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HolobiomicsLab

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1. ▌
   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.
   2 installs
2. ▌
   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.
   2 installs
3. ▌
   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.
   2 installs
4. ▌
   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
5. ▌
   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
6. ▌
   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;
   1 install
7. ▌
   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
8. ▌
   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
9. ▌
   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.
   2 installs
10. ▌
    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.
    2 installs
11. ▌
    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
12. ▌
    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
13. ▌
    Graph Based Link Representation Visualization · holobiomicslab

    Use when after NPLinker computes scored links between genomic and metabolomic entities using a scoring method (e.
    2 installs
14. ▌
    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
15. ▌
    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
16. ▌
    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
17. ▌
    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
18. ▌
    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
19. ▌
    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
20. ▌
    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.
    0 installs
21. ▌
    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.
    2 installs
22. ▌
    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
23. ▌
    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.
    2 installs
24. ▌
    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
25. ▌
    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
26. ▌
    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
27. ▌
    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
28. ▌
    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
29. ▌
    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.
    2 installs
30. ▌
    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.
    2 installs
31. ▌
    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
32. ▌
    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
33. ▌
    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
34. ▌
    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;
    1 install
35. ▌
    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.
    2 installs
36. ▌
    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
37. ▌
    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
38. ▌
    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 .
    0 installs
39. ▌
    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
40. ▌
    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
41. ▌
    Summarized Experiment Data Structure Handling · holobiomicslab

    Use when you have high-dimensional metabolomics or genomics data stored as a SummarizedExperiment object (e.
    2 installs
42. ▌
    Transcriptome Metabolome Correlation Analysis · holobiomicslab

    Use when you have paired spatial transcriptome and metabolome feature matrices (e.g., from .
    2 installs
43. ▌
    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.
    2 installs
44. ▌
    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.
    2 installs
45. ▌
    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.
    0 installs
46. ▌
    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.
    2 installs
47. ▌
    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
48. ▌
    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.
    0 installs
49. ▌
    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
50. ▌
    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.
    2 installs
51. ▌
    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.
    2 installs
52. ▌
    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.
    2 installs
53. ▌
    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.
    0 installs
54. ▌
    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
55. ▌
    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
56. ▌
    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.
    2 installs
57. ▌
    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
58. ▌
    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
59. ▌
    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
60. ▌
    Extracted Ion Chromatogram Peak Shape Similarity · holobiomicslab

    Use when after features have been grouped by retention time similarity and abundance correlation across samples, but before downstream annotation or compound identification.
    0 installs
61. ▌
    Ft Icr Ms Data Preprocessing And Quality Control · holobiomicslab

    Use when when you have raw or processed FT-ICR MS peak-abundance .
    1 install
62. ▌
    High Resolution Mass Spectrometry Interpretation · holobiomicslab

    Use when you have centroided LC- or GC-HRMS data (in mzML format, ideally from data-dependent acquisition) and need to identify potential PFAS candidates from a large feature list.
    0 installs
63. ▌
    Isotopic Envelope Generation At Fixed Enrichment · holobiomicslab

    Use when when you have a peptide sequence, MS2 fragment charge states, and a known isotope enrichment fraction (e.g., 1.
    0 installs
64. ▌
    Machine Learning Model Application To Lipidomics · holobiomicslab

    Use when you have MS-DIAL lipid identifications from an Orbitrap or TOF mass spectrometer and need to remove spurious or low-confidence assignments before downstream metabolomics analysis.
    2 installs
65. ▌
    Mass Binning And Tokenization For Topic Modeling · holobiomicslab

    Use when you have extracted and intensity-normalized fragment ion masses and neutral loss values from MS/MS spectra and need to prepare them for unsupervised topic modeling to discover recurring fragmentation motifs.
    0 installs
66. ▌
    Mass Spectrometry Data Visualization With Pandas · holobiomicslab

    Use when your input is a Pandas DataFrame containing mass spectrometry measurements (m/z and intensity columns for spectra, retention time and intensity for chromatograms, or x, y, z for 2D/3D peak maps) and you need to generate static plots (matplotlib) or interactive web-based visualizations.
    0 installs
67. ▌
    Mass Spectrometry Dataset Handling Preprocessing · holobiomicslab

    Use when you have raw or semi-processed MS/MS spectra in MSP format (e.g., from GNPS, Orbitrap instruments) and need to feed them into MSBERT or similar transformer-based embedding models for library matching, clustering, or similarity scoring.
    0 installs
68. ▌
    Mass Spectrometry Instrument Resolution Modeling · holobiomicslab

    Use when when correcting LC-MS fractional abundances of measured isotopologues (FAM) from isotope labeling experiments where instrument resolution (e.
    0 installs
69. ▌
    Mass Spectrometry Reference Database Integration · holobiomicslab

    Use when you have individual MS/MS spectra or batch .mgf files from untargeted metabolomics experiments and need to search them against domain-specific reference libraries (e.
    2 installs
70. ▌
    Metabolite Feature Extraction And Quantification · holobiomicslab

    Use when after retention-time correction and data alignment have been completed on centroided LC-MS data (mzML or mzXML format).
    0 installs
71. ▌
    Multidimensional Feature Extraction From Spectra · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to transform spectra into fixed-dimensional molecular embeddings for candidate matching against a reference database, especially when direct spectral comparison or classical fingerprinting.
    0 installs
72. ▌
    Neural Network Based Molecular Formula Inference · holobiomicslab

    Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting where spectrum database matching is unavailable or undesirable.
    0 installs
73. ▌
    Peak Intensity Chromatographic Property Analysis · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering) containing m/z, retention time, and peak intensity metrics, and you need to group LC-MS features into clusters to reduce redundancy before parental signal extraction.
    0 installs
74. ▌
    Peptide Modification Representation And Handling · holobiomicslab

    Use when when you have an observed MS/MS spectrum and need to annotate fragment peaks against a known modified peptide sequence. Specifically: (1) you possess a peptide amino acid sequence with known or predicted post-translational modifications at specific positions;
    0 installs
75. ▌
    Python Module Integration And Pipeline Extension · holobiomicslab

    Use when you have developed new scoring logic (e.g., average inchikey score, neighbourhood score) for an MS/MS spectral analogue search tool and need to embed these components into an existing production pipeline that uses a random forest to combine multiple features for candidate re-ranking.
    0 installs
76. ▌
    Quantum Chemistry Based Fragmentation Prediction · holobiomicslab

    Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z values and intensities) to compare against experimental LC-IM-MS/MS data before performing CCS prediction or downstream.
    0 installs
77. ▌
    R Bioconductor Summarizedexperiment Manipulation · holobiomicslab

    Use when when converting raw metabolomics data (tab-delimited text files, Sciex OS exports) into a structured object for batch processing, or when you need to organize compound-level measurements (assays), sample metadata (colData), and feature annotations (rowData) in a single container that.
    0 installs
78. ▌
    Retention Time Calibration Via Lowess Regression · holobiomicslab

    Use when after mass track extraction and alignment across samples, when preparing to detect elution peaks on composite mass tracks. Use this when inter-sample retention time variation exceeds acceptable alignment tolerance (e.
    0 installs
79. ▌
    Spectral Tensor Representation And Preprocessing · holobiomicslab

    Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT. Specifically: you have raw spectral data with variable peak counts and need fixed-size tensor inputs;
    2 installs
80. ▌
    Systematic Mass Calibration And Drift Correction · holobiomicslab

    Use when when processing multiple LC-MS samples in a cohort study and MassGrid construction reveals that anchor mass tracks (13C/12C isotope or Na/H adduct pairs) in non-reference samples deviate systematically from the reference sample's m/z values by >1 ppm.
    0 installs
81. ▌
    Targeted Peak Detection Screening And Validation · holobiomicslab

    Use when you have centroided mzML LC–MS data, a curated list of target compounds (with theoretical m/z, expected retention time, and polarity), and you need to confirm target presence and extract quantitative metrics (area under curve, max intensity, signal-to-noise ratio, peak correlation, point.
    0 installs
82. ▌
    Transition List Formatting For Targeted Analysis · holobiomicslab

    Use when you have generated or assembled a lipid spectral library with precursor m/z values, adduct information, and fragmentation patterns, and you need to import those spectra into Skyline for targeted data-independent or parallel-reaction-monitoring (PRM) analysis.
    1 install
83. ▌
    Molecular Structure Prediction Out Of Distribution · holobiomicslab

    Use when your goal is to assess whether a pretrained NMR2Struct model trained on molecules ≤19 heavy atoms can generalize to larger, more complex molecules, or whether accuracy degrades significantly.
    0 installs
84. ▌
    Environment Validation And Verification · holobiomicslab

    Use when after installing ENPKG or any component of the workflow via conda/pip dependency manifests and before executing workflow scripts.
    0 installs
85. ▌
    File Path Abstraction And Normalization · holobiomicslab

    Use when a Shiny application or R package is confirmed to work on one OS (e.g., Windows only) but fails to initialize or run on others due to unresolved file path conventions, system library calls, or OS-specific package dependencies.
    0 installs
86. ▌
    Hypergeometric Distribution Calculation · holobiomicslab

    Use when when you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying sizes, and you need to make those scores comparable across links with different GCF sizes (#G), MF sizes (#m), and.
    0 installs
87. ▌
    Installation Validation And Diagnostics · holobiomicslab

    Use when after installing a package via conda or pip from a distribution channel (e.g., Bioconda, PyPI), run this skill to confirm the installation succeeded and that critical submodules are importable before proceeding to use the package in analysis workflows.
    2 installs
88. ▌
    Metabolic Gap Filling Community Context · holobiomicslab

    Use when you have consensus metabolic reconstructions for all members of a microbial or plant community (e.
    2 installs
89. ▌
    Molecular Ccs Prediction Model Training · holobiomicslab

    Use when you have a curated dataset of small molecules with SMILES, optional 3D coordinates, adduct information, and experimentally measured CCS values (in Ångströms or similar units), and you want to train a GNN model to predict CCS on held-out test molecules.
    0 installs
90. ▌
    Ms Signal Correction Strategy Selection · holobiomicslab

    Use when you have loaded raw MS intensity tables into QuantyFey and observe or suspect intensity drift artifacts across your measurement sequence. Drift is especially likely in long-running targeted MS experiments where calibration curves or internal standards show systematic variation over time.
    0 installs
91. ▌
    Natural Product Chemical Representation · holobiomicslab

    Use when you have a set of natural product molecules (or suspected natural products) in SMILES, InChI, or SDF format and need a chemical representation suitable for biosynthetic classification, structural screening, or machine learning tasks where standard generic fingerprints (e.
    0 installs
92. ▌
    Neural Network Projection Module Design · holobiomicslab

    Use when when you have 512-dimensional (or other fixed-size) representation vectors output from paired encoders processing augmented versions of the same input (e.
    2 installs
93. ▌
    Nps Structural Diversity Stratification · holobiomicslab

    Use when you have a trained PS2MS deep learning model, a set of evaluation compounds (especially novel NPS analogues), and want to understand whether prediction confidence (softmax probabilities, uncertainties) degrades gracefully or sharply as structural distance from the training set increases.
    2 installs
94. ▌
    Pathway Database Filtering By Detection · holobiomicslab

    Use when you have run a metabolomics experiment with incomplete coverage of a reference pathway database (e.g., 10–100% of database metabolites detected), and you plan to use ORA for pathway enrichment. The skill is essential if your detection method has known sensitivity limits (e.
    0 installs
95. ▌
    Plotly 3d Surface Scatter Visualization · holobiomicslab

    Use when you have mass spectrometry data (m/z, retention time, intensity) loaded into a Pandas DataFrame and need to explore the full 3D structure of a peak map interactively, particularly when static 2D heatmaps obscure important intensity relationships or when stakeholders require browser-based.
    1 install
96. ▌
    Pooled Statistical Significance Testing · holobiomicslab

    Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test whether a combined scoring strategy (e.
    0 installs
97. ▌
    Python Class Design With Dunder Methods · holobiomicslab

    Use when when you need to enable bracket notation (e.g., handler[5]) for random access to blocks within a large compressed or remote data source, or when you want to support both random access and sequential iteration over data without materializing all records upfront.
    0 installs
98. ▌
    Python Package Installation From Source · holobiomicslab

    Use when when you need to verify a Python package installs successfully from a cloned or local repository, validate that all tests pass after installation, or prepare a development environment for contributing to the package.
    0 installs
99. ▌
    Regression Model Evaluation Mae Metrics · holobiomicslab

    Use when when you have trained a regression model on experimental retention times or similar continuous molecular property predictions and need to quantify its generalization performance on held-out test data.
    0 installs
100. ▌
     State Dict Serialization And Extraction · holobiomicslab

     Use when after training a multi-component neural network architecture (e.
     0 installs