← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 11k skills
• 0 followers
• last month last updated

1. ▌
   Simulation Based Validation · holobiomicslab

   Use when when you need to verify that a statistical correction (e.
   2 installs
2. ▌
   Statistical Test Comparison · holobiomicslab

   Use when when you have run differential methylation analysis in methylKit and need to validate whether overdispersion correction (overdispersion='MN') produces appropriately stringent statistical tests.
   0 installs
3. ▌
   API Endpoint Communication · holobiomicslab

   Use when you have fingerprint or spectrum data that requires compound-class annotation but prefer not to run SIRIUS locally, or need to integrate predictions into an automated analysis pipeline.
   0 installs
4. ▌
   Build Status Documentation · holobiomicslab

   Use when when you need to validate that a development build release workflow (such as dev_build_release.yml for a mass spectrometry data processing project) executes without failure and generates artifacts for downstream testing or distribution.
   0 installs
5. ▌
   Ccs Library Format Parsing · holobiomicslab

   Use when when you have received or cloned a CCS reference library (such as the DTCCSN2 library for U13C labeled lipids) bundled with lipidomics software and need to verify its integrity, understand its lipid class composition, or extract metadata before using it for CCS bias calculation or.
   0 installs
6. ▌
   CI Status Badge Deployment · holobiomicslab

   Use when you have configured a GitHub Actions workflow that executes build, test, and quality checks, and you want to embed a machine-readable, auto-updating badge in your repository README to signal pipeline status at a glance.
   1 install
7. ▌
   Graph Tensor Serialization · holobiomicslab

   Use when after constructing feature tensors encoding atom adjacency matrices, bond types, and chemical properties from canonical SMILES—and before feeding graphs into a GNN training loop—to enable reproducible, portable, and memory-efficient storage of graph objects that will be loaded in batches.
   2 installs
8. ▌
   Hdf5 Feature Table Loading · holobiomicslab

   Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for multi-dimensional alignment, CCS calibration, or isotope detection.
   0 installs
9. ▌
   JSON Directive Application · holobiomicslab

   Use when when you have extracted intermediate JSON conforming to the Experiment Description Specification and need to restructure, filter, sort, or aggregate records (e.
   0 installs
10. ▌
    Jupyter Notebook Execution · holobiomicslab

    Use when you have access to a published study that provides a Jupyter notebook (.ipynb) containing executable code for reproducing simulations, analyses, or figures, and you need to verify that the reported results can be regenerated in your own environment or adapt the code for a related analysis.
    2 installs
11. ▌
    Module Import Verification · holobiomicslab

    Use when after installing a Python package (especially one with optional dependencies) to confirm that: (1) core modules are accessible and importable;
    1 install
12. ▌
    Mzpeak Format File Parsing · holobiomicslab

    Use when you have an mzPeak file (uncompressed ZIP archive containing Parquet files) and need to extract and work with spectrum metadata (scan descriptions, precursors, selected ions), spectrum signal data (profile or centroid m/z and intensity arrays), or chromatogram data.
    0 installs
13. ▌
    REST API Endpoint Querying · holobiomicslab

    Use when you have a SMILES string or batch of SMILES strings representing chemical structures and need to obtain NP Classifier predictions programmatically.
    0 installs
14. ▌
    Richness Index Computation · holobiomicslab

    Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular species across experimental conditions—for example, to test whether inoculation or environmental perturbation alters the.
    0 installs
15. ▌
    S4 Class Method Inspection · holobiomicslab

    Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on NumericList or similar container objects, rather than inefficient loops or apply functions.
    0 installs
16. ▌
    Workflow Status Monitoring · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
    0 installs
17. ▌
    Batch Design Specification · holobiomicslab

    Use when before applying any batch effect correction function in dbnorm (dbnormPcom, dbnormNPcom, dbnormBer, dbnormBagging, Visodbnorm, or hclustdbnorm), you must first prepare and validate a batch assignment vector that maps each sample to its analytical run or batch.
    2 installs
18. ▌
    Batch Effect Visualization · holobiomicslab

    Use when you have multi-batch metabolomics data in SummarizedExperiment format and need to demonstrate that batch clustering or run-order signal drift persists in raw/imputed assays but is eliminated after hRUV normalisation (intra-batch loess + RUV-III, followed by inter-batch concatenation).
    2 installs
19. ▌
    Batch Structure Processing · holobiomicslab

    Use when you have a collection of 100+ molecules in SMILES, SDF, MOL, or MOL2 format and need to compute a unified feature representation combining physicochemical descriptors and structural fingerprints for downstream machine learning.
    0 installs
20. ▌
    Build Automation Scripting · holobiomicslab

    Use when when you have a Windows-only .NET Framework 4.
    0 installs
21. ▌
    Build System Configuration · holobiomicslab

    Use when when you have a Python package with source modules that need to be documented, want to generate API stubs automatically from docstrings, and need to produce browsable HTML documentation for distribution or hosting (e.g., on ReadTheDocs).
    2 installs
22. ▌
    Class Hierarchy Extraction · holobiomicslab

    Use when you need to understand the extensibility surface of a modular object-oriented codebase, particularly when planning to contribute new modules, extend existing functionality, or onboard developers unfamiliar with the architecture.
    0 installs
23. ▌
    Compound Metric Tabulation · holobiomicslab

    Use when after completing doAnalysis on a SummarizedExperiment object with mzQuality, when you need to share compound-level metrics with non-R users, integrate results into downstream reporting systems, or perform meta-analyses across multiple metabolomics experiments.
    2 installs
24. ▌
    Conformer Generation Rdkit · holobiomicslab

    Use when when you have ionized adduct structures (SMILES or MOL format) from an ionization-state determination step and need to create an ensemble of relaxed 3D geometries for each molecule prior to expensive conformation filtering (e.g., ASE-ANI or quantum methods).
    0 installs
25. ▌
    Count Matrix Preprocessing · holobiomicslab

    Use when after count matrix quantification (e.g., from Salmon) and before differential expression analysis, when you have: (1) a raw or unfiltered count matrix with potentially low-abundance features; (2) known batch effects or technical covariates documented in sample metadata;
    0 installs
26. ▌
    Cross Domain Token Mapping · holobiomicslab

    Use when when building a unified sequence model (e.
    2 installs
27. ▌
    Cross Platform Compilation · holobiomicslab

    Use when when releasing a new version of a tool, onboarding to a new development platform, or validating that a tool meets its documented platform support claims (e.g., Windows 10, Ubuntu 22.04, macOS 12+ ARM64). Apply this skill before publishing binaries or claiming multi-platform support.
    2 installs
28. ▌
    Django Backend Development · holobiomicslab

    Use when you need to build a web-based data ingestion layer that accepts raw MS files (.raw, .mzML, .mzXML) from users, validates them before storage, and tracks their processing status through a data management pipeline.
    0 installs
29. ▌
    Edge Case Boundary Testing · holobiomicslab

    Use when when implementing or validating a quantitative formula (e.g., resource sizing, memory allocation, worker count calculation) that will be applied across a range of input values, especially when the formula involves division, clamping, or has implicit domain constraints (e.
    0 installs
30. ▌
    Feature Importance Ranking · holobiomicslab

    Use when after training logistic regression, random forest, and/or XGBoost classifiers on metabolomics data (e.
    0 installs
31. ▌
    Formula Annotation Ranking · holobiomicslab

    Use when after generating candidate formula/adduct pairs from m/z database matching but before final metabolite annotation. Use it when you have observed isotopic patterns from feature detection (e.
    0 installs
32. ▌
    Genomic Coordinate Mapping · holobiomicslab

    Use when after sub-clusters have been detected by PRESTO-STAT or PRESTO-TOP statistical methods on tokenised and redundancy-filtered BGCs, and you need to report their precise genomic positions, gene locus tags, and orientations for integration with natural product substructure predictions or for.
    0 installs
33. ▌
    Graph Isomorphism Matching · holobiomicslab

    Use when when comparing two or more lipid structures and you need to determine which atoms and bonds in one structure correspond to those in another, prior to computing a distance metric. Specifically, when input lipids have variable fatty acyl chain compositions (e.
    0 installs
34. ▌
    Graph Network Construction · holobiomicslab

    Use when you have trained ML models that predict pairwise relationships (e.
    0 installs
35. ▌
    Interactive Plot Rendering · holobiomicslab

    Use when you have validated omics data loaded into R (expression matrices, fold-change and p-value pairs, gene ontology enrichment statistics, survival or distribution data) and need to generate publication-quality figures that must be explored interactively via a web browser, support pan/zoom, and.
    0 installs
36. ▌
    Isobaric Ion Detection Msi · holobiomicslab

    Use when you have loaded MSI data with an extracted peak list and need to annotate matrix-related signals, particularly when the dataset may contain isobaric ions or peaks with overlapping spatial distributions that could be misclassified during downstream annotation filtering.
    0 installs
37. ▌
    JSON Configuration Parsing · holobiomicslab

    Use when you need to implement a converter or standardization system that must map multiple incompatible nomenclature styles (e.g., lipid abbreviations from 5+ databases and 17+ software programs) into a single unified format.
    0 installs
38. ▌
    Lipid Graph Representation · holobiomicslab

    Use when when you have multiple lipid structures (from lipidomics data in CSV, XLSX, or mzTab-M format) and need to compute pairwise structural distances, identify lipids responsible for shaping a lipidome, or perform hierarchical clustering of lipidomes.
    0 installs
39. ▌
    Lipid Nomenclature Parsing · holobiomicslab

    Use when you have received raw lipid identification output from LipidSearch or LIQUID in CSV or TSV format containing lipid species names or identifiers, and you need to extract their structural components and map them to standardized LIPID MAPS categories before building a quantitative data matrix.
    0 installs
40. ▌
    Long Format Data Reshaping · holobiomicslab

    Use when when you have a wide-format feature intensity table (samples in rows, analyzed compounds in columns) and need to conduct multiple regression linear models (lm or lmer) to estimate associations between independent variables (fixed effects) and each metabolomic feature as a dependent.
    0 installs
41. ▌
    Longitudinal Data Analysis · holobiomicslab

    Use when you have imputed metabolomics data in long format (with id, time, categorical grouping variable, metabolite names, and numeric values) and need to rank metabolites by evidence of difference across groups or time trajectories.
    0 installs
42. ▌
    Massbank Record Validation · holobiomicslab

    Use when you have a collection of MassBank records (in plain-text or structured format) that need to be systematically validated for conformance to MassBank format specification—particularly in a continuous integration context where validation must run on every commit or pull request to maintain.
    0 installs
43. ▌
    Mean Intensity Aggregation · holobiomicslab

    Use when after importing imzML or vendor-specific MSI data into napari and visualizing the raw spectral dataset.
    2 installs
44. ▌
    Metabolite Feature Ranking · holobiomicslab

    Use when you have an imputed, long-format metabolomics dataset with repeated measurements across subjects and a grouping variable (e.
    0 installs
45. ▌
    Metabolite Pathway Mapping · holobiomicslab

    Use when after metabolite detection and normalization from Metabolomics Workbench format data, when you have a table of metabolite names or identifiers (rows=metabolites, columns=samples) and need to assign pathway membership to compute pathway-level enrichment statistics or visualize.
    0 installs
46. ▌
    Metabolite Peak Annotation · holobiomicslab

    Use when after peak detection has identified significant m/z and retention time features in untargeted or targeted mass spectrometry data (as a .raw, .d, or mzXML file).
    0 installs
47. ▌
    Metadata Structure Mapping · holobiomicslab

    Use when you have mzML-format raw data files from mass spectrometry experiments and need to ingest them into MS-DIAL for untargeted metabolomics or lipidomics analysis.
    0 installs
48. ▌
    Metfrag Settings Injection · holobiomicslab

    Use when when deploying the ipbhalle/metfragweb container and you need to configure MetFrag parameters such as ChemSpider tokens, proxy settings for web services (MoNA, KEGG, MetaCyc), or local database connections (PubChem via MySQL/PostgreSQL) without modifying the container image itself.
    0 installs
49. ▌
    Mzpeak File Format Parsing · holobiomicslab

    Use when when you have mass spectrometry data stored in mzPeak format (ZIP archive containing Parquet files) and need to read spectrum metadata, chromatogram metadata, and signal data (m/z and intensity arrays) for analysis. Use this skill if your input is an .
    0 installs
50. ▌
    Per Pixel Array Arithmetic · holobiomicslab

    Use when you have multiple registered LA-ICP-MS elemental images (e.g., P31, Zn66 intensity maps) and need to compute a new derived image by applying per-pixel operations—such as elemental ratios, thresholding, masking, or conditional logic—across channels.
    2 installs
51. ▌
    Pfam Domain Hit Extraction · holobiomicslab

    Use when you have BGC sequences (in FASTA or GenBank format) and need to identify conserved biosynthetic domains to build a feature vector for BGC similarity clustering or to annotate gene functions.
    0 installs
52. ▌
    Port Mapping Configuration · holobiomicslab

    Use when when you have a containerized web application with a fixed internal port (e.g., Tomcat on port 8080) and need to expose it on a different localhost port for local access or testing.
    2 installs
53. ▌
    Principal Curve Projection · holobiomicslab

    Use when you have per-sample metabolite abundance data and a metabolite-pathway association table, and you need to quantify dysregulation of individual samples across multiple metabolic pathways.
    0 installs
54. ▌
    Projected Area Computation · holobiomicslab

    Use when you have 3D optimized molecular conformers (RDKit mol objects or SDF files) and need to extract shape-based features for collision cross section prediction, graph neural network input, or conformer comparison.
    0 installs
55. ▌
    Pubchem Metadata Retrieval · holobiomicslab

    Use when after compound database dereplication (via SIRIUS or MetFrag) has produced per-spectrum candidate annotation lists with putative compound identifiers, and before applying selection criteria to rank and filter candidates.
    1 install
56. ▌
    Python Environment Pinning · holobiomicslab

    Use when when you have access to a research repository or README documenting a machine learning implementation (e.g., Keras/TensorFlow-based deep learning model) and need to reproduce the computational environment exactly. Triggers include: (1) README explicitly lists pinned versions (e.
    1 install
57. ▌
    Python Unit Test Execution · holobiomicslab

    Use when after rewriting or modifying a Python module (such as calculate_feature_overlap.py in a metabolomics analysis tool) and you need to verify that the refactored code maintains backward compatibility and correctness against the original test suite.
    0 installs
58. ▌
    R List Object Manipulation · holobiomicslab

    Use when you have extracted metadata or spectral information from a Thermo Fisher Scientific .
    0 installs
59. ▌
    R Package Function Mapping · holobiomicslab

    Use when you have a working R package (e.g., IonFlow for ionomics analysis) with documented functions and parameters, and you need to wrap it as a Galaxy tool so end users can invoke the R workflow through Galaxy's web interface without command-line expertise.
    0 installs
60. ▌
    Redis Queue Job Submission · holobiomicslab

    Use when you have an OpenMS workflow ready to execute in online_deployment:true mode with Redis available, and you need to submit it as a queued job artifact rather than blocking the Streamlit thread. Trigger conditions: (1) online_deployment flag is true in settings;
    0 installs
61. ▌
    Rust Build And Compilation · holobiomicslab

    Use when when you have Rust source code (such as the mzPeak format implementation at the repository root) and need to generate executable binaries or libraries for converting mass-spectrometry file formats, validating output files, or reading/writing domain-specific formats like mzPeak.
    0 installs
62. ▌
    Shiny Reactive Programming · holobiomicslab

    Use when you have an R package with analytical functions (e.g., meta-analysis, statistical modeling, visualization) and need to expose it as an interactive web interface where end-users can upload data, adjust parameters, and view results in real time without rewriting backend logic.
    0 installs
63. ▌
    Smiles Sdf Format Handling · holobiomicslab

    Use when you have downloaded or obtained a dataset of small molecules with structures encoded as SMILES strings or SDF files (e.
    0 installs
64. ▌
    Spectral Bucket Assignment · holobiomicslab

    Use when you have a collection of mass spectrometry spectral data (m/z and intensity pairs) that must be indexed for fast neighbor retrieval or similarity search, and you need to trade some precision in similarity matching for substantial gains in query speed and memory efficiency across large.
    0 installs
65. ▌
    Spectral Metadata Grouping · holobiomicslab

    Use when processing a mass spectrometry dataset (in FragHub JSON format or similar) where duplicate spectral records are suspected or known to exist. The input dataset should already be in a standardized format with computed or retrievable SPLASH keys.
    0 installs
66. ▌
    Statistical Power Analysis · holobiomicslab

    Use when you have implemented or obtained a statistical method (e.g., PaIRKAT) and need to quantify its statistical power—the probability of correctly rejecting a false null hypothesis—across a range of realistic experimental scenarios before applying it to real data or publishing results.
    0 installs
67. ▌
    Twim Ms Data Preprocessing · holobiomicslab

    Use when you have raw or processed TWIM-MS experimental data (arrival times, m/z, ion mobility parameters) and need to compute class-conditioned CCS values or assign biomolecular class labels directly from high-dimensional ion mobility measurements.
    0 installs
68. ▌
    Unwanted Variation Removal · holobiomicslab

    Use when metabolomics featuredata exhibits unwanted variation from batch effects, matrix effects, or confounding factors;
    0 installs
69. ▌
    Validator Tool Integration · holobiomicslab

    Use when you have a repository of structured records (e.g., mass spectrometry data, metadata, or domain-specific formats) and need to enforce validation rules systematically across all records.
    0 installs
70. ▌
    Weka Format Pathway Export · holobiomicslab

    Use when you have computed a pathway dysregulation score matrix (PDSmatrix) from metabolomics data and need to rank pathways by their relevance to a binary or multi-class phenotype label using information-gain scoring, then export the ranked set for use in machine learning classifiers (SVM, Random.
    0 installs
71. ▌
    Accurate Mass Database Search · holobiomicslab

    Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z values to a reference database and want to recover HMDB identifiers, molecular formulas, and structural annotations for.
    0 installs
72. ▌
    Ce Ms Data Import And Parsing · holobiomicslab

    Use when you have raw CE-MS instrument output in mzML or netCDF format and need to extract specific ion traces (by m/z value), filter by effective mobility windows, or apply transformations to migration time data.
    0 installs
73. ▌
    Cosine Similarity Computation · holobiomicslab

    Use when when comparing two MS/MS spectra (query and reference) to quantify their spectral resemblance for compound identification or molecular networking, particularly when you need a simple, symmetric measure that is insensitive to precursor mass differences and does not require peak alignment.
    2 installs
74. ▌
    Mobility Scale Transformation · holobiomicslab

    Use when analyzing CE-MS(/MS) data where electroosmotic flow fluctuations cause variable migration times for the same compounds across runs.
    2 installs
75. ▌
    Ms2 Annotation Interpretation · holobiomicslab

    Use when after GNPS spectral library search has returned matched chemical annotations (with m/z values and cosine similarity scores) for MS/MS spectra.
    0 installs
76. ▌
    Multi Platform Ms Integration · holobiomicslab

    Use when you have untargeted metabolomics data from multiple MS instruments (e.
    0 installs
77. ▌
    Bleu Score Metric Computation · holobiomicslab

    Use when you have a trained sequence-to-sequence model (such as GCMSFormer) that predicts mass spectra from overlapped peaks, and you need to evaluate model performance on a held-out test set.
    0 installs
78. ▌
    Chromatogram Artifact Removal · holobiomicslab

    Use when raw NetCDF-format GCxGC-MS chromatograms exhibit steady or increasing baseline intensity caused by instrumental contamination, column bleeding, or thermal drift;
    2 installs
79. ▌
    Coeluting Compound Resolution · holobiomicslab

    Use when analyzing complex GC-MS mixtures where two or more chemical compounds elute at similar or identical retention times, producing overlapping or merged peaks in the raw chromatogram.
    2 installs
80. ▌
    Feature Table Matrix Assembly · holobiomicslab

    Use when when you need to generate a realistic LC/GC-MS feature table (peak intensity matrix) with controlled, quantifiable condition effects (e.g., differential metabolite abundance across disease states) and batch effects (e.g., instrument drift, sample processing day).
    0 installs
81. ▌
    Fixed Size Integration Method · holobiomicslab

    Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.
    2 installs
82. ▌
    Gc Ms Abundance Preprocessing · holobiomicslab

    Use when after autoQ has extracted isotopologue peak area measurements from mz(X)ML files and you need to prepare the integrations data frame for visualization with metBarPlot or comparative analysis.
    2 installs
83. ▌
    Gc Ms Chromatogram Processing · holobiomicslab

    Use when when working with raw GC-MS data in NetCDF (ANDI) format that requires peak detection, baseline removal, and retention time alignment before spectral matching against reference libraries such as PNNLMetV20191015.MSL.
    0 installs
84. ▌
    Gcims Dataset Object Creation · holobiomicslab

    Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS preprocessing pipeline.
    2 installs
85. ▌
    Gnps Spectral Data Processing · holobiomicslab

    Use when your input is raw or semi-processed MS/MS spectra fetched from GNPS or a compatible library (e.g., EMBL-MCF 2.0, NIST23) and you need to prepare them for neural-network-based formula prediction.
    0 installs
86. ▌
    Level 4 Annotation Assignment · holobiomicslab

    Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
    0 installs
87. ▌
    Mass Spectrum Tensor Encoding · holobiomicslab

    Use when when you have parsed EI-MS spectrum data (m/z and intensity values) and need to feed it into a pre-trained MWFormer transformer model for direct molecular weight prediction.
    2 installs
88. ▌
    Metabolite Cluster Evaluation · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to cross-validate the two available scoring methods (findMain and RAMClustR internal scoring) to identify cases where they.
    0 installs
89. ▌
    Metabolomic Feature Alignment · holobiomicslab

    Use when you have two or more CSV feature tables from independent metabolomic experiments (each with RT, m/z, intensity, isotope, and adduct columns), and you need to merge them into a single aligned feature matrix for downstream batch effect removal, marker identification, or pathway analysis.
    0 installs
90. ▌
    Ms Data Format Identification · holobiomicslab

    Use when when receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline. Specifically, apply this skill when: (1) input files arrive without documented instrument type or chromatographic/mobility dimensionality;
    2 installs
91. ▌
    Nps Classification Prediction · holobiomicslab

    Use when you have an unknown mass spectrum from a suspicious analyte and need to determine whether it matches a known NPS or a derivative thereof. The analyte's mass spectrum is available in MSP or equivalent format, and you have a core drug structure to enumerate derivatives from.
    0 installs
92. ▌
    Qc Sample Type Classification · holobiomicslab

    Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization steps.
    0 installs
93. ▌
    Tandem Ms Data Reorganization · holobiomicslab

    Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment fields rather than in dedicated SMILES/InChIKey fields, or when positive and negative ionization mode spectra are commingled.
    0 installs
94. ▌
    Adduct Mass Offset Assignment · holobiomicslab

    Use when when you have an LC-MS feature table with m/z and retention time columns and need to identify which observed ions correspond to the same neutral compound under different ionization conditions and isotopic enrichment.
    0 installs
95. ▌
    Adduct Mass Shift Calculation · holobiomicslab

    Use when when you have a list of observed m/z values from LC/MS feature detection and need to identify candidate metabolites by testing whether those m/z values correspond to known database compounds in specific ionization forms.
    0 installs
96. ▌
    Adduct Regex Pattern Matching · holobiomicslab

    Use when ingesting mass spectrometry spectra from heterogeneous databases or libraries where adduct annotations may be incomplete, incorrectly formatted, or inconsistent with the ionization mode. Use it before downstream analysis (e.
    0 installs
97. ▌
    Anchor Feature Pair Selection · holobiomicslab

    Use when after completing feature m/z grouping and pairwise alignment detection on two LC-MS datasets acquired under non-identical conditions.
    0 installs
98. ▌
    Baseline Comparative Analysis · holobiomicslab

    Use when your research proposes a new spectral embedding, matching algorithm, or retrieval method and you need to quantify its improvement over known baselines. Specifically, when you have a test dataset (e.
    0 installs
99. ▌
    Binary Additive Flag Encoding · holobiomicslab

    Use when constructing HPLC column feature vectors from raw metadata that includes additive composition flags (e.g., presence/absence or concentration of formic acid, acetic acid, TFA, or phosphoric acid in mobile phase eluents A and B).
    2 installs
100. ▌
     Bioactivity Score Aggregation · holobiomicslab

     Use when when you have both (1) a molecular network graph from GNPS with aligned MS/MS features (nodes and edges) and (2) a bioassay-guided fractionation activity matrix (fractions × bioactivity measurements), and you need to determine which molecular features are responsible for observed.
     0 installs