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HolobiomicsLab

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1. ▌
   R Graphics Customization · holobiomicslab

   Use when when you have completed a comprehensive ranking of preprocessing workflows (e.
   0 installs
2. ▌
   R Object Slot Inspection · holobiomicslab

   Use when after calling a data import function (such as read_chrom on a NetCDF chromatogram file) that returns a structured S4 object, inspect its slots to confirm the object was constructed correctly, validate that retention times and modulation parameters were parsed as expected, and ensure the.
   2 installs
3. ▌
   R Pipe Operator Chaining · holobiomicslab

   Use when when you have a metabolomics dataset loaded into a SummarizedExperiment and need to apply a sequence of analysis steps (data loading, annotation, statistical analysis, visualization, reporting) in a reproducible, self-contained pipeline where each function's output becomes the next.
   0 installs
4. ▌
   Retention Time Windowing · holobiomicslab

   Use when you have a complete TIC (total ion current) table indexed by retention time and need to visualize or analyze only a specific time interval—for example, when isolating a chromatographic peak region (9–10 min) before plotting or when a mass spectrometry run spans a time range wider than the.
   0 installs
5. ▌
   Smiles Molecular Parsing · holobiomicslab

   Use when when you have a list of candidate metabolite identifiers in SMILES or mol format and need to programmatically apply chemical transformations (e.g., derivatization reactions), compute molecular weights, or enumerate adduct ions for mass spectrometry matching.
   2 installs
6. ▌
   Smiles String Validation · holobiomicslab

   Use when you have MSBERT-preprocessed spectral datasets (GNPS, MoNA, or MTBLS1572 format) with SMILES annotations before training a spectral embedding or compound identification model.
   0 installs
7. ▌
   Spectral Image Filtering · holobiomicslab

   Use when when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
   0 installs
8. ▌
   Tautomer Standardization · holobiomicslab

   Use when ingesting raw SMILES strings from curated structure inventories where the same chemical may be represented in multiple tautomeric forms (e.g., keto–enol pairs, lactam–lactim forms) across different literature sources or input databases.
   0 installs
9. ▌
   Threshold Sweep Analysis · holobiomicslab

   Use when when you have predicted probabilities and binary true labels from a classifier and need to evaluate its discriminative ability across multiple operating points, or when you need to generate a publication-quality ROC curve with AUC to compare classifiers or communicate model performance to.
   0 installs
10. ▌
    Type I Error Computation · holobiomicslab

    Use when when you need to verify that reported Type I error rates from a statistical method (here, PaIRKAT) can be independently reproduced, or when you require baseline false positive rate estimates across multiple simulation conditions (sample sizes, effect configurations, significance.
    0 installs
11. ▌
    C Stream Io Debugging · holobiomicslab

    Use when when a C++ program writes records to an output stream (e.g., SAM alignment file) and the final output file contains fewer records than expected based on upstream counts (e.g., salmon's NumReads total in quant.sf exceeds SAM record count), indicating buffered data loss at stream closure.
    2 installs
12. ▌
    Salmon Output Parsing · holobiomicslab

    Use when when you have salmon quant.sf.gz output files from pseudoalignment-based transcript quantification and need to convert transcript-level abundance estimates and counts into gene-level matrices for differential expression analysis with edgeR, DESeq2, or limma-voom.
    2 installs
13. ▌
    Matlab Scientific Computing · holobiomicslab

    Use when you have mass spectrometry data in mzXML or mzML format and need to systematically extract regions of interest (ROIs) from multi-dimensional m/z-intensity-time arrays, normalize feature values, and augment datasets for untargeted metabolomics workflows.
    0 installs
14. ▌
    Msflo Metabolite Annotation · holobiomicslab

    Use when after MS-DIAL has completed feature detection and peak alignment on .mzML LC-HRMS data, producing an aligned feature table. Use MSFLO when you need to assign metabolite identities to detected features and filter results by significance criteria before downstream interpretation.
    0 installs
15. ▌
    R Data Structure Conversion · holobiomicslab

    Use when you have preprocessed MSI data in Cardinal format (post-peakBin) and need to apply mass2adduct's adduct-detection workflow, OR you have exported MSI intensity data as CSV from third-party software (SCiLS, MSiReader) and must convert it into a standardized R object for downstream analysis.
    0 installs
16. ▌
    Spectral Similarity Scoring · holobiomicslab

    Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g., PNNLMetV20191015.MSL) to identify the unknown compound.
    0 installs
17. ▌
    Spectrum Similarity Scoring · holobiomicslab

    Use when you have an unknown MS/MS spectrum (query spectrum with m/z and intensity pairs) and a reference spectral library (local or public: GNPS, MASSBANK, DrugBANK), and you need to identify the -matching compounds by ranking library entries by spectral similarity.
    0 installs
18. ▌
    Vendor Data Standardization · holobiomicslab

    Use when you have raw MS data files directly from a vendor instrument (Thermo .raw, Agilent .d, Waters .ms, etc.) and need to process them through AriumMS or any other metabolomics pipeline that accepts only .mzXML or .mzML formats.
    0 installs
19. ▌
    Binary Data Base64 Encoding · holobiomicslab

    Use when when converting simulated or real LC/GC-MS spectral data (m/z–retention-time intensity matrices) into mzML format for archival, sharing, or downstream processing.
    0 installs
20. ▌
    Ei Mass Spectrum Simulation · holobiomicslab

    Use when when you have a molecular structure (XYZ or equivalent format) and need to predict its EI mass spectrum including major fragment ions and their relative intensities, particularly for validation against experimental data or when experimental spectra are unavailable;
    0 installs
21. ▌
    Gcms Spectrum Deconvolution · holobiomicslab

    Use when input GC-MS data (netCDF or mzML format) exhibits overlapping chromatographic peaks where multiple analytes co-elute at the same retention time, resulting in composite mass spectra that conflate signals from distinct molecular species.
    0 installs
22. ▌
    Instrument Metadata Parsing · holobiomicslab

    Use when when you have raw or semi-processed mass spectrometry data files in mixed formats (e.g., vendor-native .raw, .d, .
    2 installs
23. ▌
    Java Source Code Inspection · holobiomicslab

    Use when when you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format types (e.
    2 installs
24. ▌
    Lipid Feature Normalization · holobiomicslab

    Use when after raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate statistical analysis to identify differential lipids and metabolites.
    2 installs
25. ▌
    Mass Chromatogram Alignment · holobiomicslab

    Use when after chromatographic peak detection on preprocessed LC-MS data, when you have detected features (peaks) in multiple samples and need to establish which peaks across samples represent the same molecular species.
    1 install
26. ▌
    Mass Spectrum Peak Matching · holobiomicslab

    Use when when you have a query electron ionization mass spectrum (as m/z and intensity pairs) and need to identify it against a spectral library stored in msp format.
    0 installs
27. ▌
    Mzml File Format Generation · holobiomicslab

    Use when when you need to generate reproducible synthetic LC/GC-MS raw data files with known ground-truth peak properties (m/z, retention time, intensity) for benchmarking peak detection, feature extraction, normalization, or batch correction algorithms;
    2 installs
28. ▌
    Network Topology Comparison · holobiomicslab

    Use when after executing a molecular networking workflow on GC-MS data that has been processed through auto-deconvolution, and a published reference network exists from a prior analysis of the same or analogous dataset.
    0 installs
29. ▌
    Network Topology Validation · holobiomicslab

    Use when after retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra. Use this skill to confirm the network structure is sound before performing chemical similarity searches, community detection, or annotation.
    2 installs
30. ▌
    R Data Structure Processing · holobiomicslab

    Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100 s) and drift time (5–16 ms) ranges, or when you need to apply smoothing, decimation, or baseline correction to raw GCIMS.
    2 installs
31. ▌
    Reactant Ion Peak Exclusion · holobiomicslab

    Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion source) would otherwise be misidentified as an analyte peak, causing false positives in the peak list.
    2 installs
32. ▌
    Spectral Feature Annotation · holobiomicslab

    Use when after auto-deconvolution has resolved co-eluting GC-MS peaks into individual component spectra.
    2 installs
33. ▌
    Spectral Feature Extraction · holobiomicslab

    Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.
    0 installs
34. ▌
    Spectrum Metadata Filtering · holobiomicslab

    Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality. Use when you observe spectra annotated with negative adducts (e.
    0 installs
35. ▌
    Transformer Model Inference · holobiomicslab

    Use when you have electron ionization mass spectrum data (m/z and intensity pairs) and a pre-trained transformer model checkpoint, and you need to predict molecular weight directly from the spectrum without manual feature engineering or rule-based methods.
    0 installs
36. ▌
    Two Dimensional Tic Folding · holobiomicslab

    Use when immediately after acquiring raw GCxGC-MS data in NetCDF format (.cdf files) and before any signal enhancement (smoothing, baseline correction) or alignment steps.
    0 installs
37. ▌
    Unique Compound Enumeration · holobiomicslab

    Use when you have a GC-MS results table with a Match.Factor column (representing identification confidence) and you need to understand how many distinct compounds survive at different quality cutoffs (e.g., ≥65, ≥80, ≥90).
    0 installs
38. ▌
    Benchmark Harness Execution · holobiomicslab

    Use when you have post-processed clustering results from multiple tools (msCluster, Falcon, MaRaCluster) on the same tandem MS dataset and need to generate a comparative performance report with quality metrics and runtime statistics to determine which tool suits your metabolomics workflow.
    0 installs
39. ▌
    Chemical Class Node Mapping · holobiomicslab

    Use when you have a GNPS mass spectral molecular network (in graphml or cytoscape format) and want to enrich its nodes with chemical class information derived from GNPS public library spectral matches.
    2 installs
40. ▌
    Command Line Tool Execution · holobiomicslab

    Use when you have tandem MS/MS spectrum data in standard peak file formats (mzML, mzXML, or MGF) and need to cluster spectra based on precursor mass and fragment ion similarity.
    0 installs
41. ▌
    Compound Count Verification · holobiomicslab

    Use when after modifying a FIDDLE configuration file to add or remove instrument types from the allowlist (e.g., adding 'ftms' to gnps_orbitrap), run the full preprocessing pipeline and validate that the resulting training and test set sizes match documented targets.
    0 installs
42. ▌
    Confusion Matrix Generation · holobiomicslab

    Use when after training or evaluating a classification model (e.g., MS2DeepScore or other neural networks) when you have paired arrays of predicted class labels and ground-truth labels and need to assess per-class prediction accuracy, false positive/negative rates, or class imbalance effects.
    0 installs
43. ▌
    Cross Assay Feature Linkage · holobiomicslab

    Use when when you have structural clusters from multiple LC-MS assays (e.g., positive and negative ion modes, or reversed-phase and HILIC methods) and need to identify which features across assays represent the same underlying metabolite.
    2 installs
44. ▌
    Cross Method Rt Calibration · holobiomicslab

    Use when when you have predicted retention times from a DNN model trained on one chromatographic method (CM) and need to rank or filter metabolite candidates on a different chromatographic method, but have only a small set of calibration molecules (≥10) with known RTs on both source and target.
    0 installs
45. ▌
    D Ratio Threshold Filtering · holobiomicslab

    Use when after signal drift correction (step 4) has computed per-feature D-Ratio values, and before normalization (step 7).
    0 installs
46. ▌
    Database Similarity Scoring · holobiomicslab

    Use when you have one or more MS/MS spectra (query spectra in mzML, mzXML, or MGF format) and need to identify unknown compounds by comparing them against curated spectral databases organized by biological domain (microbe, plant, tissue, microbiome, food).
    2 installs
47. ▌
    Dia Data Format Recognition · holobiomicslab

    Use when you have raw mass spectrometry data from a DIA acquisition method and need to determine whether it is MS^E, All-Ion Fragmentation (AIF), or SWATH-MS before loading into IDSL.CSA for fragmentation spectra deconvolution.
    2 installs
48. ▌
    Dia File Quality Prediction · holobiomicslab

    Use when you have a batch of DIA mass spectrometry raw files (.raw, .d, or .wiff formats) from known instrument types (timsTOF, TripleTOF, or Orbitrap) and need to classify each file as pass/fail or assign a quality label.
    0 installs
49. ▌
    Feature Fidelity Prediction · holobiomicslab

    Use when you have a feature table (CSV with m/z and retention time columns) and corresponding .mzXML or .mzML mass spectrometry files from an LC-MS metabolomics experiment, and you need to filter out false or low-quality chromatographic peaks before downstream analysis.
    2 installs
50. ▌
    Feature Metadata Annotation · holobiomicslab

    Use when you have processed mass spectrometry data consisting of three separate tables (quantification features, sample metadata, and spectral annotations) and need to combine them into a single, queryable artifact that preserves relationships between features, samples, and their chemical.
    0 installs
51. ▌
    Feature Table Normalization · holobiomicslab

    Use when you have peak/feature tables from one or more peak picking tools (MZmine, XCMS, MS-DIAL, Compound Discoverer) and need to ingest them into LipidMatch or combine results from multiple tools in a single lipidomics workflow.
    0 installs
52. ▌
    Formula Stratified Sampling · holobiomicslab

    Use when when preparing MS/MS spectral training data where: (1) the initial TCN train/test split contains imbalanced positive and negative examples, (2) certain molecular formulas are over-represented in the positive class, (3) you are training a Siamese architecture rescore model that requires.
    0 installs
53. ▌
    Gnps Data Schema Validation · holobiomicslab

    Use when after extracting a GNPS molecular networking job archive using GNPSExtractor, before calling npl.load_data().
    2 installs
54. ▌
    Gpu Accelerated Computation · holobiomicslab

    Use when when processing large-scale mass spectrometry datasets (>1 million spectra) where CPU-based clustering runtime would exceed minutes to hours, and when the analysis pipeline includes: (1) encoding raw spectra into high-dimensional binary vectors, (2) computing pairwise distance matrices.
    0 installs
55. ▌
    Graph Enrichment Operations · holobiomicslab

    Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived substructural motifs (from classical or feature-based LDA experiments) in a single integrated operation, typically for.
    2 installs
56. ▌
    Lcms Feature Classification · holobiomicslab

    Use when you have an LCMS feature table annotated with MS2 spectral data and need to distinguish in-source fragments (mass loss patterns, same retention time, MS2 spectral relationships) from true metabolite features.
    0 installs
57. ▌
    Lcms Result Table Structure · holobiomicslab

    Use when after completing Part 4 (Identification of ISF Features) in the ISFrag workflow, when you have an analysis results object containing identified ISF features and need to generate a shareable, tabular export that documents feature annotations, hierarchical parent–fragment relationships, and.
    0 installs
58. ▌
    Lcms Workflow Orchestration · holobiomicslab

    Use when starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z, retention time, and intensity values across all samples.
    0 installs
59. ▌
    Lipid Library Format Schema · holobiomicslab

    Use when you have identified lipid species unique to your experimental system (e.
    0 installs
60. ▌
    Mass Accuracy Ppm Filtering · holobiomicslab

    Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
    2 installs
61. ▌
    Mass Spectral M Z Alignment · holobiomicslab

    Use when after you have (1) identified putative labelled features with intensity and m/z measurements from LC/MS data (e.g., via basepeak_finder output in geoRge), (2) defined a list of expected ionization adducts (e.
    2 installs
62. ▌
    Mass Spectrum M Z Alignment · holobiomicslab

    Use when when working with multidimensional MS data (LC–IM–MS/MS) converted to MZA format where spectra are stored in jagged arrays with m/z values distributed across individual HDF5 datasets per scan, and you need to ensure m/z consistency for downstream peak detection, isotope analysis, or.
    0 installs
63. ▌
    Mass Spectrum Preprocessing · holobiomicslab

    Use when you have raw MS/MS spectra in MGF format with variable peak quality, mixed charge states, or instrument artifacts that could confound clustering or similarity measures.
    0 installs
64. ▌
    Mass Spectrum Visualization · holobiomicslab

    Use when when you have extracted m/z and intensity arrays from an MZA file (or similar HDF5-backed MS data structure) and need to visually inspect a single MS1 or MS2 spectrum, verify peak characteristics, or diagnose data quality issues before downstream analysis (peak fitting, isotope pattern.
    0 installs
65. ▌
    Md Defect Ratio Calculation · holobiomicslab

    Use when you have a feature table from LC- or GC-HRMS data (either detected via pyOpenMS or imported as a custom feature list) containing m/z, retention time, and intensity values, and you want to rapidly filter to candidate PFAS features that exhibit the elevated mass defects typical of.
    2 installs
66. ▌
    Metabolite Feature Flagging · holobiomicslab

    Use when after drift correction and before imputation, when you have a MetaboSet object with LC-MS peak abundances and need to remove features with insufficient detection consistency across QC samples.
    0 installs
67. ▌
    Metabolite Ms Ms Annotation · holobiomicslab

    Use when when you have SWATH-MS raw data (mzML or vendor format) containing multiplexed MS/MS spectra from multiple co-eluting precursor ions and need to separate these spectra into individual, annotatable component spectra for metabolite identification.
    2 installs
68. ▌
    Metadata Integrity Checking · holobiomicslab

    Use when after processing LCMS feature data through Blueshift or Gravity but before finalizing results.
    0 installs
69. ▌
    Model Ablation Study Design · holobiomicslab

    Use when you need to measure how much a specific model capability or architectural feature contributes to prediction performance, especially when that capability is non-obvious or orthogonal to baseline methods.
    2 installs
70. ▌
    Model Comparison Evaluation · holobiomicslab

    Use when when you have multiple candidate spectrum prediction models (e.g., FFN vs. GNN encoders, NEIMS vs. MassFormer vs. ICEBERG) and need to determine which performs better on a shared task like tandem mass spectrum prediction.
    0 installs
71. ▌
    Molecular Candidate Ranking · holobiomicslab

    Use when after a trained CNN model has generated molecular embeddings for query spectra, and you need to retrieve the most likely candidate molecules from a reference database.
    2 installs
72. ▌
    Ms Ms Spectrum Purification · holobiomicslab

    Use when processing LC-MS/MS data acquired in DDA mode that contains chimeric (co-fragmented) MS/MS spectra—i.e., when a single MS/MS scan contains fragments from multiple precursor ions due to co-isolation.
    2 installs
73. ▌
    Ms2 Spectral Interpretation · holobiomicslab

    Use when you have extracted an MS1 feature table (from XCMS or custom CSV with m/z, retention time, and intensity columns) and one or more DDA mzXML files from the same or related LC-MS runs, and you need to annotate features with MS2 spectral data and match them against a standard spectral library.
    0 installs
74. ▌
    Multi Module Joint Training · holobiomicslab

    Use when when you have a pretrained encoder that captures domain knowledge (e.g., spectral feature extraction) and need to train task-specific decoder or scoring modules on top of it without degrading the encoder's learned representations.
    0 installs
75. ▌
    Nextflow Workflow Execution · holobiomicslab

    Use when you have .mzML or .abf LC-HRMS metabolomics raw data files and need to perform peak detection, feature identification, and chromatogram alignment reproducibly across different compute environments (local workstations, HPC clusters).
    0 installs
76. ▌
    Organism Metadata Retrieval · holobiomicslab

    Use when when a project JSON document contains genome identifiers but lacks corresponding organism name annotations, and you need to link MS/MS mass spectra with genomic context for downstream biosynthetic gene cluster or chemical ecology analysis.
    0 installs
77. ▌
    Pairwise Matrix Computation · holobiomicslab

    Use when when you have a cleaned MS/MS dataset with chemical structure annotations (SMILES, InChI, or InChIKey) and need to generate ground-truth structural similarity labels for training a deep learning model.
    1 install
78. ▌
    Parent Tp Mapping Structure · holobiomicslab

    Use when you have generated a TP object (from generateTPs) with structural information (SMILES) for predicted or library-derived transformation products, and you need to either (1) construct a MetFrag-compatible database that preserves parent compound records alongside TPs, or (2) componentize.
    2 installs
79. ▌
    Peak Detection In Lcms Data · holobiomicslab

    Use when after retention-time correction has been completed on centroided LC-MS data (mzML or mzXML format) and you need to identify all detected peaks as a unified feature table across a cohort of samples.
    0 installs
80. ▌
    Peak Table Format Detection · holobiomicslab

    Use when when receiving a peak or feature table output from an unknown or variable upstream peak-picking tool, and you need to route it to the correct ingestion adapter (e.g., in LipidMatch) to normalize and validate it before lipid identification.
    0 installs
81. ▌
    Pfas Feature Prioritization · holobiomicslab

    Use when you have detected features in LC- or GC-HRMS data (via pyOpenMS or custom feature tables) and need to systematically rank them for likelihood of being PFAS compounds.
    0 installs
82. ▌
    Project Metadata Validation · holobiomicslab

    Use when when a user uploads a JSON project document to the Pairing Omics Data Platform, before accepting it into the repository or indexing it for search. Use this skill to catch missing required fields, incorrect field types, and constraint violations early in the submission workflow.
    2 installs
83. ▌
    Pubchem Structure Retrieval · holobiomicslab

    Use when you have an experimental tandem mass spectrum and chemical formula for an unknown compound, and need to identify the true structure among all PubChem entries with that formula.
    0 installs
84. ▌
    Annotation Scoring And Ranking · holobiomicslab

    Use when you have experimental mass spectra from untargeted metabolomics and need to assign compound identities with confidence estimates.
    0 installs
85. ▌
    Chemical Shift Data Formatting · holobiomicslab

    Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar TensorFlow Serving-backed molecular classification system that expects peaks as JSON rather than raw spectroscopic files.
    0 installs
86. ▌
    Fragment To Structure Assembly · holobiomicslab

    Use when when you have spectroscopic measurements (1D ¹H or ¹³C NMR) that have been decomposed into predicted substructures or fragments, and you need to reconstruct the full molecular formula and connectivity graph.
    0 installs
87. ▌
    Inadequate Spectral Processing · holobiomicslab

    Use when you have raw INADEQUATE NMR spectrum files (e.g., in standard NMR formats) that require initial processing before metabolite annotation.
    0 installs
88. ▌
    Mass Spectral Query Submission · holobiomicslab

    Use when you have one or more individual MS/MS spectra (in mzML, mzXML, or JSON format) and need to identify the compound(s) and their biological source by searching against a domain-specific spectral library.
    0 installs
89. ▌
    Modification Site Localization · holobiomicslab

    Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally related modified (unknown) compound—and need to identify which atom(s) in the structure carry the modification.
    0 installs
90. ▌
    Nmr Modality Ablation Analysis · holobiomicslab

    Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal contribution of each NMR modality or justify multimodal input design.
    2 installs
91. ▌
    Plasma Serum Sample Comparison · holobiomicslab

    Use when you have NMR-based metabolomics measurements from a cohort containing both plasma and serum samples with associated processing delay metadata (pre- and post-centrifugation times), and you need to determine whether metabolic parameter stability differs between the two sample types or to.
    0 installs
92. ▌
    R Package Function Integration · holobiomicslab

    Use when you have a published predictive model with known coefficients and feature requirements (e.g., MetaboAge from a peer-reviewed study), a target R package with an established data pipeline (e.
    2 installs
93. ▌
    Spectral Library Matching Gnps · holobiomicslab

    Use when you have MS2 product-ion spectra in open formats (.mzML or .mzXML) from public mass spectrometry datasets (e.g., from MassIVE with a valid accession) and need to identify chemical compounds by comparing fragmentation patterns against the GNPS reference spectral library.
    0 installs
94. ▌
    Spectral Mixture Deconvolution · holobiomicslab

    Use when you have an NMR spectrum of a mixture sample and a library of reference spectra for individual compounds, and you need to determine which compounds are present and in what proportions.
    0 installs
95. ▌
    Spectral Peak Network Grouping · holobiomicslab

    Use when after peak picking has been completed on INADEQUATE NMR spectra and you need to group correlated peaks into compound-specific networks before matching against a metabolite database.
    2 installs
96. ▌
    Webworker File Access Enabling · holobiomicslab

    Use when you need to run a local HTML file that uses WebWorker or WebAssembly (such as COLMARvista for NMR spectra analysis) and the browser raises cross-origin or file-access policy errors preventing WebWorker initialization or WebAssembly module loading.
    0 installs
97. ▌
    Cooler File Format Handling · holobiomicslab

    Use when you have a Hi-C dataset stored in cooler format (e.
    2 installs
98. ▌
    Gc Content Bias Calculation · holobiomicslab

    Use when you have a SummarizedExperiment object containing peak counts from single-cell or bulk ATAC-seq/DNAse-seq data and need to prepare it for unbiased motif deviation analysis.
    0 installs
99. ▌
    Methylation Data Clustering · holobiomicslab

    Use when after merging methylation call files across all samples into a unified methylBase object (via unite()), when you need to assess whether biological replicates cluster together, identify unexpected sample groupings, or visualize global methylation similarity relationships before proceeding.
    2 installs
100. ▌
     Motif Peak Overlap Matching · holobiomicslab

     Use when you have a filtered set of non-overlapping peaks from ATAC-seq data and a collection of motifs (typically from JASPAR or similar databases), and you need to identify which peaks contain matches to which motifs as a prerequisite for computing motif-based deviation scores across samples.
     2 installs