize each peak cluster's properties.
    0 installs
14. ▌
    Ppm Tolerance Filtering In Mass Spectrometry · holobiomicslab

    Use when when you have assigned molecular formulas to m/z peaks or computed mass differences between peaks in FT-ICR MS data, and you need to distinguish true chemical matches from noise or random coincidences.
    0 installs
15. ▌
    Python Package Installation Development Mode · holobiomicslab

    Use when when you have cloned a Python package repository locally and need to test code changes, run the package's test suite, or contribute to development without reinstalling the package after each modification.
    0 installs
16. ▌
    Quality Control Sample Selection And Marking · holobiomicslab

    Use when your metabolomics dataset contains samples analyzed across multiple batches or runs, and you have sample-level metadata (sampledata) with a 'type' or classification field. You intend to apply QC-aware normalization methods (e.
    0 installs
17. ▌
    Quantitative Mode Metabolomics Configuration · holobiomicslab

    Use when when you have metabolomics results from multiple studies reporting compound identifiers, p-values, fold-changes, and study sizes (N), and you need to prepare them for quantitative meta-analysis using weighted Fisher's method and logarithmic fold-change combination.
    2 installs
18. ▌
    Rdkit Descriptor And Fingerprint Calculation · holobiomicslab

    Use when you need to (1) compare structural similarity between generated compounds and target/reference structures using Tanimoto similarity scores, (2) extract molecular descriptors for machine learning models that predict reaction feasibility, (3) implement compound filtering based on chemical.
    2 installs
19. ▌
    Reaction Activity Score Computation From Gpr · holobiomicslab

    Use when you have RNA-seq FPKM abundance data for genes across multiple cell lines or samples, a metabolic model with embedded GPR associations, and need to translate differential gene expression into reaction-level constraints for flux prediction.
    0 installs
20. ▌
    Repository Cloning With Recursive Submodules · holobiomicslab

    Use when you need to set up a development environment for a project that declares Git submodules (typically listed in .gitmodules), particularly when the build system (qmake, make, Maven, etc.) expects all dependencies to be present in the working tree.
    2 installs
21. ▌
    Rna Seq Preprocessing Pipeline Orchestration · holobiomicslab

    Use when when you have raw FASTQ files (from SRA or local storage) and need to produce normalized transcript quantification (quant.sf) files for a multi-sample RNA-seq cohort.
    2 installs
22. ▌
    Roc Auc Computation For Phenotype Prediction · holobiomicslab

    Use when you have constructed consensus-clustered microbe and metabolite modules from microbiome-metabolome interaction data and wish to test whether these module-level features have clinically predictive value for a binary phenotype (e.g., disease vs. healthy).
    0 installs
23. ▌
    Spectra Object Serialization Deserialization · holobiomicslab

    Use when you have Spectra objects in an R environment and need to apply Python MS algorithms (e.g., matchms similarity scoring, spectrum normalization, or filtering) that operate on Python spectral objects, then return results back to R for further analysis or visualization.
    0 installs
24. ▌
    Spectral Array Extraction And Reconstruction · holobiomicslab

    Use when your input is an mzPeak archive (ZIP of Parquet files) and you need to recover spectrum signal data (m/z values and intensities) for downstream analysis, visualization, or format conversion. Use this skill when working with profile or centroid mode spectra stored in `spectra_data.
    0 installs
25. ▌
    Spectral Similarity Scoring With Mass Shifts · holobiomicslab

    Use when you have an unknown query spectrum suspected to carry a post-translational modification and need to match it against a library of unmodified reference spectra.
    0 installs
26. ▌
    Standardized Region Export For Deep Learning · holobiomicslab

    Use when you have LC-HRMS profile-mode data with detected local maxima (from gradient-descent peak finding) and need to prepare them as input for a convolutional neural network trained to classify peaks vs. background signal or to estimate peak boundaries and centers.
    0 installs
27. ▌
    Tensor Shape Validation Through Forward Pass · holobiomicslab

    Use when after assembling a Graphormer backbone with DGL molecular graph encoders, column-parameter embedding layers, and gradient-slope feature concatenation, but before training on the full dataset.
    0 installs
28. ▌
    Topic Label Validation Distribution Analysis · holobiomicslab

    Use when after LDA topic inference has assigned dominant topic labels to mass spectra, and before those labels are passed to MLP or GNN multi-task training.
    0 installs
29. ▌
    Univariate Statistical Output Interpretation · holobiomicslab

    Use when after running omu_summary (t-test) or omu_anova (ANOVA) on metabolomics count data with a defined contrast (e.g., numerator vs. denominator treatment levels), when you need to filter and visualize metabolites by statistical significance and effect size.
    0 installs
30. ▌
    W4m Three Table Format Conformance · holobiomicslab

    Use when moving a feature table between Workflow4Metabolomics tools and the dataMatrix, sampleMetadata and variableMetadata files must agree on identifiers, order and R-name validity before a statistics step silently analyses mislabelled samples.
    0 installs
31. ▌
    Dask Array Materialization And Collection · holobiomicslab

    Use when you have performed lazy dask-backed feature extraction on an ImageContainer using im.calculate_image_features and need to persist the computed spatial features into the AnnData object while controlling when and how dask graph computation is triggered.
    1 install
32. ▌
    Differential Splicing Statistical Testing · holobiomicslab

    Use when you have PSI (percent-spliced-in) matrices for multiple samples grouped into two or more biological conditions, along with corresponding transcript expression quantification, and need to identify events or transcripts with statistically significant changes in inclusion levels between.
    0 installs
33. ▌
    Gene Level Summarization From Transcripts · holobiomicslab

    Use when you have transcript-level quantification files (salmon quant.sf.gz, kallisto h5, or Sailfish output) and need to perform gene-level differential expression analysis.
    0 installs
34. ▌
    Multiple Testing Correction Visualization · holobiomicslab

    Use when after running fgsea() on a preranked gene list and obtaining a results table with raw pval, padj, ES, NES, and size columns, use this skill to: (1) subset results to top enriched pathways (e.g., top 10 upregulated ES > 0 and top 10 downregulated ES < 0 by adjusted p-value);
    1 install
35. ▌
    Rna Seq Experimental Design Specification · holobiomicslab

    Use when before constructing a DESeqDataSet from count data or tximport output, when you have raw RNA-seq samples that need to be annotated with experimental conditions, treatment groups, batch effects, or other covariates.
    0 installs
36. ▌
    Salmon Quantification Output Verification · holobiomicslab

    Use when after running salmon quant with the --writeMappings/-z flag to produce SAM output, or when investigating discrepancies between the number of mapped reads reported in quant.sf and the actual number of records written to the output SAM file.
    0 installs
37. ▌
    Sparse Matrix Verification And Validation · holobiomicslab

    Use when after calling squidpy.gr.spatial_neighbors or any graph-building operation that outputs sparse matrices to adata.
    2 installs
38. ▌
    Transcript Abundance Correlation Analysis · holobiomicslab

    Use when when validating a new or reimplemented quantification tool against a reference implementation on the same dataset and index, or when investigating whether changes to seed representation, chain pruning thresholds, or other algorithmic parameters affect downstream abundance estimates.
    0 installs
39. ▌
    Uncertainty Aware Significance Assessment · holobiomicslab

    Use when you have PSI matrices for two or more conditions with replicates per condition, and you need to determine which alternative splicing events show significant changes between conditions while accounting for measurement uncertainty that scales with transcript expression levels.
    1 install
40. ▌
    Approximate Nearest Neighbor Index Construction · holobiomicslab

    Use when when you have a large collection of reference MS/MS spectra (spectral library) and need to search unknown query spectra against it rapidly, particularly for open modification searching where the modification mass is unknown and candidate space is large.
    0 installs
41. ▌
    Ce Ms Migration Time To Mobility Transformation · holobiomicslab

    Use when your CE-MS dataset exhibits migration time drift between runs due to electroosmotic flow (EOF) variation, and you have identified two internal mobility markers (e.g., Paracetamol and Procaine) with known charges whose migration times can be measured in the raw data.
    2 installs
42. ▌
    Chromatographic Peak Detection And Segmentation · holobiomicslab

    Use when you have raw LC-MS data (mzML or vendor format) and need to discover and characterize all chromatographic features present, without prior knowledge of target analytes.
    0 installs
43. ▌
    Marker Feature Identification Chromatography Ms · holobiomicslab

    Use when when processing raw chromatography–mass spectrometry data (GC–MS or LC–MS) as a 2D m/z vs retention time map and you need to identify and visualize marker features for analyte discrimination without relying on conventional peak picking.
    2 installs
44. ▌
    Mass Spectral Missing Word Fraction Computation · holobiomicslab

    Use when when applying a pre-trained Spec2Vec Word2Vec model to new mass spectra (particularly those outside the model's training distribution), you need to assess whether peaks and neutral losses in query spectra have been seen during model training.
    0 installs
45. ▌
    Mass Spectral Similarity Scoring Across Samples · holobiomicslab

    Use when after XCMS feature detection, grouping, and retention time correction when you have aligned features with consistent retention times and intensity patterns across samples.
    0 installs
46. ▌
    Metabolite Feature Clustering By Retention Time · holobiomicslab

    Use when after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table with retention times and intensity profiles across multiple samples and need to collapse redundant features into.
    0 installs
47. ▌
    Performance Metric Extraction From Publications · holobiomicslab

    Use when you have identified a claim that one tool outperforms another (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms') in a research article's abstract or introduction, but the specific metrics and results table are not included in the introductory text.
    0 installs
48. ▌
    Bag Of Words Document Representation Generation · holobiomicslab

    Use when you have raw MS/MS spectral data in standard mass spectrometry formats and need to prepare it for unsupervised substructure discovery via topic modeling.
    0 installs
49. ▌
    Biochemical Relation Integration For Annotation · holobiomicslab

    Use when when you have LC/MS feature data (m/z, retention time, intensity) that must be annotated against a metabolic database and you have access to (or can construct) knowledge about biochemical reaction networks, expected isotope patterns, and instrument-specific adduct formation rules.
    0 installs
50. ▌
    Bioconductor Summarized Experiment Construction · holobiomicslab

    Use when after successfully reading and validating a tab-delimited metabolomics file (containing mandatory columns: aliquot, compound, area, type, injection_time, batch) using readData, and before applying batch correction, outlier detection, or other QC filters.
    0 installs
51. ▌
    Blank Sample Background Interference Estimation · holobiomicslab

    Use when after MS1 feature detection and accurate mass annotation, when you have identified a set of blank injections (negative controls) run in the same analytical sequence segment as your biological or study samples.
    0 installs
52. ▌
    Checkpoint Selection Based On Validation Metric · holobiomicslab

    Use when training neural networks on MS/MS spectra (or similar scientific data) where you need to preserve model states that improve validation performance.
    0 installs
53. ▌
    Chemical Structure Transformation Documentation · holobiomicslab

    Use when when you have access to source code or algorithmic documentation of a metabolite generation pipeline (such as MAGMa's job subproject) and need to understand, validate, or reconstruct the transformations that convert a parent compound into enumerated metabolite candidates.
    2 installs
54. ▌
    Collision Cross Section Matching And Annotation · holobiomicslab

    Use when when you have LC-IM-MS/MS data with measured collision cross section (CCS) values and m/z assignments, and you need to disambiguate sterol isomers (particularly N-Me derived unsaturated sterols) by matching against a curated database of predicted CCS values and MS/MS fragmentation patterns.
    2 installs
55. ▌
    Collision Energy Optimization For Fragmentation · holobiomicslab

    Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with collision-energy-dependent m/z values and intensities for downstream CCS prediction or LC-IM-MS/MS library matching.
    0 installs
56. ▌
    Concentration Prediction From Calibration Model · holobiomicslab

    Use when you have (1) a set of calibration samples with known spiked concentrations of target compounds, (2) measured compound/internal-standard ratios for both calibration and study samples, and (3) need to convert ratios to absolute concentrations for reporting.
    0 installs
57. ▌
    Dynamic Exclusion Weighting Strategy Evaluation · holobiomicslab

    Use when you have prototyped a novel data-dependent acquisition strategy that uses dynamic exclusion with intensity or ROI weighting, and you need to quantitatively compare its MS/MS coverage and intensity performance against a simpler baseline (TopN) before testing on real instrumentation.
    2 installs
58. ▌
    Internal Standard Peak Detection And Validation · holobiomicslab

    Use when you have loaded processed LC-MS data (mzML or vendor format) and need to establish baseline instrument performance before evaluating sample analytes. Use it at the start of each LC-MS batch or run to ensure that internal standard detection passes predefined thresholds;
    0 installs
59. ▌
    Ionization Mode Specific Preprocessing Handling · holobiomicslab

    Use when you have raw MS/MS spectra in supported formats (.mgf, .mzML, or .msp) from mixed ionization modes and need to prepare them for downstream topic modeling (LDA) or motif discovery.
    1 install
60. ▌
    Isotope Pattern Annotation In Feature Detection · holobiomicslab

    Use when when performing feature detection on centroided DDA mzML files from LC- or GC-HRMS and you need to confirm the elemental composition or differentiate between candidate features—particularly for PFAS screening where isotopic signatures (chlorine, bromine, fluorine) are diagnostic.
    0 installs
61. ▌
    JSON Structure Validation For Metabolomics Data · holobiomicslab

    Use when after serializing empirical compound collections to JSON format via khipu's build_empCpds command, or before ingesting empCpd.
    0 installs
62. ▌
    Mass Spectrometry Preprocessing Quality Control · holobiomicslab

    Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).
    0 installs
63. ▌
    Mass Spectrum Peak Annotation And Normalization · holobiomicslab

    Use when you have raw MS/MS spectra in MSP format or as numpy arrays and need to standardize them for comparison or library matching. Specifically, use it before performing electronic or chemical denoising, or before computing entropy-similarity metrics between query and reference spectra.
    0 installs
64. ▌
    Mass Track Construction From Centroided Spectra · holobiomicslab

    Use when when you have centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment. Apply this skill at the start of an untargeted metabolomics workflow, before building a cross-sample MassGrid.
    0 installs
65. ▌
    Metabolite Feature Normalization Across Batches · holobiomicslab

    Use when after data merging and cleanup (blank removal) and before univariate or multivariate statistical analysis, when your merged feature table (samples as columns, metabolite features as rows) contains samples processed in different MS batches or instrumental runs that may introduce systematic.
    0 installs
66. ▌
    Metabolite Feature Quantification Table Parsing · holobiomicslab

    Use when when you have completed feature detection in MZmine3 or similar tools and produced a feature quantification table (rows = features, columns = samples with intensity values), and you possess a separate sample metadata file (sample identifiers, treatment groups, batch information).
    0 installs
67. ▌
    Molecular Conformer Generation And Optimization · holobiomicslab

    Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational and electronic structure data as input to a machine-learning CCS prediction model.
    0 installs
68. ▌
    Molecular Formula Prediction From Fragmentation · holobiomicslab

    Use when you have MS/MS fragmentation spectra (from Orbitrap or Q-TOF instruments) in MGF format with known precursor m/z, adduct type, and collision energy, and you need to generate ranked molecular formula candidates.
    0 installs
69. ▌
    Molecular Network Construction For Metabolomics · holobiomicslab

    Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown metabolites.
    0 installs
70. ▌
    Ms Ms Spectrum Statistical Significance Testing · holobiomicslab

    Use when you have aligned fragment ion pairs from two MS/MS spectra (via maximum weight matching or other methods) and need to assign p-values or Z-scores to each matched pair to distinguish true biological/chemical relationships from random noise.
    0 installs
71. ▌
    Organism Specific Metabolism Pathway Assignment · holobiomicslab

    Use when you have observed metabolites (from LC-MS/MS, chromatography, or spectroscopy) whose identities are unknown, and you wish to constrain the candidate pool by leveraging organism-specific metabolism predictions.
    0 installs
72. ▌
    Untargeted Metabolomics Data Quality Assessment · holobiomicslab

    Use when after imputation and signal drift correction (OUKS steps 3–4), when you have a QC-annotated feature intensity table with replicated QC samples and need to assess which features have stable, reproducible signals before filtering and statistical testing.
    0 installs
73. ▌
    Untargeted Metabolomics Workflow Implementation · holobiomicslab

    Use when you have LC-MS/MS data acquired in DDA mode from untargeted metabolomics experiments and need to remove chimeric (co-fragmented) MS/MS spectra that result from multiple precursor ions fragmented simultaneously.
    0 installs
74. ▌
    Biotransformation Rule Application To Metabolites · holobiomicslab

    Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated database of biotransformation rules (e.g., from KEGG, RetroRules, or domain-specific repositories).
    0 installs
75. ▌
    Metabolomics Database Search And Formula Matching · holobiomicslab

    Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time values.
    2 installs
76. ▌
    Atac Seq Clustering Performance Interpretation · holobiomicslab

    Use when when you need to assess whether a given ATAC-seq clustering method (or variant) is competitive on your data or when evaluating which published method to adopt.
    0 installs
77. ▌
    Deviation Score Computation And Interpretation · holobiomicslab

    Use when you have filtered ATAC-seq peak counts, matched motifs to those peaks, and want to measure which transcription factor motifs show elevated or reduced accessibility relative to GC-content and accessibility-matched background expectations—particularly when annotating TF motif usage across.
    0 installs
78. ▌
    Eigenvector Digitization Into Compartment Bins · holobiomicslab

    Use when you have computed eigenvector values from a prior eigs_cis calculation on a cooler Hi-C matrix and need to classify genomic regions into discrete A/B compartment categories before performing saddle analysis or computing compartment-level contact asymmetry metrics.
    0 installs
79. ▌
    Repository Cloning And Dependency Verification · holobiomicslab

    Use when you have identified a published computational tool (e.
    2 installs
80. ▌
    Tn5 Insertion Position Extraction And Counting · holobiomicslab

    Use when you have ATAC-seq BAM files and a set of genomic coordinates (e.g., transcription factor motif sites, peak regions) and need to quantify the spatial distribution of Tn5 cleavage events relative to those coordinates.
    0 installs
81. ▌
    Background Distribution Threshold Calibration · holobiomicslab

    Use when when you have trained a predictive model (e.g., neural network or regression model) that outputs continuous scores (such as Spearman correlation coefficients) for individual features (e.
    2 installs
82. ▌
    Centered Log Ratio Transformation Application · holobiomicslab

    Use when apply CLR transformation when working with microbiome or metabolomic relative abundance tables that will be input to multivariate regression or neural network models.
    2 installs
83. ▌
    Col Mode Augmentation Pipeline Implementation · holobiomicslab

    Use when when you have preprocessed mass spectrometry imaging (MSI) ion images and need to generate augmented image pairs for contrastive learning in co-localized ion discovery tasks.
    0 installs
84. ▌
    Collision Cross Section Prediction Evaluation · holobiomicslab

    Use when you have a pre-trained GNN CCS prediction model and need to assess its predictive performance and cross-dataset generalizability. Use it specifically when evaluating whether models trained on one CCS database (e.
    0 installs
85. ▌
    Cross Dataset Model Generalization Assessment · holobiomicslab

    Use when you have trained a neural network or regression model on one paired microbiome-metabolome dataset and wish to test whether it can predict metabolite abundances in an independent, externally-sourced dataset collected from different patient cohorts or study populations.
    0 installs
86. ▌
    Documentation Mining For Project Architecture · holobiomicslab

    Use when you have access to a multi-component research software repository (e.
    0 installs
87. ▌
    Mass Spectrometry Imaging Data Interpretation · holobiomicslab

    Use when when you have preprocessed MALDI-MSI data (in msimat format) and want to determine whether abundant peaks are actually molecular adducts of simpler parent ions rather than distinct metabolites.
    0 installs
88. ▌
    Message Passing Neural Network Implementation · holobiomicslab

    Use when when you have molecular input data (SMILES strings or graph representations) and need to predict molecular properties or spectra using graph neural networks. Apply this skill specifically when the base chemprop MPNN must be extended with new feature modules (e.
    0 installs
89. ▌
    Metabolite Abundance Normalization Comparison · holobiomicslab

    Use when you have normalized peak intensities using MetaboDirect's data preprocessing step and are preparing to perform PERMANOVA or NMDS ordination on a bacterium-phage or environmental metabolomics dataset (36+ samples).
    2 installs
90. ▌
    Multi Criterion Score Combination And Ranking · holobiomicslab

    Use when you have generated hypothetical links (e.g., GCF–MF pairs) and computed multiple independent scoring functions on them (e.g., strain co-occurrence, IOKR structural fingerprint matching), but individual scores show incomplete discrimination power.
    0 installs
91. ▌
    Package Installation Verification And Testing · holobiomicslab

    Use when a Python package has been relocated to a new repository location, reorganized to conform to new organizational standards (e.g., metabolomics-cloud conventions), or its dependencies, metadata, or CI/CD workflows have been modified.
    0 installs
92. ▌
    Peak Intensity Normalization Method Selection · holobiomicslab

    Use when after peak filtering (by m/z, isotopic presence, formula assignment error, and sample prevalence) and before multivariate analysis (PCA, NMDS, PERMANOVA) when comparing peak abundance patterns across samples with potential differences in ionization efficiency, ion suppression, or total ion.
    0 installs
93. ▌
    Performance Metric Comparison Across Backends · holobiomicslab

    Use when when you have access to a set of gallery or benchmark scripts executed across multiple plotting backends and need to quantify which backend delivers the fastest median execution time for specific mass spectrometry plot types (chromatogram, mobilogram, peakmap, peakmap-marginals, spectrum.
    0 installs
94. ▌
    S4 Class Extension For Backend Implementation · holobiomicslab

    Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly into workflows that use the Spectra package.
    2 installs
95. ▌
    Smiles String Translation And Standardization · holobiomicslab

    Use when you have raw SMILES strings from multiple external database sources (e.g., PubChem, ChEMBL, vendor databases) that need to be integrated into a unified structure registry. Indicators include: (1) raw SMILES table exists at a known interim input path (e.
    0 installs
96. ▌
    Source Code Analysis For Algorithm Extraction · holobiomicslab

    Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the software performs in silico generation, enumeration, or filtering of candidate molecular structures and the published paper or.
    0 installs
97. ▌
    Spearman Rank Correlation Statistical Testing · holobiomicslab

    Use when you have paired in silico and experimental measurements from multiple biological samples (e.
    2 installs
98. ▌
    Spectral Annotation And Overlay Visualization · holobiomicslab

    Use when after correlation testing has validated putative parent–adduct ion pairs (e.g., via corrPairsMSI() on a massdiff object annotated with adductMatch results), use this skill to annotate and visualize the mass spectrum plot to confirm that identified pairs exhibit expected overlap—e.
    0 installs
99. ▌
    Url Validation And Accessibility Verification · holobiomicslab

    Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
    2 installs
100. ▌
     Visualization Comparative Performance Metrics · holobiomicslab

     Use when you have execution-time data for the same set of plotting operations (e.g., chromatogram, spectrum, peakmap rendering) across two or more backend implementations (e.
     0 installs