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HolobiomicsLab

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1. ▌
   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
2. ▌
   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.
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3. ▌
   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
4. ▌
   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.
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5. ▌
   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
6. ▌
   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
7. ▌
   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).
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8. ▌
   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
9. ▌
   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
10. ▌
    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
11. ▌
    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
12. ▌
    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
13. ▌
    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.
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14. ▌
    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.
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15. ▌
    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
16. ▌
    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.
    0 installs
17. ▌
    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.
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18. ▌
    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
19. ▌
    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.
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20. ▌
    Repository Cloning And Dependency Verification · holobiomicslab

    Use when you have identified a published computational tool (e.
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21. ▌
    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.
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22. ▌
    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.
    0 installs
23. ▌
    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.
    0 installs
24. ▌
    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.
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25. ▌
    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
26. ▌
    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
27. ▌
    Documentation Mining For Project Architecture · holobiomicslab

    Use when you have access to a multi-component research software repository (e.
    0 installs
28. ▌
    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
29. ▌
    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
30. ▌
    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).
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31. ▌
    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.
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32. ▌
    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.
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33. ▌
    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
34. ▌
    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.
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35. ▌
    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.
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36. ▌
    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
37. ▌
    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
38. ▌
    Spearman Rank Correlation Statistical Testing · holobiomicslab

    Use when you have paired in silico and experimental measurements from multiple biological samples (e.
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39. ▌
    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
40. ▌
    Url Validation And Accessibility Verification · holobiomicslab

    Use when when compiling or maintaining a catalog of web-accessible scientific tools (e.
    0 installs
41. ▌
    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
42. ▌
    Anndata Object Initialization And Structuring · holobiomicslab

    Use when when you have imzML and accompanying ibd (ion binary data) files from spatial metabolomics experiments and need to load them into a unified AnnData object representation for integration with spatial transcriptomics or other spatial multi-omics data.
    0 installs
43. ▌
    Background Contamination Threshold Assessment · holobiomicslab

    Use when after batch correction of metabolomics data when you need to identify and remove compounds whose signal in background/blank samples exceeds a tolerable contamination level.
    0 installs
44. ▌
    Bayesian Dimensionality Reduction Application · holobiomicslab

    Use when your input is a filtered metabolite abundance matrix with remaining sporadic missingness (after removing features with >80% missingness) and you need to produce a complete feature table for subsequent normalization and statistical analysis without data loss or listwise deletion.
    0 installs
45. ▌
    Chromatographic Peak Isolation And Refinement · holobiomicslab

    Use when after sliding-window analysis has identified candidate TIC peaks but before extracting chromatographic parameters (retention time, peak width, intensity) from extracted ion chromatograms.
    0 installs
46. ▌
    Composite Mass Track Summation Across Samples · holobiomicslab

    Use when after mass tracks have been aligned across samples into a MassGrid structure (m/z-aligned, same mass-to-charge ratio) and retention time calibration dictionaries have been computed for each sample.
    0 installs
47. ▌
    Compute Service Local Transformation Registry · holobiomicslab

    Use when initializing a chemical metadata annotation pipeline and you need to: (1) establish which identifier conversions are available across your installed converter suite (CIR, CTS, PubChem, IDSM, BridgeDb, RDKit, custom); (2) validate that each conversion route can actually be invoked;
    0 installs
48. ▌
    Connected Component Decomposition And Pruning · holobiomicslab

    Use when after identifying pairwise feature connections via correlation and retention-time windowing, when you need to partition the feature space into coherent groups where each feature has sufficient connectivity to its peers.
    0 installs
49. ▌
    Data Format Validation And Integrity Checking · holobiomicslab

    Use when after converting raw Bruker .d/.baf or other proprietary mass spectrometry imaging formats using pyBaf2Sql or ProteoWizard MSConvert, or after running MSIGen's get_image_data() function.
    0 installs
50. ▌
    Environmental Microbial Metabolism Prediction · holobiomicslab

    Use when you have a small molecule structure (SMILES, MOL, or SDF format) and need to understand how soil or aquatic microbiota would metabolize it.
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51. ▌
    Feature Matrix Correction Integration Context · holobiomicslab

    Use when after integrating feature matrices from multiple analytical experiments (batches) into a single MutileAlign matrix. Batch effects manifest as systematic differences in metabolite intensities across batches even when analyzing the same samples.
    0 installs
52. ▌
    Fingerprint Feature Extraction Retention Time · holobiomicslab

    Use when when you have a collection of small molecules with known chemical structures (SMILES, SDF, mol, mol2, or hin format) and need to train or apply a retention time prediction model.
    0 installs
53. ▌
    Functional Level Similarity Index Computation · holobiomicslab

    Use when when you have two metabolic networks (e.g., from KEGG) and need to measure similarity not by network topology but by the metabolic functions and pathway annotations each organism possesses. Use this skill when your research question focuses on functional overlap—e.
    0 installs
54. ▌
    Graph Based Link Representation Visualization · holobiomicslab

    Use when after NPLinker computes scored links between genomic and metabolomic entities using a scoring method (e.
    0 installs
55. ▌
    Hierarchical Clustering Dendrogram Generation · holobiomicslab

    Use when you have a normalized and imputed metabolite abundance matrix (as a MultiAssayExperiment object) and want to identify groups of co-expressed metabolites.
    0 installs
56. ▌
    High Resolution Mass Spectral Data Processing · holobiomicslab

    Use when you have high-resolution mass-spectrometry data (Orbitrap, GC-CI-MS) from stable-isotope labeling experiments and need to quantify isotopologue abundances for a defined list of target compounds.
    0 installs
57. ▌
    In Silico Fragmentation Simulation Validation · holobiomicslab

    Use when you have experimental peak lists (m/z, retention time, intensity) from UHPLC-HRMS/MS or direct infusion MS/MS data and need to assign lipid identities with confidence scores. Use it when your instrument produces high-resolution tandem mass spectra (e.
    0 installs
58. ▌
    Intensity Value Aggregation Across Replicates · holobiomicslab

    Use when after peak recognition has identified features (m/z and retention time pairs) across one or more MS replicates, and you need to collapse multiple intensity measurements per feature into a single representative value per sample.
    0 installs
59. ▌
    Internal Standardization Correction Lipidomes · holobiomicslab

    Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and measured CCS values need bias assessment or correction.
    0 installs
60. ▌
    Ion Mobility Spectrometry Data Interpretation · holobiomicslab

    Use when you have raw ion mobility-mass spectrometry data (drift time and m/z measurements) from DTIMS-MS, TWIMS-MS, or SLIM-based IMS-MS instruments and need to derive collision cross section values for molecular ion characterization. Use it specifically when calibrant standards (e.
    0 installs
61. ▌
    Locality Sensitive Hashing Index Construction · holobiomicslab

    Use when you have a large collection of mass spectrometry spectra (m/z and intensity pairs) and need to perform rapid similarity-based retrieval or clustering without computing all pairwise distances.
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62. ▌
    Machine Learning Based Conformation Filtering · holobiomicslab

    Use when when you have generated multiple 3D conformations for a molecule or set of ionized adducts (e.g., via RDKit) and need to retain only the most energetically favorable structures before expensive quantum calculations.
    0 installs
63. ▌
    Machine Learning Pipeline Integration Testing · holobiomicslab

    Use when you have adapted an ML pipeline (e.g., MSNovelist) to consume a non-standard fingerprint representation (Morgan 4096-bit instead of bundled SIRIUS 6 fingerprints) and need to verify that the model's input layer correctly reshapes and processes the new fingerprint format before committing.
    0 installs
64. ▌
    Mass Spectrometry Feature Similarity Modeling · holobiomicslab

    Use when when you have an untargeted metabolomics dataset with MS2 fragmentation spectra and need to annotate metabolites beyond what reference databases alone provide.
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65. ▌
    Mass Spectrometry Imaging Data Representation · holobiomicslab

    Use when you have raw mass spectrometry imaging data (2D or 3D spatial coordinates with full mass-to-charge spectra) and want to train a probabilistic deep learning classifier for tumor delineation or tissue classification.
    0 installs
66. ▌
    Mass Spectrum Preprocessing And Normalization · holobiomicslab

    Use when when you have raw MS/MS spectra in MGF or mzML/mzXML formats and need to feed them into Casanovo or similar transformer-based de novo sequencing models.
    0 installs
67. ▌
    Matrix Ion Spatial Distribution Visualization · holobiomicslab

    Use when after rMSIcleanup has classified ions as matrix-related or non-matrix, and you need to audit, validate, or communicate the annotation decisions. Use it when overlapping or isobaric peaks are present in the dataset and you must document misclassification risks per annotation.
    0 installs
68. ▌
    Metabolite Prediction Threshold Determination · holobiomicslab

    Use when after training and cross-validating a regression model (e.g., neural network or Elastic Net) that predicts metabolite abundances from microbiome features, you have Spearman correlation coefficients (SCCs) for each metabolite between predicted and observed values.
    0 installs
69. ▌
    Metabolite Vote Counting Qualitative Analysis · holobiomicslab

    Use when you have metabolomic results from multiple studies with only compound identifiers, directional trend labels (up-regulated, down-regulated, or no trend), and bibliographic references — and you want to quantify agreement on metabolite behavior direction across studies without requiring.
    0 installs
70. ▌
    Model Validation On Chromatographic Standards · holobiomicslab

    Use when after training a CNN model on labeled rt×mz two-dimensional areas extracted from LC-HRMS data, use this skill to quantify model performance on a held-out test set of reference chromatograms before deploying the model for peak detection on new samples.
    0 installs
71. ▌
    Molecular Fingerprint Representation Learning · holobiomicslab

    Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES), and need to perform metabolite annotation by ranking candidate compounds based on spectral similarity.
    0 installs
72. ▌
    Multi Way Join Operations On Reference Tables · holobiomicslab

    Use when you have independently cleaned and validated organism, structure, and reference tables (each keyed by organism_id, structure_id, and reference_id respectively) and need to consolidate them into a single denormalized curated table that maintains traceability to the original integrated table.
    0 installs
73. ▌
    Peak Preservation Vs Noise Reduction Tradeoff · holobiomicslab

    Use when you have raw or baseline-corrected mass spectra from MSImagingArrays or MSImagingExperiment objects and need to decide between smoothing methods before peak picking or statistical analysis.
    0 installs
74. ▌
    Preprocessing Pipeline Parameter Optimization · holobiomicslab

    Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d) or UIMF format with jagged peaks and low-abundance ions that require signal enhancement, but you need to decide whether to apply smoothing, and at what strength, to avoid over-smoothing real signals or under-removing artifacts.
    0 installs
75. ▌
    Principal Component Analysis For Metabolomics · holobiomicslab

    Use when after loading a Metaboprep object containing metabolomic abundance data when you need to: (1) identify samples that are statistical outliers in multivariate metabolite space; (2) determine the number of statistically significant principal components;
    0 installs
76. ▌
    Protein Domain Homology Search And Annotation · holobiomicslab

    Use when after predicting coding potential (via CPAT) on differentially expressed isoforms and you need to assign functional annotations based on protein domain homology.
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77. ▌
    Replicate Based Unwanted Variation Estimation · holobiomicslab

    Use when when you have metabolomics data organised across multiple experimental batches with deliberately embedded sample replicates within batches (short replicates) and across batches (batch replicates), and you observe batch effects or signal drift in PCA plots that obscure biological patterns.
    0 installs
78. ▌
    Scaffold Extraction From Molecular Structures · holobiomicslab

    Use when when pre-training or fine-tuning a molecular representation model on natural products and you need to encode scaffold-derived evolutionary patterns as a distinct learning signal. Trigger: input is SMILES strings or molecular graphs from natural product databases (e.
    0 installs
79. ▌
    Signal Quality Enhancement Low Abundance Ions · holobiomicslab

    Use when you observe jagged or noisy peak profiles in low-abundance ions after loading raw IM-MS data (Agilent MassHunter .
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80. ▌
    Signal To Noise Filtering For Peak Candidates · holobiomicslab

    Use when immediately after peak detection in the IDSL.IPA workflow, when you have a list of candidate peaks extracted from EIC data and need to remove noise-dominated signals before downstream peak property evaluation and annotation.
    0 installs
81. ▌
    Singular Value Decomposition Pathway Analysis · holobiomicslab

    Use when when you have a peak intensity matrix (rows = metabolite features, columns = samples) with corresponding compound annotations (peak ID → KEGG/ChEBI ID mapping), and you need to rank pathways or metabolite set groupings (KEGG pathways, Reactome pathways, GNPS Molecular Families, MS2LDA.
    0 installs
82. ▌
    Summarized Experiment Data Structure Handling · holobiomicslab

    Use when you have high-dimensional metabolomics or genomics data stored as a SummarizedExperiment object (e.
    0 installs
83. ▌
    Transcriptome Metabolome Correlation Analysis · holobiomicslab

    Use when you have paired spatial transcriptome and metabolome feature matrices (e.g., from .
    0 installs
84. ▌
    Anndata Object Manipulation And Inspection · holobiomicslab

    Use when after executing a Squidpy spatial analysis function (e.g., gr.spatial_neighbors, gr.nhood_enrichment, gr.sepal, im.
    0 installs
85. ▌
    Git Repository Cloning And Fork Management · holobiomicslab

    Use when you need to set up a local copy of a scientific software project (e.g., Scanpy) to run its test suite, modify source code, or prepare a feature or bugfix contribution. The canonical repository is hosted on GitHub and you do not have direct push access.
    0 installs
86. ▌
    Matplotlib Plot Reference Image Comparison · holobiomicslab

    Use when you need to verify that visualization functions produce graphically correct output that matches previously validated baseline images. Use it as part of automated testing workflows (e.
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87. ▌
    Rna Seq Quantification Selective Alignment · holobiomicslab

    Use when you have paired-end or single-end RNA-seq reads (FASTQ format) and a reference transcriptome (FASTA), and you need to estimate transcript-level abundances (NumReads and TPM per transcript) rather than gene-level counts.
    0 installs
88. ▌
    Sample Metadata Preparation And Assignment · holobiomicslab

    Use when before constructing a DESeqDataSet from any count matrix (whether from tximport, HTSeq, featureCounts, or raw counts). You have sample identifiers (run IDs, file names, or row names) and must link them to condition labels (e.
    0 installs
89. ▌
    Selective Alignment Sensitivity Evaluation · holobiomicslab

    Use when when comparing mapping outputs between two selective-alignment implementations (e.g., C++ vs. Rust port) on byte-identical reference indices and observing a multi-percentage-point gap in mapping rate or read assignments.
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90. ▌
    Seurat Workflow Orchestration For Scrnaseq · holobiomicslab

    Use when you have a raw or Seurat object-backed scRNA-seq expression matrix and need to: (1) stabilize variance across genes with SCTransform normalization, (2) extract feature loadings in reduced dimensionality space via reverse PCA to use as input for GESECA or other coregulation-based enrichment.
    0 installs
91. ▌
    Transcript Abundance Quantification Import · holobiomicslab

    Use when you have transcript abundance files (e.g., Salmon quant.sf.gz, kallisto abundance.h5, RSEM .isoforms.results) from a quantification tool and need to construct a gene-level count matrix for DESeq2 analysis.
    0 installs
92. ▌
    Mass Spectrometry Fragmentation Pattern Modeling · holobiomicslab

    Use when when building a re-usable spectral reference library for lipidomics workflows where you need to match experimental MS/MS spectra against a comprehensive theoretical fragmentation model.
    0 installs
93. ▌
    Kovats Retention Index Extraction And Assignment · holobiomicslab

    Use when you have compiled a multi-source EI library (NIST, RIKEN, MoNA, SWGDRUG) into a single msp object and want to enrich it with experimental retention index metadata. Apply this skill when you have access to NIST library installation files (ri.dat and USER.
    0 installs
94. ▌
    Sample Study Size Stratified Algorithm Selection · holobiomicslab

    Use when when beginning mass alignment in a multi-sample LC-MS metabolomics study, before constructing the MassGrid.
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95. ▌
    Within Batch Randomization By Metadata Attribute · holobiomicslab

    Use when you have already assigned samples to batches (inter-batch balance is fixed) and need to shuffle injection order within each batch to decorrelate sample properties from time-dependent instrumental effects. Use it when your metadata table includes a randomization dimension (e.
    0 installs
96. ▌
    Chromatography Mass Spectrometry Data Processing · holobiomicslab

    Use when when you have raw GC–MS or LC–MS data (m/z vs retention time chromatography-mass spectrometry maps) and need to identify analyte signals and marker features without conventional peak picking;
    0 installs
97. ▌
    Composite Mass Track Assembly And Peak Detection · holobiomicslab

    Use when after mass tracks have been aligned across all samples into a MassGrid (via sample-wise or centroid-based alignment), you have a unified set of m/z features tracked across the entire study.
    0 installs
98. ▌
    Dataset Object Serialization And Deserialization · holobiomicslab

    Use when you have mass spectrometry data arriving through heterogeneous input formats (Task ID from GNPS, Universal Spectrum Identifiers, or Feature-Based Molecular Networking identifiers) and need to load, validate, and store them as a single standardized dataset object for interactive peak.
    0 installs
99. ▌
    Embedding Space Visualization And Interpretation · holobiomicslab

    Use when after training or loading a pre-trained deep learning model that produces high-dimensional embeddings (e.g., 200-dimensional vectors from MS2DeepScore). Use this skill when you have a set of spectra with known chemical class annotations (e.
    0 installs
100. ▌
     Empirical Compound Annotation And Representation · holobiomicslab

     Use when you have a tab-delimited feature table (m/z, retention time, intensities) from LC-MS preprocessing and need to group related ions (isotopologues, adducts, in-source fragments) into compound-level annotations with inferred neutral mass.
     0 installs