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HolobiomicsLab

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1. ▌
   Statistical Score Distribution Analysis · holobiomicslab

   Use when when you have run the same mass spectrum through molecular formula assignment under different parameter settings (e.
   0 installs
2. ▌
   Structured Data Compilation From Readme · holobiomicslab

   Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic coverage) in its README, and you need to create a machine-readable inventory for downstream indexing, validation, or reuse.
   0 installs
3. ▌
   Two Layer Architecture Dispatch Testing · holobiomicslab

   Use when when you need to verify that a wrapper package (e.g., rawrr) correctly bridges R and a managed .NET assembly (such as RawFileReader), specifically to confirm that internal dispatch functions can retrieve assembly location and version string before attempting actual spectral data extraction.
   0 installs
4. ▌
   Abstract Method Subclassing Filter Base · holobiomicslab

   Use when when you need to apply domain-specific filtering logic to compounds during Pickaxe expansion—for example, retaining only compounds within a Tanimoto similarity threshold to known targets, or compounds matching experimentally detected masses.
   0 installs
5. ▌
   Batch Effect Correction In Metabolomics · holobiomicslab

   Use when you have a preprocessed and normalized lipid abundance matrix with documented batch identifiers and experimental group assignments, and you need to perform differential abundance testing across simple or complex experimental designs (multi-factor, repeated measures) where batch effects.
   0 installs
6. ▌
   Batch Effect Correction Reference Based · holobiomicslab

   Use when when you have log-transformed metabolite abundance data from multiple batches (e.
   1 install
7. ▌
   Candidate Set Generation For Annotation · holobiomicslab

   Use when when you have raw or unprocessed PubChem compound records and need to produce a curated set of candidate metabolite structures for input to MAGMa job calculations.
   0 installs
8. ▌
   Cardinal Object Structure Understanding · holobiomicslab

   Use when when you have loaded a raw or processed Cardinal MSImagingExperiment object from MS imaging data and need to (1) extract spectral intensities and m/z feature information for conversion to other formats (e.g., Seurat), (2) verify that normalization or spatial segmentation (e.
   0 installs
9. ▌
   Cell Type Protein Profiling Integration · holobiomicslab

   Use when you have co-registered IMC (protein imaging mass cytometry) and SIMS (secondary ion mass spectrometry for metabolites) data from the same tissue regions, cell segmentation masks, and need to assign cell types based on protein expression patterns, then overlay those assignments onto.
   0 installs
10. ▌
    Chemical Structure Format Normalization · holobiomicslab

    Use when when integrating chemical structure data from multiple source databases that represent the same compound in different notations (e.
    0 installs
11. ▌
    Collision Cross Section Bias Estimation · holobiomicslab

    Use when when you have IM-MS lipidomics data spiked with U13C labeled lipid internal standards (e.g., fully labeled yeast extract) and want to assess whether measured CCS values deviate systematically from expected values in the DTCCS_N2 reference library.
    0 installs
12. ▌
    Community Metabolic Pathway Integration · holobiomicslab

    Use when you have multiple draft metabolic models (in JSON, XML, or SBML format) representing individual members or assembly variants of a community—such as Arabidopsis thaliana-associated microbiota—and need a single integrated model that captures the consensus metabolic potential while resolving.
    2 installs
13. ▌
    Conformer Filtering Threshold Selection · holobiomicslab

    Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before quantum-chemical single-point energy evaluation.
    0 installs
14. ▌
    Cross File Version Consistency Checking · holobiomicslab

    Use when before initiating a release branch workflow for a multi-module Maven project, particularly when the repository contains multiple pom.xml files at different directory levels and a release branch naming convention (e.g., 'release/X.Y.Z') is planned.
    0 installs
15. ▌
    Cross Validation Performance Evaluation · holobiomicslab

    Use when when you have paired microbiome and metabolome count data and need to estimate how well a neural network or regression model can predict metabolite abundances from microbial features without overfitting to a single held-out test set.
    0 installs
16. ▌
    CSV Delimiter Parsing And Configuration · holobiomicslab

    Use when when uploading a new mass spectrometry data file to Punc'data in CSV or delimited-text format, before attempting to map columns to their semantic roles (m/z value, intensity, formula).
    0 installs
17. ▌
    Dataset Serialization For Deep Learning · holobiomicslab

    Use when after generating aligned multimodal feature tensors from molecular structures (graph-based features, Morgan fingerprints, and physicochemical descriptors) and before initiating model training loops.
    0 installs
18. ▌
    Deep Learning Model Architecture Design · holobiomicslab

    Use when you have extracted molecular features (voxel projected areas, molecular graphs, m/z values, adduct encodings) and need to build a predictive model to map these features to a continuous molecular property (CCS).
    2 installs
19. ▌
    Dictionary Lookup And Cross Referencing · holobiomicslab

    Use when after integrating and curating raw structure-organism pairs from multiple heterogeneous databases, use this skill when you need to verify that each pair and its associated metadata (literature citations, organism taxonomy, chemical identifiers) exist in your authoritative reference.
    2 installs
20. ▌
    Distance Matrix Computation For Samples · holobiomicslab

    Use when after batch effect removal and data integration, when you have a feature-by-sample matrix (finalData) and wish to separate and visualize sample groups by their metabolomic profiles using clustering methods such as hierarchical clustering analysis (HCA).
    0 installs
21. ▌
    Docker Containerized Pipeline Execution · holobiomicslab

    Use when you have raw mass spectrometry data converted to MS1 format and need to predict peptide features (charge, isotope count, retention time) without installing complex dependencies or configuring GPU/Python environments locally.
    2 installs
22. ▌
    Dynamic Branch Cutting Module Detection · holobiomicslab

    Use when after constructing a hierarchical dendrogram from a biweight midcorrelation dissimilarity matrix of metabolite measurements, when your dendrogram exhibits complicated structure (multiple scales, varying branch heights) that would be poorly captured by a single fixed-height cutoff, and you.
    0 installs
23. ▌
    Elemental Ratio Histogram Visualization · holobiomicslab

    Use when after loading a numeric elemental ratio column (H/C, O/C, N/C, etc.) from a CSV file into Punc'data, when you need to visualize the distribution of molecular formulas across a sample and want bin spacing to adapt automatically: narrow bins (0.1) for low-range data (span ≤ 3.
    0 installs
24. ▌
    Enrichment Visualization And Annotation · holobiomicslab

    Use when after pathway enrichment analysis has been executed by clusterProfiler or biotranslator on differentially expressed features filtered by layer-specific p-value cutoffs (genes_genespval=1, mirna_genespval=1, proteins_genespval=0.5, lipids_genespval=0.5).
    1 install
25. ▌
    Fold Change Significance Interpretation · holobiomicslab

    Use when when you have differential expression results with both fold-change and p-value columns from a CSV file (e.g., volcano_example.
    2 installs
26. ▌
    Gpu Accelerated Neural Network Training · holobiomicslab

    Use when when you have a trainable neural network model (e.g., MSNovelist), labeled training data with known input/output pairs, GPU resource availability on a compute cluster, and need to optimize model weights via backpropagation.
    0 installs
27. ▌
    Gpu Capability Detection And Validation · holobiomicslab

    Use when after setting up a conda/pip environment with PyTorch and CUDA, before loading pretrained model weights or running inference/training pipelines.
    0 installs
28. ▌
    HTTP Endpoint Connectivity Verification · holobiomicslab

    Use when after deploying a web service in a Docker container with port mapping (e.g., -p 8888:8080), verify that the application is running and responding to HTTP requests at the mapped endpoint.
    2 installs
29. ▌
    Instrumental Noise Spike Identification · holobiomicslab

    Use when you have raw LA-ICP-MS image data (line-by-line, spot-wise, or ablation-time-aligned) that exhibits isolated high-intensity or low-intensity pixels inconsistent with neighboring pixels.
    0 installs
30. ▌
    Internal Standard Intensity Calibration · holobiomicslab

    Use when you have added a known internal standard compound to your nano-DESI MSI sample and want to correct for pixel-to-pixel variation in ionization efficiency or sample deposition.
    2 installs
31. ▌
    Isotope Mass Table Reference Management · holobiomicslab

    Use when when building a mass spectrometry analysis pipeline that requires exact mass lookups, molecular formula validation, or isotope abundance predictions. Specifically: (1) you are constructing a MolecularFormula class that needs to validate element symbols against known isotopes;
    0 installs
32. ▌
    Lexical Tokenization And Grammar Design · holobiomicslab

    Use when you need to enable users to express complex domain-specific queries in a natural, succinct syntax—particularly when SQL patterns are familiar but must be augmented with domain assumptions (e.
    0 installs
33. ▌
    Log Transformation And Scale Adjustment · holobiomicslab

    Use when raw metabolomics peak intensity data exhibits right-skewed distributions with heteroscedastic variance across metabolites and samples, or when combining multiple normalization methods (e.
    0 installs
34. ▌
    M Z Annotation Reduction Quantification · holobiomicslab

    Use when you have spatial metabolomics data with semi-colon-delimited multi-isomer annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you want to quantify the benefit of RefineLipids simplification with lipid_info='simple' parameter.
    2 installs
35. ▌
    Machine Learning Model Training Sklearn · holobiomicslab

    Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites with experimentally validated CCS values, and you plan to predict CCS values on target datasets containing 10,000+.
    0 installs
36. ▌
    Mass Grid Index Traversal And Retrieval · holobiomicslab

    Use when when you have constructed a MassGrid (m/z-aligned mass tracks across multiple samples) and need to retrieve all sample-specific mass tracks for a given m/z value in order to sum their intensities, apply retention time calibration, or construct composite mass track objects for peak.
    0 installs
37. ▌
    Mass Recalibration Lock Mass Correction · holobiomicslab

    Use when converting mzML files to imzML format for imaging mass spectrometry data and you have a known internal standard (lock mass) whose exact m/z value is available. Use it specifically during the metadata annotation stage (iw_utils.
    2 installs
38. ▌
    Mass Spectrometry Drift Time Processing · holobiomicslab

    Use when when you have raw ion mobility-mass spectrometry data (drift times, m/z values, and frame metadata) from DTIMS-MS, TWIMS-MS, or SLIM-based instruments and need to compute CCS values for structural characterization or database matching.
    0 installs
39. ▌
    Matrix Subsetting With Index Reordering · holobiomicslab

    Use when when you need to subset a backend containing multiple MS spectra to a user-defined subset (e.
    0 installs
40. ▌
    Metabolite Benchmark Dataset Validation · holobiomicslab

    Use when after mzRAPP has exported a benchmark CSV file from processing a batch of centroided mzML files (e.
    0 installs
41. ▌
    Metabolite Feature Grouping By Compound · holobiomicslab

    Use when after XCMS feature detection and retention time correction, when you have a feature table (CSV or XCMS object) with m/z and retention time values aligned across samples.
    0 installs
42. ▌
    Metabolite Stability Database Retrieval · holobiomicslab

    Use when you have measured metabolites or lipids from blood samples (plasma or serum) and need to assess whether quantitative results may be compromised by pre-analytical handling.
    0 installs
43. ▌
    Model Evaluation Metrics Interpretation · holobiomicslab

    Use when you have retrained or modified a neural network model (e.g., MSNovelist) to accept a different input fingerprint representation (e.
    0 installs
44. ▌
    Model Performance Evaluation Roc Curves · holobiomicslab

    Use when you have a binary classification task on metabolomics data (e.g., covid_data) and need to benchmark multiple algorithms to determine which produces the highest discriminative power.
    0 installs
45. ▌
    Molecular Class Annotation For Networks · holobiomicslab

    Use when after molecular formulas have been assigned to detected peaks (via CoreMS, Formularity, or equivalent) and you are constructing biochemical transformation networks where node interpretation requires understanding what chemical classes are being transformed.
    0 installs
46. ▌
    Molecular Complexity Metric Computation · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the structural diversity, elemental stoichiometry patterns, or complexity landscape of the organic mixture.
    2 installs
47. ▌
    Molecular Graph Representation Handling · holobiomicslab

    Use when when you have molecular structure data (SMILES or molecular IDs) from chemistry databases (e.g., PubChem, HMDB) and need to feed it into a neural network architecture like TransG-Net that expects multimodal inputs combining graph-structured molecular topology with learned embeddings.
    1 install
48. ▌
    Molecular Structure To Graph Conversion · holobiomicslab

    Use when when you have validated RDKit molecule objects from chemical databases (PubChem, HMDB) and need to generate graph-structured features for machine learning models that consume molecular topology as input.
    2 installs
49. ▌
    Molecular Structure Tokenization Smiles · holobiomicslab

    Use when when you have molecular structures encoded as SMILES strings and need to incorporate them into a multi-modal language model (such as BART) that also processes mass spectra.
    0 installs
50. ▌
    Msi Intensity Matrix Isotope Correction · holobiomicslab

    Use when you have loaded a feature-by-pixel intensity matrix (HDF5 format following Cardinal::HDF5 layout) from imzML MSI data in positive ion mode and you have identified paired [M+H]+ and [M+Na]+ features for the same neutral lipid species (differing by ~22 Da in m/z).
    0 installs
51. ▌
    Multi Backend Visualization Abstraction · holobiomicslab

    Use when when building a mass spectrometry visualization library that must support multiple plotting backends (matplotlib for static output, bokeh and plotly for interactive exploration) with a uniform DataFrame-based API, and where different plot kinds (spectrum, chromatogram, mobilogram, peakmap).
    0 installs
52. ▌
    Multi Branch Representation Integration · holobiomicslab

    Use when when building an end-to-end deep learning model that predicts multiple related properties from a single input (e.
    0 installs
53. ▌
    Multi Organism Metabolic Data Retrieval · holobiomicslab

    Use when when you have identifiers for two organisms available in KEGG and need to compare their metabolic networks quantitatively and visually at both structural (node–edge topology) and functional (pathway role) levels for applications in drug engineering, medical science, or systems biology.
    2 installs
54. ▌
    Multiclass Biomarker Quality Assessment · holobiomicslab

    Use when you have a multi-class metabolomic peak table with quality control (QC) samples included, and you need to select an optimal preprocessing workflow for downstream biomarker discovery or differential profiling.
    0 installs
55. ▌
    Multiple Testing Correction Application · holobiomicslab

    Use when when performing statistical tests (e.g., t-tests, ANOVA) across many metabolites in a MultiAssayExperiment object to identify differentially abundant metabolites between sample groups.
    0 installs
56. ▌
    Multistage Neural Architecture Training · holobiomicslab

    Use when you have paired mass spectra and molecular structure datasets and need to train a model that jointly understands both modalities for tasks like structure elucidation. Specifically, use it when: (1) you have large unlabeled or weakly-labeled pretraining data with both spectra and molecules;
    2 installs
57. ▌
    Natural Product Database Schema Parsing · holobiomicslab

    Use when when ingesting raw data from multiple external natural-product databases with different formats, field naming conventions, and data structures.
    0 installs
58. ▌
    Noise Perturbation Sensitivity Analysis · holobiomicslab

    Use when when comparing pathway analysis methods on metabolomics peak data and you need evidence that one method is more robust than another to the noise and missing peaks that are prevalent in real metabolomics experiments.
    2 installs
59. ▌
    Noise Smoothing Chromatographic Signals · holobiomicslab

    Use when when you have raw LC-HRMS profile-mode data (rt × mz intensity matrices) and need to detect chromatographic peaks using gradient-descent or local-maxima algorithms.
    0 installs
60. ▌
    Noise Threshold Filtering Spectral Data · holobiomicslab

    Use when working with raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains low-abundance background noise, isolated high-intensity artifacts, or jagged peaks characteristic of low-abundance ions.
    2 installs
61. ▌
    Normalized Enrichment Score Computation · holobiomicslab

    Use when you have differential analysis results (p-values and log2 fold changes) from metabolomics data and need to assess whether predefined sets of metabolites (metabolic pathways) show coordinated enrichment patterns.
    0 installs
62. ▌
    Omics Network Visualization Preparation · holobiomicslab

    Use when after constructing a correlation-based network from omics data (nodes and edges defined), when you need to assign visual positions to nodes for rendering.
    0 installs
63. ▌
    Over Representation Enrichment Analysis · holobiomicslab

    Use when you have p-values and effect sizes from two independent association studies (metabolomic GWAS and meta-genome GWAS) and want to identify whether variants associated with disease phenotypes co-occur with metabolites that share biochemical pathways or protein interactions.
    0 installs
64. ▌
    Pairwise Similarity Matrix Construction · holobiomicslab

    Use when after XCMS feature detection and retention time correction, when you have a feature abundance table aligned across samples and need to group features that likely arise from the same compound before downstream annotation.
    2 installs
65. ▌
    Pearson Correlation Statistical Testing · holobiomicslab

    Use when when you have two co-registered LA-ICP-MS element images and need to determine whether the spatial distribution of one element correlates significantly with another.
    2 installs
66. ▌
    Pixel Replacement With Local Statistics · holobiomicslab

    Use when lA-ICP-MS image data contains isolated spike outliers (single or few pixels with anomalously high or low intensities relative to their local neighborhood) that distort quantitative analysis or visualization.
    0 installs
67. ▌
    Python Binding Generation With Nanobind · holobiomicslab

    Use when when you have a C++ library (such as OpenMS) with nanobind binding specifications in a designated bindings directory and need to create a Python module that exposes C++ classes, functions, and data types to Python code.
    0 installs
68. ▌
    Python Dependency Management With Conda · holobiomicslab

    Use when you have a requirements file (e.g., jestr_requirements.
    0 installs
69. ▌
    Qc Sample Filtering Multi Step Criteria · holobiomicslab

    Use when after feature extraction from XCMS, MS-Dial, or similar tools (producing a feature intensity matrix with samples in rows and compounds in columns), and after sample type annotation (blank, curve, qc, unknown).
    0 installs
70. ▌
    R Tibble Object Creation And Validation · holobiomicslab

    Use when when you have raw metabolomics results from multiple studies in heterogeneous file formats (xls/xlsx, csv, or txt) and need to harmonize them into a single, machine-readable tibble structure with required columns (compound identifier, p-value, fold-change, study size N, reference) for.
    2 installs
71. ▌
    Relative Standard Deviation Computation · holobiomicslab

    Use when when you have preprocessed metabolomics data with pooled QC samples and assigned internal standards, and need to select the optimal internal standard for each compound by comparing ratio stability across candidate standards.
    0 installs
72. ▌
    Signal Anomaly Detection Chromatography · holobiomicslab

    Use when you have raw total ion current (TIC) traces extracted from mass spectrometry samples (e.g., from qTOF, orbitrap, or FTICR instruments) and need to identify and flag scans with anomalous peak intensities before feature detection.
    0 installs
73. ▌
    Small Molecule 3d Structure Preparation · holobiomicslab

    Use when when you have ionized adduct structures (SMILES or MOL format) from a prior ionization-state determination step and need to create multiple low-energy 3D conformations before filtering with machine-learning potentials (ASE-ANI) or quantum calculations.
    0 installs
74. ▌
    Smiles Formula Representation Chemistry · holobiomicslab

    Use when when obtaining transformation products through mixed algorithmic backends (library, CTS, BioTransformer, metabolic logic rules) that require different chemical representations: structure-based algorithms need SMILES strings with optional log P values, while formula-based algorithms need.
    0 installs
75. ▌
    Software Distribution File Organization · holobiomicslab

    Use when you have edited one or more core algorithm scripts (Modular.r, genEIC.r, MS1Spectragen.r, or Stats.R) in a shared developer repository (e.g., Core-Match on GitHub) and need to integrate those changes into an already-installed LipidMatch-4.2 or FluoroMatch distribution on disk.
    0 installs
76. ▌
    Spatial Segmentation Shrunken Centroids · holobiomicslab

    Use when apply SSC when you have preprocessed and normalized MS imaging data (e.g., after TIC normalization and peak processing) and need to discover spatially distinct metabolite regions without prior tissue annotation.
    0 installs
77. ▌
    Spectrum Metadata Extraction Validation · holobiomicslab

    Use when when ingesting heterogeneous MS spectral data from multiple open-access libraries (OMS libraries) where metadata completeness and correctness are uncertain.
    0 installs
78. ▌
    Statistical Model Ranking And Selection · holobiomicslab

    Use when you have trained multiple machine learning algorithms (e.
    0 installs
79. ▌
    Structure Organism Consistency Checking · holobiomicslab

    Use when after curating structure-organism pairs from multiple source databases (1_curating stage), when you need to filter curated pairs into high-confidence subsets for downstream analysis.
    0 installs
80. ▌
    Summarizedexperiment Assay Manipulation · holobiomicslab

    Use when when working with multi-batch metabolomics studies where you need to create intermediate normalized assays (e.
    0 installs
81. ▌
    Table Consolidation And Denormalization · holobiomicslab

    Use when when you have cleaned, normalized organism, structure, and reference tables from separate cleaning pipelines (e.g., after 2_curating stage) and must integrate them into a single queryable table while maintaining referential integrity and generating lookup dictionaries.
    0 installs
82. ▌
    Targeted Peak Detection And Integration · holobiomicslab

    Use when you have centroided LC–MS data in .mzML format, a validated table of target compounds with adjusted expected retention times (RT in minutes), and you need to extract peak areas and quality metrics across all sample runs.
    0 installs
83. ▌
    Training Metric Monitoring Torchmetrics · holobiomicslab

    Use when during supervised model training loops when you need to log loss and validation metrics at each epoch to assess whether the model is learning properly and to determine when to stop training.
    0 installs
84. ▌
    Trust Score Propagation Directed Graphs · holobiomicslab

    Use when you have (1) a directed edge list representing a global network (e.
    0 installs
85. ▌
    Genome Scale Metabolic Flux Modeling Workflow · holobiomicslab bundle

    Use when you have a genome-scale constraint-based metabolic model (GEM, SBML/JSON) for one or more organisms and want predicted flux states grounded in your own omics data — integrate transcriptomics / metabolomics-derived constraints (eFlux-style Reaction Activity/Propensity Scores, extracellular uptake-secretion rates) into the model, sample the feasible flux space with optGpSampler, interpret and compare the resulting flux distributions across samples or conditions, and, when multiple organism or community-member models exist, gap-fill and merge them into a consensus community model (COMMIT-style) — connecting metabolomics features to predicted flux states.
    0 installs
86. ▌
    Chain Pruning Threshold Optimization · holobiomicslab

    Use when when comparing mapped read counts between two RNA-seq quantification implementations (e.
    0 installs
87. ▌
    Gene Expression Matrix Normalization · holobiomicslab

    Use when when you have raw or unnormalized gene expression data from microarray experiments (e.
    0 installs
88. ▌
    Log Fold Change Shrinkage Estimation · holobiomicslab

    Use when after running DESeq() and extracting base results with results(), apply shrinkage when you have differential expression estimates and want to reduce the variance of log fold change estimates while preserving signal.
    0 installs
89. ▌
    Method Comparison Differential Calls · holobiomicslab

    Use when you have applied two or more competing analysis workflows to the same RNA-seq or microarray dataset and need to assess whether they yield consistent or divergent differential expression results. Typical triggers: (1) comparing a new normalization method (e.
    0 installs
90. ▌
    Overdispersion Estimation Validation · holobiomicslab

    Use when after using edgeR::DGEListFromTximport with divide=TRUE on tximport output containing Gibbs sample or bootstrap replicates.
    2 installs
91. ▌
    Precision Weight Calculation Rna Seq · holobiomicslab

    Use when you have raw RNA-seq read counts and a set of normalization factors (e.g., TMM-computed library size scales from edgeR's calcNormFactors), and you plan to fit a linear model to detect differential expression.
    2 installs
92. ▌
    Psi Matrix Loading And Normalization · holobiomicslab

    Use when you have generated PSI matrices for alternative splicing events or transcripts across two or more biological conditions using SUPPA's psiPerEvent or psiPerIsoform subcommand, and you need to align and standardize these matrices with corresponding transcript expression quantification files.
    0 installs
93. ▌
    Selective Alignment Parameter Tuning · holobiomicslab

    Use when you observe discrepancies in mapping rate or per-transcript quantification between two salmon implementations, or when the default chain-pruning thresholds (orphanChainSubThresh, postMergeChainSubThresh) are leaving a substantial fraction of reads unmapped (e.
    0 installs
94. ▌
    Group Wise Chemical Enrichment Calculation · holobiomicslab

    Use when when comparing GNPS chemical annotations across two or more groups of samples (defined by ReDU sample-information categories such as sample type, extraction method, or ionization source) where the groups contain different numbers of files.
    0 installs
95. ▌
    Interactive Spectral Visualization Emperor · holobiomicslab

    Use when when you have computed PCA coordinates from chemical annotation matrices (e.
    0 installs
96. ▌
    Mass Spectrometry Library Search Retrieval · holobiomicslab

    Use when when you have an unknown MSMS spectrum (precursor m/z and fragment ions) and need to discover structurally related compounds from a spectral library.
    0 installs
97. ▌
    Peak Detection And Boundary Identification · holobiomicslab

    Use when when you have CE-MS raw data (mzML or netCDF format) with extracted ion traces for target compounds and need to identify peak boundaries and extract quantitative peak properties (retention time on µeff scale, peak intensity, peak area) within a specified mobility window.
    2 installs
98. ▌
    Sodium Adduct Detection And Classification · holobiomicslab

    Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in the range of ~20–25 Da (characteristic of Na adducts).
    2 installs
99. ▌
    Spectral Library Annotation Interpretation · holobiomicslab

    Use when you have received chemical annotations from GNPS spectral library matching and need to (1) assess annotation confidence and validity for downstream analysis, (2) understand why the same chemical may appear under multiple GNPS annotation IDs, or (3) decide whether to collapse or deduplicate.
    0 installs
100. ▌
     Tabular Results Aggregation And Comparison · holobiomicslab

     Use when when you have chemical annotations (GNPS matches) distributed across multiple sample groups (e.g., by sample type, extraction method, ionization source) with unequal numbers of files per group, and you need to compare enrichment fairly without group-size bias.
     0 installs