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HolobiomicsLab

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1. ▌
   Format Conversion Conditional Logic 2 · holobiomicslab

   Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass spectrometry analysis on either an Orbitrap (via Excalibur DDA) or via Skyline's transition-based workflow.
   0 installs
2. ▌
   High Resolution Ms2 Peak Assignment 2 · holobiomicslab

   Use when you have high-resolution MS2 data in .ms2 format from lipid A samples and need to perform automated structure annotation to identify lipid A molecular variants and their fragmentation patterns at scale.
   0 installs
3. ▌
   Hplc Column Parameter Normalization 2 · holobiomicslab

   Use when when you have raw HPLC column specifications from RepoRT or similar metadata repositories and need to prepare them as input features for machine learning models. Apply this skill before featurizing molecular structures or training graph transformers for retention time prediction.
   2 installs
4. ▌
   Identity Search Spectrum Annotation 2 · holobiomicslab

   Use when you have experimental MS/MS spectra and need to assign definitive molecular identities by matching against a curated spectral library.
   2 installs
5. ▌
   Intensity Vector Manipulation Numpy 2 · holobiomicslab

   Use when you have extracted mass tracks (EICs) from multiple LC-MS samples aligned into a MassGrid structure, and you need to combine their intensity vectors into a single composite intensity vector for peak detection on the aggregate signal rather than per-sample.
   0 installs
6. ▌
   Interactive Data Exploration Design 2 · holobiomicslab

   Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs. serum, cohort identifiers) and need to interactively explore how variation in processing conditions drives changes in metabolic.
   0 installs
7. ▌
   Interference Profile Identification 2 · holobiomicslab

   Use when after running saturation repair or multidimensional smoothing on IM-MS data when you need to validate whether corrected peaks are reliable or whether overlapping coeluting/comobiling ions may have caused incorrect signal reconstruction.
   0 installs
8. ▌
   Ion Adduct Isotope Pattern Matching 2 · holobiomicslab

   Use when you have a preprocessed feature table (m/z, retention time, intensities) from LC-MS and need to group features into empirical compounds.
   0 installs
9. ▌
   Ion Mobility Feature Classification 2 · holobiomicslab

   Use when you have high-dimensional TWIM-MS data (arrival time and m/z dimensions) from a multi-omic sample and need to associate experimental features with biomolecular classes *before* running peak detection or feature identification pipelines.
   0 installs
10. ▌
    Isotopologue Mass Delta Calculation 2 · holobiomicslab

    Use when when constructing a reference mass-matching framework for untargeted metabolomics or isotope-tracing LC-MS data, before pattern-matching observed features to isotopic and adduct variants.
    0 installs
11. ▌
    Mass Spectral Relationship Matching 2 · holobiomicslab

    Use when after peak detection and feature table generation when you have a collection of m/z, retention time, and intensity values and need to identify which features are related variants (isotopes, adducts, or fragments) of the same parent compound.
    0 installs
12. ▌
    Mass Spectrometry Adduct Annotation 2 · holobiomicslab

    Use when you have tabulated pairwise mass differences from a MALDI-MS imaging dataset (via massdiff()) and need to identify which observed mass differences correspond to known chemical adducts (e.g., [M+H]+, [M+Na]+, [M-H2O]+).
    0 installs
13. ▌
    Msms Spectrum Metadata Preservation 2 · holobiomicslab

    Use when removing invalid or malformed entries (e.g., SMILES validation, format errors) from large spectral datasets (GNPS, MoNA, MTBLS1572, MassBank).
    0 installs
14. ▌
    Msp File Parsing Edge Case Handling 2 · holobiomicslab

    Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final dataset or explicitly logged with a reason for exclusion.
    0 installs
15. ▌
    Natural Product Database Validation 2 · holobiomicslab

    Use when after curating and integrating structure-organism pairs from multiple source databases, and before publishing or using the dataset for computational research. Apply this skill when you have aggregated organism counts binned by structural diversity (e.
    2 installs
16. ▌
    Network Based Functional Prediction 2 · holobiomicslab

    Use when you have an untargeted metabolomics feature table with m/z values, retention times, intensity measurements, and p-values from statistical testing, but lack or wish to bypass metabolite identification.
    1 install
17. ▌
    Numeric Array Round Trip Validation 2 · holobiomicslab

    Use when after implementing or modifying a numerical compression codec (such as MSNumpressCoder for m/z and intensity arrays in mass-spectrometry workflows) to verify that round-trip encode–decode cycles preserve numerical values within expected tolerance.
    0 installs
18. ▌
    Poisson Noise Injection For Imaging 2 · holobiomicslab

    Use when augmenting mass spectrometry ion images for contrastive learning, particularly when the model must generalize across different detector conditions or signal-to-noise ratios.
    2 installs
19. ▌
    Pre Analytical Delay Stratification 2 · holobiomicslab

    Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect metabolic parameter stability within a plasma or serum sample cohort.
    0 installs
20. ▌
    Response Status Code Interpretation 2 · holobiomicslab

    Use when when you need to confirm that a documented web service endpoint is deployed and accessible before using it for analysis, or when troubleshooting tool availability in a bioinformatics pipeline. Apply this skill after obtaining a service URL (e.
    2 installs
21. ▌
    Retention Time Intensity Tabulation 2 · holobiomicslab

    Use when when you have a resolved mzML or mzXML spectrum file and need to visualize or analyze the temporal intensity profile of a specific analyte (defined by its m/z value).
    0 installs
22. ▌
    Sample Information Metadata Parsing 2 · holobiomicslab

    Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
    0 installs
23. ▌
    Spectral Correlation Interpretation 2 · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a prominent but structurally ambiguous peak.
    2 installs
24. ▌
    Spectral Entropy Quality Assessment 2 · holobiomicslab

    Use when after feature detection and alignment in untargeted MS data processing, when you need to filter or rank candidate metabolite annotations by spectral quality before committing to xenobiotic metabolite assignments. Use when combining fragmentation similarity scores (e.
    0 installs
25. ▌
    Spectral Library Record Structuring 2 · holobiomicslab

    Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, molecular weight, annotation fields) that you need to bind together into a queryable spectral library record for local compound.
    0 installs
26. ▌
    Two Dimensional Ms Image Processing 2 · holobiomicslab

    Use when you have raw GC–MS or LC–MS data represented as a two-dimensional map (m/z axis vs. retention time axis) and need to identify chemo-/biomarker features across multiple analytes simultaneously, especially when conventional peak picking produces high false-positive or false-negative rates.
    2 installs
27. ▌
    Untargeted Lc Ms Data Preprocessing 2 · holobiomicslab

    Use when when you have raw untargeted LC-MS metabolomics data and need to detect low-quality or mis-integrated peaks in an XCMS-processed xcmsSet object before performing metabolite annotation, statistical analysis, or biomarker discovery.
    1 install
28. ▌
    Weighted Loss Function Optimization 2 · holobiomicslab

    Use when when training a dual-encoder architecture (bi-encoder + cross-encoder) on NMR spectral data where independent encoding and joint pair processing produce competing or imbalanced gradient signals.
    0 installs
29. ▌
    Mass Spectrum Peak Detection 2 · holobiomicslab

    Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct infusion MS (DI-MS), ASAP-MS, or other high-throughput ambient ionization methods, and need to identify which m/z signals represent true peaks of interest rather than noise or baseline drift.
    0 installs
30. ▌
    Peak Labeling And Annotation 2 · holobiomicslab

    Use when immediately after automatic peak detection on a raw or processed MS spectrum when you have a list of candidate peaks with m/z and intensity values but lack systematic identifiers, confidence estimates, or ranked ordering.
    0 installs
31. ▌
    Force Field Minimization Mmff94 2 · holobiomicslab

    Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum calculations.
    2 installs
32. ▌
    Data Type Constraint Verification 2 · holobiomicslab

    Use when when ingesting or updating MassBank records in plain-text or structured format, and you need to verify that metadata fields (accession, name, formula, mass, spectrum peaks) comply with type definitions, presence requirements, and allowed value ranges.
    0 installs
33. ▌
    Docker Volume Mount Configuration 2 · holobiomicslab

    Use when deploying the ipbhalle/metfragweb container and you need to supply custom MetFrag settings (ChemSpider tokens, proxy servers, local database connections) without modifying the container image.
    0 installs
34. ▌
    Fatty Acid Composition Generation 2 · holobiomicslab

    Use when you need to systematically enumerate all possible lipid species within a defined analytical scope—specifically when you have specified one or more lipid classes (e.g., phosphatidylcholine, triacylglycerol) and fatty acid composition ranges (e.
    0 installs
35. ▌
    Github Actions Workflow Execution 3 · holobiomicslab

    Use when you have a GitHub repository containing scientific records (e.
    2 installs
36. ▌
    Hash Based Deduplication Workflow 2 · holobiomicslab

    Use when when processing open mass spectrometry library (OMSL) data that may contain duplicate spectral records (e.
    1 install
37. ▌
    Lipid Metadata Annotation Mapping 2 · holobiomicslab

    Use when when exporting in-memory generated spectra as MSP-format spectral libraries, you must first map each spectrum record to required MSP fields (NAME, PRECURSORMZ, SPECTRUM) and optional metadata annotations.
    0 installs
38. ▌
    Hdf5 Cardinal Format Preservation 2 · holobiomicslab

    Use when after performing isotopic correction, quantitation, or other pixel-level transformations on a feature-by-pixel intensity matrix imported from an imzML file via Cardinal's HDF5 layout.
    0 installs
39. ▌
    Hdf5 File Structure Specification 2 · holobiomicslab

    Use when when exporting quantified MSI data (feature-by-pixel intensity matrices with associated ion m/z, lipid annotations, and pixel spatial coordinates) from LipidQMap and you need to produce a standards-compliant HDF5 container that can be read by Cardinal and other MSI analysis tools.
    0 installs
40. ▌
    Lipid Feature Identifier Matching 2 · holobiomicslab

    Use when you have an isotope-corrected or raw MSI dataset stored in HDF5 format following Cardinal::HDF5 conventions, a user-provided internal standard definition (sample identifier and/or feature name), and need to locate and extract the intensity row for that lipid before performing ratio-based.
    2 installs
41. ▌
    Lipid Nomenclature Simplification 2 · holobiomicslab

    Use when you have spatial metabolomics data with semicolon-delimited isomer name annotations (such as the 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to reduce annotation complexity before pathway analysis, statistical testing, or visualization.
    2 installs
42. ▌
    Mass Difference Network Construction 2 · holobiomicslab

    Use when you have a filtered peak list (CSV with m/z values and assigned molecular formulas) from FT-ICR MS and want to infer biochemical transformations occurring in microbial or environmental samples.
    2 installs
43. ▌
    Mass Spectrometry Data Preprocessing 2 · holobiomicslab

    Use when you have raw mass spectra or processed feature matrices from liquid chromatography–mass spectrometry (LC-MS) or direct infusion MS that must be ingested by a deep learning model for substance identification.
    2 installs
44. ▌
    Spectrum Vector Similarity Searching 2 · holobiomicslab

    Use when you have millions of MS/MS spectra represented as low-dimensional vectors (via feature hashing) and need to compute pairwise distances only between similar spectra rather than comparing every spectrum to every other spectrum.
    0 installs
45. ▌
    2d Nmr Pulse Sequence Implementation 2 · holobiomicslab

    Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and spin-system J-coupling data, and you want to simulate realistic peak patterns including indirect-dimension evolution and phase.
    0 installs
46. ▌
    Activity Score Robustness Assessment 2 · holobiomicslab

    Use when after computing PLAGE-derived activity scores for pathways or metabolite sets (Molecular Families, Mass2Motifs) from log2-standardized metabolomics intensity data.
    0 installs
47. ▌
    Bayesian Meta Learning Model Fitting 2 · holobiomicslab

    Use when you have a pre-trained DNN RT predictor (e.g., trained on METLIN SMRT with 80,038 experimental RTs) and need to adapt it to predict retention times in a new or external chromatographic method for which you have only 10–50 calibration molecules with known RTs.
    0 installs
48. ▌
    Categorical Grouping And Aggregation 2 · holobiomicslab

    Use when you have a flat table of structure-organism pairs or entity records and need to summarize their distribution across categorical bins (e.g., organism counts binned by number of associated structures in categories: 1, 1–10, 10–100, >100).
    0 installs
49. ▌
    Chemical Database Query And Matching 2 · holobiomicslab

    Use when when you have mass-to-charge (m/z) values from mass spectrometry imaging or other MS experiments and need to assign molecular formulae with high precision, especially in spatially-resolved metabolomics where traditional LC-MS annotation methods are insufficient.
    2 installs
50. ▌
    Coefficient Of Variation Computation 2 · holobiomicslab

    Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association modeling.
    2 installs
51. ▌
    Cosine Similarity Matrix Computation 2 · holobiomicslab

    Use when after generating normalized dense embeddings for both query and reference MS/MS spectra using a pre-trained model like SpecEmbedding.
    2 installs
52. ▌
    Detection Limit Threshold Definition 2 · holobiomicslab

    Use when when preparing metabolomics abundance tables with left-censored missingness (values below instrument detection limit or quantification limit) for imputation.
    0 installs
53. ▌
    Few Shot Learning Calibration Design 2 · holobiomicslab

    Use when you have experimental retention times measured on a source chromatographic method and want to predict RTs on a target chromatographic method, but possess only a small set (10–100) of molecules with ground-truth measurements on both methods.
    0 installs
54. ▌
    Fragmentation Pattern Classification 2 · holobiomicslab

    Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
    0 installs
55. ▌
    Graph Based Knowledge Representation 2 · holobiomicslab

    Use when annotating metabolites in untargeted metabolomics experiments where both established biochemical pathways and experimental MS2 similarity patterns must be simultaneously leveraged.
    2 installs
56. ▌
    Heterogeneous Graph Embedding Design 2 · holobiomicslab

    Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time prediction across different chromatographic columns, methods, or conditions).
    2 installs
57. ▌
    Hit Metric Evaluation Fold Averaging 2 · holobiomicslab

    Use when when you have a trained MS/MS spectral embedding model and need to measure compound identification accuracy on a held-out test set, but want to mitigate sensitivity to a single random train/test split. Use this skill if the original training set split is fixed (e.
    2 installs
58. ▌
    Ion Mobility Dimension Interpolation 2 · holobiomicslab

    Use when when processing raw IM-MS data (Agilent MassHunter .
    2 installs
59. ▌
    Isotope Adduct Anchor Identification 2 · holobiomicslab

    Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a cohort.
    2 installs
60. ▌
    Kegg Pathway Prediction From Spectra 2 · holobiomicslab

    Use when you have untargeted MS2 spectral data (in MS2MP-compatible format) and need to assign KEGG pathway annotations to unknown metabolites.
    2 installs
61. ▌
    Left Censored Missingness Simulation 2 · holobiomicslab

    Use when when you have a complete metabolomics abundance table (e.g., targeted LC/MS or untargeted GC/MS counts) and need to generate synthetic left-censored missingness for evaluating imputation algorithm performance.
    0 installs
62. ▌
    Lineshape Convolution And Broadening 2 · holobiomicslab

    Use when after generating theoretical spin multiplets for individual metabolites via first-order or density-matrix NMR simulation, but before combining spectra or applying Fourier transformation.
    0 installs
63. ▌
    M Z Alignment And Mass Grid Assembly 2 · holobiomicslab

    Use when when processing multiple centroided mzML LC-MS files from the same study and you need to identify which mass tracks represent the same metabolite across samples.
    0 installs
64. ▌
    Mass Spectrometry Data Normalization 2 · holobiomicslab

    Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed peak information into a transformer-based spectral embedding model that expects normalized, fixed-length tensor inputs.
    0 installs
65. ▌
    Mass Spectrometry Data Preprocessing 3 · holobiomicslab

    Use when you have raw LCMS data in mzML or mzXML format from DDA, DIA, or fullscan analyses and need to extract metabolite features with unified m/z, retention time, and intensity values across multiple samples before performing MS2 annotation or in-source fragment analysis.
    0 installs
66. ▌
    Mass Spectrometry Spectral Alignment 2 · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally modified variant of that compound—and you need to identify which atoms in the structure likely bear the modification.
    2 installs
67. ▌
    Massgrid Construction And Validation 2 · holobiomicslab

    Use when after individual mass tracks (EICs) have been extracted from each sample's mzML file and you need to create a unified, cross-sample m/z reference structure. Triggered when: (1) you have ≥2 samples in a cohort; (2) mass tracks have been binned at 0.
    0 installs
68. ▌
    Metabolic Network Graph Construction 2 · holobiomicslab

    Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensities) and aim to predict functional pathway activity without explicit metabolite identification.
    0 installs
69. ▌
    Metabolite Quality Metric Assessment 2 · holobiomicslab

    Use when after drift correction has been applied to a MetaboSet object, and before imputation and batch correction.
    0 installs
70. ▌
    Metabolomics Data Structure Handling 2 · holobiomicslab

    Use when you have metabolomics data already formatted as a SummarizedExperiment object containing multiple assays (raw counts, log-transformed, imputed, or normalized versions) and need to access specific assay layers alongside batch annotation metadata to perform comparisons (e.
    0 installs
71. ▌
    Metabolomics Intensity Normalization 2 · holobiomicslab

    Use when your input is a raw metabolomics intensity matrix (compounds × samples) with known batch assignment and QC sample labels, and you observe signal drift across the analytical sequence or batch-to-batch variation.
    0 installs
72. ▌
    Missing Data Mechanism Specification 2 · holobiomicslab

    Use when when you have a metabolomics abundance table with missing values and need to decide which imputation method to apply, or when designing a simulation to evaluate imputation performance.
    0 installs
73. ▌
    Ms Adduct Annotation And Recognition 2 · holobiomicslab

    Use when when processing LC-MS peak tables from isotope tracing experiments where multiple ionization adducts ([M+H]+, [M+Na]+, [M+NH4]+, etc.) and in-source fragments have generated redundant features at different m/z values that represent the same underlying metabolite.
    0 installs
74. ▌
    Neural Network Hyperparameter Tuning 2 · holobiomicslab

    Use when when training a multilayer perceptron to predict metabolomic features from microbiome abundances, you need dataset-specific hyperparameter configurations because prediction performance (Spearman correlation and well-predicted metabolite counts) varies substantially across microbiome.
    0 installs
75. ▌
    Nmr Metabolite Identity Confirmation 2 · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
    0 installs
76. ▌
    Organism Count Distribution Analysis 2 · holobiomicslab

    Use when you have a flat file of structure-organism pairs (e.
    2 installs
77. ▌
    Parent Product Relationship Tracking 2 · holobiomicslab

    Use when when you have applied biotransformation rules to generate candidate product structures from a set of input molecules (represented as SMILES strings) and need to document which product structures were derived from which parent structures.
    0 installs
78. ▌
    Peak Quality Classifier Optimization 2 · holobiomicslab

    Use when after calculating 12 peak-quality metrics on a development set of extracted ion chromatograms (EICs) and labeled peaks, when you need to select both the classification algorithm and its optimal hyperparameters before training a final model on held-out test data.
    2 installs
79. ▌
    Plate Layout Parameter Configuration 2 · holobiomicslab

    Use when after uploading a sample list to InjectionDesign and before performing inter-batch balancing and intra-batch randomization.
    0 installs
80. ▌
    Ppm Error Validation In Metabolomics 2 · holobiomicslab

    Use when when annotating m/z features from Cardinal MSImagingExperiment objects or LC-MS datasets against metabolite databases (HMDB, Lipidmaps) and you need to exclude matches where the mass difference exceeds your instrumental accuracy or analysis tolerance.
    0 installs
81. ▌
    Prominence Controlled Peak Selection 2 · holobiomicslab

    Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing prominence values and need to reduce the number of detected features while maintaining signal quality.
    2 installs
82. ▌
    Repository Structure Standardization 2 · holobiomicslab

    Use when a scientific Python package is being moved to a new GitHub organization with different structural conventions (e.g., from a personal lab account to a community-led organization like metabolomics-cloud or scverse).
    0 installs
83. ▌
    Retention Time Correlation Filtering 2 · holobiomicslab

    Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts with characteristic mass shifts, neutral loss fragments) from noise or unrelated peaks.
    2 installs
84. ▌
    Rsd Threshold Parameter Optimization 2 · holobiomicslab

    Use when when preparing XCMS peak tables for quality classification and you observe that the default RSD threshold (0.3 or 30%) is either too permissive (retaining noisy EICs) or too stringent (discarding valid signals).
    2 installs
85. ▌
    Spectral Library Matching Annotation 2 · holobiomicslab

    Use when you have MS2 spectral data (precursor m/z, retention time, and fragment ion patterns) from UPLC-HRMS analysis of environmental or biological samples and need to assign compound identities by comparing against known reference spectra.
    0 installs
86. ▌
    Spectral Neutral Loss Transformation 2 · holobiomicslab

    Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment ions) rather than absolute m/z values.
    0 installs
87. ▌
    Sterol Lipid Isomer Characterization 2 · holobiomicslab

    Use when you have LC-IM-MS/MS experimental data (raw mzML or vendor format) containing signals from N-Me derived unsaturated sterol lipids and need to assign double-bond positions and stereochemistry to individual sterol isomers rather than sum compositions.
    0 installs
88. ▌
    Tsv CSV File Parsing And Aggregation 2 · holobiomicslab

    Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique structures, unique organisms, or enumerate source database identifiers to validate or report dataset scale.
    2 installs
89. ▌
    Web Application Documentation Mining 2 · holobiomicslab

    Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you need to produce a machine-readable inventory of those applications with verified live URLs and associated publications for.
    0 installs
90. ▌
    Ion Mobility Feature Engineering 2 · holobiomicslab

    Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction. Specifically, use it when you are preparing data to fit or apply a machine learning model (e.g., Sklearn v1.0.
    0 installs
91. ▌
    Polarizability Tensor Extraction 2 · holobiomicslab

    Use when after ASE-ANI has filtered conformers to remove high-energy geometries, and you need to compute electronic properties required for CCS prediction.
    0 installs
92. ▌
    Database Record Conditional Update 2 · holobiomicslab

    Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field (e.g., ionmode: 'pos'/'neg') that can deterministically populate the missing field.
    0 installs
93. ▌
    Recursive Algorithm Implementation 2 · holobiomicslab

    Use when after peak detection on LC/HRMS data (mzXML, mzML, netCDF formats) when m/z values require refinement for improved mass accuracy in untargeted metabolomics workflows.
    0 installs
94. ▌
    Autoencoder Encoder Decoder Design 2 · holobiomicslab

    Use when when working with imaging mass spectrometry (IMS) datasets where you need to extract latent low-dimensional peak features from high-dimensional peak intensity data while preserving spatial adjacency information.
    1 install
95. ▌
    Imaging Data Workspace Integration 2 · holobiomicslab

    Use when you have paired cdf files (raw mass spectrometry imaging data) and Matlab workspace (.mat) files for the same root sample, and you need to reproduce published linear-axis imaging analysis results (e.g., per-root mass spectrometry imaging metrics along a developmental or spatial axis).
    0 installs
96. ▌
    Keras Tensorflow Model Compilation 2 · holobiomicslab

    Use when you have defined a Keras model architecture (convolutional and dense layers) accepting raw mass spectrometry imaging data tensors and need to prepare it for training on tumor/non-tumor probabilistic classification without prior peak picking.
    0 installs
97. ▌
    Msi Intensity Matrix Normalization 2 · holobiomicslab

    Use when after isotope correction when you have extracted intensity matrices from imzML or HDF5 MSI data and need to convert raw or isotope-corrected ion-image intensities into quantified values using a known internal standard lipid species.
    2 installs
98. ▌
    Corpus Size Coverage Scaling Analysis 2 · holobiomicslab

    Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's learned peak embeddings sufficiently represent the peaks in your query spectra.
    0 installs
99. ▌
    Mass Spectrometry Data Format Parsing 2 · holobiomicslab

    Use when you have raw mass spectrometry instrument output (mzML, vendor binary formats, or mzPeak archives) and need to load spectrum metadata, chromatogram data, or signal arrays into memory for quality control, format conversion, or statistical analysis.
    2 installs
100. ▌
     Neutral Loss Extraction And Weighting 2 · holobiomicslab

     Use when you have a collection of annotated MS/MS spectra with precursor m/z values and fragment peak lists, and you aim to train or apply a spectral similarity model (such as Spec2Vec Word2Vec) that exploits fragmentation chemistry.
     0 installs