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HolobiomicsLab

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1. ▌
   Peak Validation Synthetic Data · holobiomicslab

   Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax or mzapy.peaks.find_peaks_1d_gauss) on synthetic mass spectra with known peak locations and heights.
   0 installs
2. ▌
   Pip Requirements File Creation · holobiomicslab

   Use when you have identified all pinned software dependencies for a Python project (typically from README, setup.py, or environment documentation) and need to create a machine-readable artifact that can reliably reconstruct that exact environment.
   0 installs
3. ▌
   Pubchem Cross Reference Lookup · holobiomicslab

   Use when you have metabolite or compound identifiers in mixed formats (chemical name, InChI, InChIKey, SMILES) across multiple studies or datasets and need to: (1) unify them to a single canonical identifier (PubChem ID) for deduplication, (2) detect and resolve duplicate entries that differ only.
   2 installs
4. ▌
   Quantile Normalization Rna Seq · holobiomicslab

   Use when apply quantile normalization after filtering a Salmon-derived count matrix for low-abundance features using edgeR, and before batch-effect correction or differential expression analysis.
   1 install
5. ▌
   Quantum Input File Preparation · holobiomicslab

   Use when you have a set of RDKit-generated conformers ranked by ASE-ANI single-point energies, and you need to submit the lowest-energy subset to quantum software (e.g. QUICK) for CCS-relevant electronic structure calculations.
   0 installs
6. ▌
   Reference Database Maintenance · holobiomicslab

   Use when when preparing to run compound metadata enrichment or structure queries, check whether your reference databases (LOTUS, DrugBank, DrugCentral) are stale or missing.
   0 installs
7. ▌
   Regression Accuracy Assessment · holobiomicslab

   Use when after fitting linear regression models to relate peak area intensities to known concentrations in targeted metabolomics curves (standard samples and quality control replicates).
   0 installs
8. ▌
   Relative Abundance Calculation · holobiomicslab

   Use when after generating a frequency count table (e.g., from count_fold_changes output showing numbers of increased vs. decreased metabolites by class) and before creating proportional visualizations (pie charts, stacked bar plots).
   1 install
9. ▌
   Repeated Measures Anova Design · holobiomicslab

   Use when you have an imputed, long-format metabolomics dataset with repeated measurements (multiple time points) per subject, a categorical grouping variable (e.
   0 installs
10. ▌
    REST API Endpoint Construction · holobiomicslab

    Use when you have pre-trained neural network models (e.g., Keras/TensorFlow) for chemical classification and need to expose them as a queryable HTTP service.
    0 installs
11. ▌
    Retention Time Range Filtering · holobiomicslab

    Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs, focus on a known analyte window, or reduce file size for faster processing.
    0 installs
12. ▌
    Rule Set Ranking And Selection · holobiomicslab

    Use when when you have a large set of generalized reaction rules (e.
    0 installs
13. ▌
    S4 Class Extension Development · holobiomicslab

    Use when you need to create a new backend for the Spectra package that provides MS data from a new source (file format, database, or computational resource) not covered by existing backends (MsBackendMzR, MsBackendMemory, MsBackendSql, etc.).
    0 installs
14. ▌
    Sdf Compound Structure Parsing · holobiomicslab

    Use when when you have fragment records (experimental or predicted) with compound identifiers or cross-reference fields that need to be validated against a reference compound database in SDF format.
    0 installs
15. ▌
    Simulation Result Reproduction · holobiomicslab

    Use when when you have access to a study's source repository containing executable simulation code in a Jupyter notebook, and you need to validate that the reported ORA results can be regenerated from the provided Python implementation.
    0 installs
16. ▌
    Smiles Adduct Form Enumeration · holobiomicslab

    Use when when you have SMILES structures of small organic molecules and need to predict CCS values for metabolite annotation in untargeted mass spectrometry workflows. Specifically, apply this skill when the same chemical entity may appear in multiple ionization states (e.
    0 installs
17. ▌
    Software Mode Routing Dispatch · holobiomicslab

    Use when you are preparing to run LipidMatch or FluoroMatch and need to select the correct analysis mode for your sample type: lipid profiling, Tween-positive surfactant analysis, or PFAS (per- and polyfluoroalkyl substances) analysis.
    0 installs
18. ▌
    Source Code Repository Cloning · holobiomicslab

    Use when you need to obtain the full source code of a scientific tool (such as LipidSpace) to build it locally, verify cross-platform compilation, inspect the codebase structure, or set up a development environment.
    0 installs
19. ▌
    Spatial Overlap Quantification · holobiomicslab

    Use when you have two co-registered LA-ICP-MS element channel images and need to determine whether their spatial distributions are correlated.
    0 installs
20. ▌
    Spectral Peak Fitting Gaussian · holobiomicslab

    Use when you have 1D MS signal data (extracted ion chromatograms, arrival time distributions, or intensity profiles) and need to resolve overlapping or closely-spaced peaks with accurate position, height, and width estimates.
    0 installs
21. ▌
    Spectral Similarity Validation · holobiomicslab

    Use when after training a Word2vec model on tokenized mass spectra and converting reference spectra into fixed-length embedding vectors, use this skill to confirm that the embedding space preserves spectral similarity before deploying it for spectrum matching.
    0 installs
22. ▌
    Statistical Test Configuration · holobiomicslab

    Use when after data transformation, normalization, and filtering are complete, and you have assigned experimental groups (main effects, covariates, pairing structure).
    1 install
23. ▌
    Structured Data Table Creation · holobiomicslab

    Use when you have obtained a raw reference library file (such as the DTCCS_N2 library for U13C labeled lipids) and need to validate its structure, verify that all expected lipid entries are present, and ensure CCS values fall within physically plausible ranges (typically 50–300 Ų for small lipids).
    0 installs
24. ▌
    Suspect List Format Conversion · holobiomicslab

    Use when you have generated a set of transformation products (TPs) from one or more parent compounds using generateTPs (via BioTransformer, CTS, or PubChemLite library algorithms) and need to screen for these TPs in your LC-HRMS feature data.
    0 installs
25. ▌
    Technical Variation Assessment · holobiomicslab

    Use when when you have a preprocessed metabolomics matrix (log2-scaled, CSV format with batch identifiers in the first column) and need to determine whether technical variation is present, which correction model (ber, ber-bagging, parametric ComBat, or non-parametric ComBat) performs on your.
    2 installs
26. ▌
    Tissue Background Segmentation · holobiomicslab

    Use when you have loaded a laser ablation ICP-MS image into pew² and need to distinguish tissue signal from instrument background or non-ablated substrate.
    0 installs
27. ▌
    Topic Modeling Lda Application · holobiomicslab

    Use when you have redundancy-filtered, tokenized BGCs (each gene represented as a Pfam domain or subPfam combination) and you want to identify fine-grained gene sub-clusters whose membership is driven by co-occurrence patterns of protein domains rather than statistical significance alone.
    0 installs
28. ▌
    Vendor Format Routing Dispatch · holobiomicslab

    Use when you have a collection of raw mass spectrometry data files from multiple instrument vendors (Agilent, Bruker, Thermo) and/or mzML exports that need to be converted to a standardized, cross-platform format for downstream software development, AI research, or multi-vendor meta-analysis.
    0 installs
29. ▌
    Vocabulary Coverage Validation · holobiomicslab

    Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before deploying the unified vocabulary in a language model.
    0 installs
30. ▌
    Workflow Configuration Parsing · holobiomicslab

    Use when you have a workflow.csv file co-located with sequence.csv in a SmartPeak session directory and need to load a default or custom workflow configuration into an executable command sequence.
    0 installs
31. ▌
    Feature Based Molecular Networking And Propagation Workflow · holobiomicslab bundle

    Use when you have untargeted LC-MS/MS MS2 data and want to spread a handful of confident annotations across whole molecular families — build a feature-based molecular network, seed it with spectral-library and SIRIUS/CANOPUS annotations, then propagate compound classes and analogue annotations across network components (MolNetEnhancer / network annotation propagation) so unannotated nodes inherit chemically-plausible identities.
    2 installs
32. ▌
    Pathway Functional Analysis Workflow · holobiomicslab bundle

    Use when you have an LC-MS metabolomics feature list (m/z, optionally p-values/fold changes) and want biological interpretation without prior identification — feature preparation, mummichog functional analysis from m/z, pathway/enrichment analysis, and pathway-level interpretation.
    0 installs
33. ▌
    Anndata Object Manipulation · holobiomicslab

    Use when you have single-cell RNA-seq count matrices or processed expression data and need to store them alongside cluster assignments (e.g., leiden cluster labels), cell metadata, and computed analysis results (e.
    2 installs
34. ▌
    Factor Design Specification · holobiomicslab

    Use when when setting up a DESeqDataSet from count matrices or transcript quantification, you must specify a design formula before running DESeq() if your experiment has batch effects, multiple treatment groups, or multi-factor designs.
    0 installs
35. ▌
    Rna Seq Count Normalization · holobiomicslab

    Use when you have transcript-level abundance estimates and inferred counts from salmon/kallisto/Sailfish (with or without Gibbs/bootstrap replicates) that must be summarized to gene or transcript level, and you plan to use count-based differential expression tools (edgeR, DESeq2, limma-voom).
    0 installs
36. ▌
    Transcript Event Extraction · holobiomicslab

    Use when you have a genome annotation GTF file and need to identify all transcript-level alternative splicing events (exon skipping, intron retention, alternative splice sites, mutually exclusive exons, alternative first/last exons) before quantifying their inclusion levels (PSI) across samples or.
    0 installs
37. ▌
    Cosine Similarity Ranking Metrics · holobiomicslab

    Use when when you have pre-computed spectral embeddings (vectors) for both query spectra and a reference library, and you need to measure retrieval performance by ranking reference compounds by similarity to each query.
    0 installs
38. ▌
    Derivatizing Matrix Configuration · holobiomicslab

    Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for metabolite annotation, and the matrix is not yet configured in your Met-ID installation.
    0 installs
39. ▌
    Effective Mobility Transformation · holobiomicslab

    Use when you have raw CE-MS data (mzML or netCDF format) with migration time measurements and need to establish a reproducible compound-specific axis that is independent of run-to-run electroosmotic flow fluctuations.
    0 installs
40. ▌
    Lcms Metabolomics Data Processing · holobiomicslab

    Use when you have raw LC-HRMS metabolomics data in .mzML or .
    0 installs
41. ▌
    Msi Feature Metadata Preservation · holobiomicslab

    Use when you are converting a processed Cardinal MSImagingExperiment object (containing normalized peaks, optional spatial shrunken centroids segmentation, and feature m/z annotations) into a Seurat object for downstream pathway analysis, differential metabolite expression, or integrative.
    2 installs
42. ▌
    Carbon Oxidation State Assessment · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peak data, when you need to classify metabolites by their redox state to predict bioavailability or lability, or when generating thermodynamic indices for chemodiversity analysis and environmental metabolomic interpretation.
    1 install
43. ▌
    Cheminformatics Database Querying · holobiomicslab

    Use when you have a list of identified or suspected chemical compound names (e.g., from GC-MS Match.
    2 installs
44. ▌
    Chromatography Data Preprocessing · holobiomicslab

    Use when you have raw spectra files from a liquid chromatography experiment (in-house or external database) and need to adapt a pretrained GNN-RT model to predict retention times for your molecules. Preprocessing is the mandatory first step before any model training or transfer learning can proceed.
    0 installs
45. ▌
    Empirical Compound Pre Annotation · holobiomicslab

    Use when after feature detection from mzML files (e.g., via Asari) when you have a feature table with m/z, retention time, and intensity columns, and before MS1 or MS2 annotation.
    1 install
46. ▌
    Ftms Raw Data Loading And Parsing · holobiomicslab

    Use when you have received raw FT-ICR transient data from Bruker Solarix or ThermoFisher instruments and need to perform signal processing, apodization, calibration, or molecular formula assignment in CoreMS. The data must be in native vendor format (.d directory with ser/fid files, or .
    2 installs
47. ▌
    Image Processing For Metabolomics · holobiomicslab

    Use when you have GC–MS or LC–MS data represented as a two-dimensional map (m/z vs retention time) and need to identify analyte signals and marker features while minimizing false peak detections.
    1 install
48. ▌
    Isotope Labeling Data Integration · holobiomicslab

    Use when you have LC-MS peak tables from parallel unlabeled and labeled (isotope-traced) sample cohorts, sample metadata defining groups and conditions, and you seek to identify metabolic intermediates that accumulate differentially in a perturbed system (e.
    0 installs
49. ▌
    Mass Spectrometry Data Formatting · holobiomicslab

    Use when you have raw GC-MS output exported as CSV (containing columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    0 installs
50. ▌
    Ms Instrument Type Classification · holobiomicslab

    Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS Imaging) is covered by at least one processing module.
    0 installs
51. ▌
    Peak Extraction Rescue Algorithms · holobiomicslab

    Use when traditional peak extraction algorithms have produced a feature table that you suspect is incomplete or missing known suspects from your target database (e.g., T3DB).
    0 installs
52. ▌
    Peak Picking Algorithm Comparison · holobiomicslab

    Use when you have claims in a paper or tool documentation that one peak picking method outperforms others (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms'), but the specific comparison metrics, numerical results, and source tables are not provided in the abstract or introduction.
    0 installs
53. ▌
    Retention Time Feature Clustering · holobiomicslab

    Use when after chromatographic peak detection (findChromPeaks) when you have a processed XcmsExperiment object with detected peaks and need to perform initial feature grouping. Use it when features of the same compound are expected to co-elute within a narrow retention-time window (e.
    2 installs
54. ▌
    Adduct Specific Model Fine Tuning · holobiomicslab

    Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
    0 installs
55. ▌
    Backend Merging And Concatenation · holobiomicslab

    Use when when you have two or more MsBackend objects (e.g., multiple MsBackendMemory, MsBackendDataFrame, or MsBackendMzR instances) containing distinct sets of MS spectra and you need to consolidate them into a single backend for downstream analysis, parallel processing, or export.
    0 installs
56. ▌
    Beam Search Decoding Optimization · holobiomicslab

    Use when using Casanovo for de novo peptide sequencing on high-stakes datasets (immunopeptidomics, paleoproteomics, or monoclonal antibody discovery) where missing the correct sequence in the top-1 prediction is costly.
    2 installs
57. ▌
    C Sharp Wrapper Invocation From R · holobiomicslab

    Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings are unavailable or impractical. Use this when the target assembly requires Windows/.
    0 installs
58. ▌
    Ccs Calibration Tunemix Execution · holobiomicslab

    Use when you have positive-mode tune mix reference data (e.g., example_tune_pos.h5) with known CCS values spanning a wide m/z range (e.g., 118.086–1522 m/z) and need to establish a CCS calibration model to convert experimental drift times or collision cross sections for downstream analysis.
    0 installs
59. ▌
    Composite Mass Track Construction · holobiomicslab

    Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you need to detect peaks across the entire cohort.
    2 installs
60. ▌
    Compound Class Annotation Parsing · holobiomicslab

    Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
    2 installs
61. ▌
    Compound Structure Representation · holobiomicslab

    Use when when you have experimental MS/MS data (peak lists, precursor m/z, charge state, adduct type) paired with a chemical structure (SMILES or structural identifier), and need to create a unified Compound object for spectral alignment, modification-site prediction, or comparative fragmentation.
    2 installs
62. ▌
    Computational Variation Detection · holobiomicslab

    Use when after peak detection and feature alignment in a metabolomic LC–MS/MS or GC–MS workflow, when you have a feature table (rows=metabolic features, columns=samples) split into separate .csv files for peak height and peak area.
    2 installs
63. ▌
    Cross Tool Performance Comparison · holobiomicslab

    Use when when you have raw tandem MS metabolomics data in vendor formats (.
    0 installs
64. ▌
    Cross Workflow Format Translation · holobiomicslab

    Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) or GNPS2 (https://gnps2.org) and need to parse spectra (spectra.mgf), molecular family networks (molecular_families.tsv), spectral library annotations (annotations.
    2 installs
65. ▌
    Data Summarization And Tabulation · holobiomicslab

    Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.
    0 installs
66. ▌
    De Novo Precursor Mass Annotation · holobiomicslab

    Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting without access to spectral libraries.
    0 installs
67. ▌
    Dependency Requirement Validation · holobiomicslab

    Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints. Use this skill when you have access to an R environment and need to confirm that R ≥4.0, XCMS ≥3.11.4, and metaMS ≥1.25.
    0 installs
68. ▌
    Differential Metabolite Detection · holobiomicslab

    Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
    0 installs
69. ▌
    Disease Classification Prediction · holobiomicslab

    Use when you have raw LC-MS metabolomics data from multiple disease groups (in .npy or .
    2 installs
70. ▌
    Environment Dependency Management · holobiomicslab

    Use when when deploying Galaxy-M or similar multi-component metabolomics platforms that depend on heterogeneous runtime environments (Python, R, MATLAB, WINE) across multiple operating systems (Ubuntu 14.
    2 installs
71. ▌
    Feature Grouping By Molecular Ion · holobiomicslab

    Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
    0 installs
72. ▌
    Feature Table Parsing And Loading · holobiomicslab

    Use when you have extracted volatile organic compound (VOC) features from individual breath samples (mzML or mzXML files) and wish to consolidate multiple per-sample feature tables into a single aligned feature table, or you need to programmatically access feature metadata (m/z, intensity, scan.
    0 installs
73. ▌
    File Format Export And Validation · holobiomicslab

    Use when after executing MassQL queries on mass spectrometry data that produce tabulated results (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to persist those results for archival, sharing, or downstream statistical analysis.
    2 installs
74. ▌
    Fragment Peak Chemical Annotation · holobiomicslab

    Use when you have MS/MS spectra with assigned precursor formulas and need to annotate the chemical composition of individual fragment peaks for metabolite structure elucidation or fragmentation pathway analysis. Apply this skill when you want to avoid external fragmentation tree computation (e.
    0 installs
75. ▌
    Fragmentation Spectrum Extraction · holobiomicslab

    Use when you have raw or peak-detected mass spectrometry data (mzXML, mzML, or netCDF format) from untargeted metabolomics or exposomics studies and need to separate composite fragmentation spectra into individual constituent spectra for annotation.
    0 installs
76. ▌
    Fuzzy Analog Search Fragmentation · holobiomicslab

    Use when when you have experimental MS/MS spectra and want to discover structurally similar compounds beyond exact spectral library matches—particularly useful for identifying chemical analogs, homologs, or isomers that share fragmentation logic but differ in molecular structure.
    0 installs
77. ▌
    In Source Fragment Identification · holobiomicslab

    Use when you have an LCMS feature table (from XCMS, MS-DIAL, MZmine2, or other feature extraction software) with m/z, retention time, and intensity columns, plus MS2 spectral annotations from DDA data, and you need to identify which features are in-source fragments rather than distinct metabolites.
    0 installs
78. ▌
    Intensity Distribution Simulation · holobiomicslab

    Use when when you need to create synthetic noisy MS/MS spectra from clean baseline spectra to validate denoising algorithms, compare denoising performance across noise levels, or generate ground-truth test datasets where the true signal and noise composition are known and controllable.
    0 installs
79. ▌
    Ion Image Quantification Workflow · holobiomicslab

    Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal standards.
    0 installs
80. ▌
    Ion Species Annotation Assignment · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across time-resolved MS scans, but before final candidate validation. Apply this skill when you need to distinguish between competing ion-species hypotheses (e.
    2 installs
81. ▌
    Isotope Pattern Spectral Matching · holobiomicslab

    Use when when you have LC/MS feature data with observed m/z and intensity values across multiple peaks (monoisotopic and isotopologues) and need to narrow candidate annotations from a metabolite database.
    2 installs
82. ▌
    Isotopologue Abundance Correction · holobiomicslab

    Use when you have LC-MS data from isotope labeling experiments where FAM measurements must be transformed to MDV values. Specifically, apply this when: (1) you have measured fractional abundances of isotopologues (FAM) in XLSX format from a high-resolution instrument (e.g., Orbitrap);
    0 installs
83. ▌
    Keras Regularizer API Integration · holobiomicslab

    Use when when extending an existing neural network class (e.g., SiameseModel) that lacks user-configurable regularization, and you need to prevent overfitting on moderate-sized training datasets (e.
    0 installs
84. ▌
    Peak Classification Validation · holobiomicslab

    Use when after training or loading a NeatMS neural network model, before applying it to filter false positive MS1 peaks in a new dataset.
    0 installs
85. ▌
    Percentile Threshold Filtering · holobiomicslab

    Use when you have computed multiple independent scoring functions (e.g., standardised strain correlation and IOKR) for a large set of potential genomic–metabolomic links and wish to identify subsets enriched for validated links.
    0 installs
86. ▌
    Pipeline Prerequisite Checking · holobiomicslab

    Use when before launching the DaDIA metabolomics pipeline or any multi-package workflow, when you have an R environment with potentially mixed or unknown package versions and need to confirm that R ≥4.0, XCMS ≥3.11.4, metaMS ≥1.25.
    0 installs
87. ▌
    Plot Customization And Styling · holobiomicslab

    Use when after generating a numerical visualization (e.g., confusion matrix, heatmap, or similarity array) using matplotlib, when you need to add axis labels, class names, colormaps, normalization annotations, colorbars, titles, and export the figure in a publication-ready format (PNG or PDF).
    0 installs
88. ▌
    Precursor Fragment Ion Pairing · holobiomicslab

    Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo, Waters, or Bruker instruments) and a list of target compounds defined by precursor m/z values (and optionally retention time windows).
    2 installs
89. ▌
    Precursor Product Mass Pairing · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment masses.
    0 installs
90. ▌
    Publication Figure Preparation · holobiomicslab

    Use when you have a mass spectrometry spectrum from a supported repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA, or MassIVE) and need to include it in a publication or supplementary material.
    0 installs
91. ▌
    Python Function Implementation · holobiomicslab

    Use when when you have classification predictions and ground-truth labels and need to generate a confusion matrix visualization with flexible normalization (by row, column, or all elements) and styling options for publication or diagnostic review.
    0 installs
92. ▌
    R Data Structure Serialization · holobiomicslab

    Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have a feature table with identified ISF features and their hierarchical fragmentation relationships, and you need to export this relationship structure for interpretation, integration with external.
    0 installs
93. ▌
    Ranking Performance Evaluation · holobiomicslab

    Use when after running retention-order prediction experiments on a test or held-out evaluation dataset.
    0 installs
94. ▌
    Reaction Pathway Interpolation · holobiomicslab

    Use when after CREST (version >= 3.0.2) has identified an ensemble of low-energy conformers and stationary points (minima and transition states), and before submitting interpolated geometries to ORCA (version >= 6.0.
    0 installs
95. ▌
    Rescore Column Standardization · holobiomicslab

    Use when after running FIDDLE v2.0.0 inference on MS/MS spectra and obtaining ranked formula candidates with confidence scores, apply this skill when the rescore model outputs columns named Rescore (0), Rescore (1), ...
    0 installs
96. ▌
    Retention Time Drift Detection · holobiomicslab

    Use when you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect misalignment of feature groups.
    0 installs
97. ▌
    Signal Intensity Normalization · holobiomicslab

    Use when after loading raw LC-MS data from multiple disease groups when you need to compute correlations between metabolite signals and disease classes, or before training a deep learning model on metabolomics profiles.
    0 installs
98. ▌
    Signal Smoothing Preprocessing · holobiomicslab

    Use when when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection. Smoothing is particularly needed when the signal-to-noise ratio is low or when gradient-based peak detection would be compromised by high-frequency noise.
    2 installs
99. ▌
    Similarity Scoring For Spectra · holobiomicslab

    Use when you have LC-MS/MS query spectra in mgf format that you need to match against a custom database (e.g., prepared with CFM-id) to identify compounds. Apply this skill when you want to rank candidate compounds by spectral similarity and return scored match results for downstream interpretation.
    2 installs
100. ▌
     Sparse Feature Vector Handling · holobiomicslab

     Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train an interpretable model (e.
     0 installs