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HolobiomicsLab

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1. ▌
   Xcms Data Import Preprocessing 3 · holobiomicslab

   Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass calibration (e.
   0 installs
2. ▌
   Annotation Scoring And Ranking 3 · holobiomicslab

   Use when you have experimental mass spectra from untargeted metabolomics and need to assign compound identities with confidence estimates.
   0 installs
3. ▌
   Arrival Time To Ccs Conversion 2 · holobiomicslab

   Use when when you have raw TWIM-MS arrival-time data and need to transform it into absolute CCS values for downstream biomolecular class assignment or comparative analysis.
   0 installs
4. ▌
   Asynchronous API Orchestration 2 · holobiomicslab

   Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to populate them by querying multiple independent web APIs in parallel.
   0 installs
5. ▌
   Asynchronous Event Aggregation 2 · holobiomicslab

   Use when your workflow fetches data from multiple external web services (e.g., CIR, CTS, PubChem, IDSM, BridgeDb) asynchronously and you need to track which services are available, how often they fail, and their response latencies during a long-running annotation job.
   0 installs
6. ▌
   Biomolecular Class Ccs Mapping 2 · holobiomicslab

   Use when after biomolecular class labels have been assigned to features in a TWIM-MS dataset and you have raw ion mobility arrival time measurements. Use it when you need to convert arrival times to standardized CCS values where calibration accuracy depends critically on the biomolecular class (e.
   0 installs
7. ▌
   Blank Sample Feature Filtering 2 · holobiomicslab

   Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data and your experimental design includes blank (negative control) samples.
   0 installs
8. ▌
   Chemical Coverage Optimization 2 · holobiomicslab

   Use when your LC-MS feature table is incomplete or has low chemical coverage because traditional peak extraction algorithms (e.g., standard XCMS workflows) systematically miss features at m/z and retention time positions corresponding to known suspect compounds in your database.
   0 installs
9. ▌
   Chemical Shift Data Formatting 2 · 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
10. ▌
    Chemical Similarity Clustering 2 · holobiomicslab

    Use when you have untargeted LC-MS/MS metabolomic data (MS1 features with MS2 fragmentation spectra) preprocessed by MZmine2 into a feature table (BIOM format) and MGF file, and you want to construct a chemically-informed hierarchy of features for alpha/beta-diversity analysis or to group features.
    0 installs
11. ▌
    Chromatogram Alignment Warping 2 · holobiomicslab

    Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference chromatogram, and you need to align peak positions across both dimensions before joining multiple samples for multiway PCA or.
    0 installs
12. ▌
    Chromatographic Noise Modeling 3 · holobiomicslab

    Use when you need to generate blank or background-only .mzML files for method validation, when you want to create synthetic negative controls with realistic instrumental noise but no analyte peaks, or when you need to simulate serum matrix background (e.
    0 installs
13. ▌
    Chromatography Data Decimation 3 · holobiomicslab

    Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g., 5–16 ms) ranges and applying Savitzky-Golay smoothing. Use it as a preprocessing step before alignment operations.
    0 installs
14. ▌
    Class Specific Ccs Calculation 2 · holobiomicslab

    Use when when you have multi-omic TWIM-MS data (raw or processed arrival-time records) and have already assigned features or detected ion features to biomolecular classes (e.
    0 installs
15. ▌
    Cluster Statistics Integration 3 · holobiomicslab

    Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did not yield detected peaks at certain cluster positions.
    0 installs
16. ▌
    Clustering Metrics Computation 2 · holobiomicslab

    Use when when you have executed multiple clustering tools on the same tandem-MS dataset and need to quantitatively compare their performance using normalized, comparable metrics rather than raw cluster assignments alone.
    0 installs
17. ▌
    Cnn Inference On Spectral Data 2 · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) in memory or on disk, a trained CNN model checkpoint available, and you need to generate molecular embedding vectors for matching against a reference database of known metabolites.
    0 installs
18. ▌
    Cross Dataset Feature Matching 2 · holobiomicslab

    Use when you have two or more feature tables in HDF5 format with detected features characterized by m/z, drift time, retention time, and intensity, and you need to match corresponding features across samples to account for systematic shifts caused by instrument variation or tuning differences.
    0 installs
19. ▌
    Cross Sample Feature Alignment 2 · holobiomicslab

    Use when you have run mass detection and chromatogram building independently on each LC-MS/MS sample and produced per-sample feature lists with m/z, retention time, and intensity values.
    0 installs
20. ▌
    Cross Spectrum Negative Mining 2 · holobiomicslab

    Use when when training a Siamese architecture rescore model for MS/MS-based molecular formula prediction and you have an imbalanced training set with far fewer negative than positive spectrum pairs.
    0 installs
21. ▌
    Data Augmentation Metabolomics 3 · holobiomicslab

    Use when you have preprocessed and normalized ROI feature data extracted from mzXML or mzML mass spectrometry files and seek to increase feature representation and robustness before statistical modeling or machine learning.
    0 installs
22. ▌
    Data Format Conversion CSV Tsv 2 · holobiomicslab

    Use when after completing data merging, cleanup, and batch correction steps in the FBMN-STATS pipeline, when you have a processed feature quantification table combined with sample metadata in memory (R data frame or Python pandas DataFrame) and need to preserve it for multivariate statistical.
    0 installs
23. ▌
    Deep Learning Model Evaluation 2 · holobiomicslab

    Use when after training a Siamese neural network on MS/MS spectrum pairs, use this skill to quantify prediction performance on a disjoint test set (e.g., 3600+ spectra from 500 unseen compounds).
    0 installs
24. ▌
    Diagnostic Fragment Annotation 2 · holobiomicslab

    Use when when you have centroided, data-dependent acquisition (ddMS2) spectra in mzML format with extracted precursor m/z values and associated fragment ion lists, and you need to discriminate PFAS features from background signals using characteristic fragmentation patterns.
    0 installs
25. ▌
    Drift Retention Time Alignment 3 · holobiomicslab

    Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature fluctuations or chromatographic column degradation, and you need to normalize sample positions before downstream peak.
    0 installs
26. ▌
    False Positive Rate Assessment 2 · holobiomicslab

    Use when you have run ORA on simulated metabolite sets with known null conditions (no true pathway enrichment) and need to measure how detection coverage, pathway database size, or other experimental parameters inflate Type I error rates.
    0 installs
27. ▌
    Feature Statistical Annotation 3 · holobiomicslab

    Use when after LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes. Use this skill when you have access to a reference list of molecules of interest (e.
    0 installs
28. ▌
    Fragment Intensity Aggregation 2 · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files but before consensus spectrum generation, when you observe high-resolution fragment lists where nearby peaks (within a specified mass tolerance, typically 0.
    0 installs
29. ▌
    Fragment Ion Spectral Matching 2 · holobiomicslab

    Use when after pointwise correlation analysis and exact mass difference refinement have identified candidate ion-species pairs that may share a common analyte origin.
    0 installs
30. ▌
    Fragment To Structure Assembly 2 · 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
31. ▌
    Full Scan Acquisition Strategy 2 · holobiomicslab

    Use when you need to assess MS1-level ionization efficiency, peak detection sensitivity, and chromatographic separation without the overhead of MS/MS fragmentation. Use it to benchmark full-scan detection across chemically diverse samples (e.
    0 installs
32. ▌
    Gc Ims Matrix Table Generation 3 · holobiomicslab

    Use when after integratePeaks has been executed with a chosen integration method (e.g., fixed_size with RIP saturation threshold of 0.1) on a clustered, baseline-corrected GC-IMS dataset.
    0 installs
33. ▌
    Gcxgc Ms Multivariate Analysis 2 · holobiomicslab

    Use when after preprocessing a set of aligned 2D-TIC (two-dimensional Total Intensity Chromatogram) matrices from GCxGC-MS experiments—when you have multiple samples across distinct biological groups (e.
    0 installs
34. ▌
    Github Actions API Integration 2 · holobiomicslab

    Use when when you need to verify that a GitHub Actions workflow (such as a development build or release pipeline) executes without fatal errors and produces expected artifacts. Use this skill when the workflow is already configured in a repository (e.g., a .yml file in .
    0 installs
35. ▌
    Graph Based Feature Annotation 2 · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and corresponding MS2LDA substructural feature assignments or chemical class predictions, and you want to systematically propagate these annotations to individual network nodes to enable feature-aware visualization and.
    0 installs
36. ▌
    Hdf5 Format Support Validation 2 · holobiomicslab

    Use when when you need to work with mzMLb (HDF5-based) proteomics data in pyteomics and want to confirm that the required h5py and hdf5plugin libraries are installed and accessible, or when troubleshooting ImportError or missing format handler issues related to mzMLb modules.
    0 installs
37. ▌
    Hierarchical Database Indexing 2 · holobiomicslab

    Use when when you have a large combinatorial chemical space (e.g., all regioisomeric positions of lipid double bonds across carbon counts and saturation levels) and need to query it repeatedly against experimental mass spectrometry spectra.
    0 installs
38. ▌
    Inadequate Spectral Processing 2 · 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
39. ▌
    Instrument Type Filtering Gnps 2 · holobiomicslab

    Use when you have a large, mixed-instrument GNPS spectral dataset and need to create an instrument-specific training set for FIDDLE or similar deep learning models. Use this skill when your configuration file specifies an instrument allowlist (e.
    0 installs
40. ▌
    Intensity Threshold Evaluation 2 · holobiomicslab

    Use when you have processed LC-MS data (mzML or vendor format) and need to validate that internal standards and target analytes produce peak intensities within expected operational ranges.
    0 installs
41. ▌
    Iokr Kernel Regression Scoring 2 · holobiomicslab

    Use when when you have paired genomics (antiSMASH-detected BGCs with MIBiG homology assignments) and metabolomics data (MS2 spectra from GNPS), and you need to score BGC-spectrum links using molecular structure similarity rather than strain co-occurrence patterns.
    0 installs
42. ▌
    Ionization Mode Classification 2 · holobiomicslab

    Use when when converting raw MS/MS spectral records (e.g. from .msp format) into metabolite fragment database entries for MetaboAnnotatoR, and the output filenames or library index must distinguish between positive and negative ionization modes to ensure correct library selection during annotation.
    0 installs
43. ▌
    Isotopic Enrichment Simulation 2 · holobiomicslab

    Use when you have a peptide sequence and need to predict its theoretical m/z values under partial or complete isotopic enrichment (e.g., 1% natural 13C abundance, 50% 13C labeling, or other SIP conditions).
    0 installs
44. ▌
    Java Build Artifact Validation 2 · holobiomicslab

    Use when when you need to verify that a Java project's automated build pipeline (GitHub Actions workflow) executes without errors and generates distributable artifacts (e.g., .deb installers, portable binaries, or .jar files).
    0 installs
45. ▌
    JSON Validation And Formatting 2 · holobiomicslab

    Use when after enriching a project JSON document with external metadata (e.g., organism names, genome identifiers) or before writing enriched JSON to disk.
    0 installs
46. ▌
    Keras Model Conversion To Hdf5 2 · holobiomicslab

    Use when you have pre-trained Keras models from the NP-Classifier repository that must be deployed via TensorFlow Serving and need to expose standardized input/output layer names ('input_2048', 'input_4096', 'output') for integration with the classification API.
    0 installs
47. ▌
    Lc Ms Peak Feature Engineering 2 · holobiomicslab

    Use when you have LC-MS feature tables with m/z and retention time coordinates paired with raw .mzXML or .mzML data files, and you need to systematically assess which features correspond to genuine chromatographic peaks versus noise or artifacts.
    0 installs
48. ▌
    Link Scoring Metcalf Algorithm 2 · holobiomicslab

    Use when you have loaded GCFs (from AntiSMASH via BigScape clustering), GNPS spectra, and molecular families (from GNPS molecular networking), and need to compute pairwise scoring between genomic and metabolomic entities to identify putative gene cluster–metabolite associations.
    0 installs
49. ▌
    Mass Fragment Pattern Querying 2 · holobiomicslab

    Use when after LDA modeling has produced an inferred motifset (JSON format) containing Mass2Motifs with fragment and neutral-loss patterns.
    0 installs
50. ▌
    Mass Spectral Query Submission 3 · 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
51. ▌
    Mass Spectrometry Data Loading 3 · holobiomicslab

    Use when you have raw MS data files from supported instruments (Agilent, Thermo, Bruker, or mzML format) and need to ingest them into IonToolPack for visualization, quality control, targeted extraction, or spectral library matching.
    0 installs
52. ▌
    Mass Spectrum De Novo Analysis 2 · holobiomicslab

    Use when you have an unknown MS/MS spectrum (m/z and intensity pairs) from positive-mode ionization and need to identify the most likely molecular formula and adduct type (e.g., [M+H]+, [M+Na]+) when no reference library match is available or desirable.
    0 installs
53. ▌
    Metabolite Coverage Simulation 2 · holobiomicslab

    Use when designing or validating a metabolomics pathway analysis experiment, especially when you have uncertainty about how many metabolites your detection platform will reliably measure relative to a pathway database. Use it if you want to understand whether your expected metabolite coverage (e.
    0 installs
54. ▌
    Mona Metadata Field Extraction 3 · holobiomicslab

    Use when when you have loaded a MoNA mass spectral library (GC-MS or LC-MS/MS) in MSP format and observe that SMILES strings are present in the Comment field rather than in a dedicated SMILES metadata field.
    0 installs
55. ▌
    Ms Data Constraint Enforcement 2 · holobiomicslab

    Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend. Triggers include: (1) implementing a replacement method (e.g., mz<- or intensity<-) for a backend class;
    0 installs
56. ▌
    Ms2lda Substructure Assignment 2 · holobiomicslab

    Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected substructural motifs to identify shared fragmentation patterns and structural classes across molecular families.
    0 installs
57. ▌
    Multi Class Network Annotation 2 · holobiomicslab

    Use when you have (1) metabolite-disease correlation matrices and protein association predictions generated by a deep learning module (e.
    0 installs
58. ▌
    Multi Sample Cohort Assessment 3 · holobiomicslab

    Use when when you have MS1 mass spectrometry data from multiple samples (a cohort) acquired across an instrument run or batch, and you need to identify which samples deviate from cohort norms or which ion targets show anomalous behavior.
    0 installs
59. ▌
    Multi Species Lipid Prediction 2 · holobiomicslab

    Use when you have candidate lipid annotations from high-throughput spectral matching (e.
    0 installs
60. ▌
    Neural Network Scoring Ranking 2 · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs), a set of candidate chemical formula–adduct pairs (enumerated via SIRIUS or another generator), and need to rank them by credibility without access to a spectrum library.
    0 installs
61. ▌
    Nextflow Profile Customization 2 · holobiomicslab

    Use when you need to execute a Nextflow metabolomics workflow (e.
    0 installs
62. ▌
    Outlier Feature Classification 2 · holobiomicslab

    Use when after peak picking by MS-DIAL and import into R, when the feature table contains m/z values with decimal components that fall within the [4, 8] interval (indicating instrumental artifacts or calibration errors).
    0 installs
63. ▌
    Peak And Neutral Loss Counting 2 · holobiomicslab

    Use when when you have matchms-processed MS2 spectra from multiple samples and need to create comparable sample-level signatures for cross-sample analysis, particularly when samples are chemodiverse, have poor feature overlap, or exhibit strong retention time shifts across LC methods or MS.
    0 installs
64. ▌
    Percentile Threshold Filtering 2 · 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
65. ▌
    Plot Customization And Styling 2 · 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
66. ▌
    Publication Figure Preparation 2 · 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
67. ▌
    Python Async Method Definition 2 · holobiomicslab

    Use when when extending MSMetaEnhancer with a new local chemical transformation (e.g., SMILES to InChI) that should execute non-blockingly within an asynchronous annotation workflow.
    0 installs
68. ▌
    Python Function Implementation 2 · 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
69. ▌
    Quality Overview Visualization 2 · holobiomicslab

    Use when you have sequential QCpool (pooled quality control) samples analyzed with Sciex Multiquant (≥v3.0.
    0 installs
70. ▌
    R Data Structure Serialization 2 · 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
71. ▌
    R Internal Function Invocation 2 · holobiomicslab

    Use when when you need to verify or retrieve package-internal metadata about compiled .NET assembly location and version before processing raw mass spectrometry files, or when testing the R↔C# dispatch mechanism in isolation without loading actual Orbitrap .raw data files.
    0 installs
72. ▌
    R Package Function Integration 2 · 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.
    0 installs
73. ▌
    Ranking Task Loss Optimization 3 · holobiomicslab

    Use when you have multiple pre-trained neural network models (e.g., MLP and GNN) that produce overlapping predictions on the same set of candidates, and your evaluation metric is rank-based (average rank, Rank@K) rather than point-wise accuracy or RMSE.
    0 installs
74. ▌
    Reaction Pathway Interpolation 2 · 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
75. ▌
    Rescore Column Standardization 2 · 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
76. ▌
    Similarity Scoring For Spectra 2 · 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.
    0 installs
77. ▌
    Spectral Data Table Conversion 2 · holobiomicslab

    Use when when you have mzPeak format spectrum files and need to work with spectrum metadata, intensity/m/z arrays, or precursor information in a tabular, columnar, or vectorized computing environment.
    0 installs
78. ▌
    Spectral Library Data Modeling 2 · holobiomicslab

    Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata filters, similarity scoring across large spectral collections, or integration into downstream tools like MS2Query that.
    0 installs
79. ▌
    Spectral Mixture Deconvolution 2 · 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
80. ▌
    Structural Type Categorization 2 · holobiomicslab

    Use when when you have a set of query chemical compounds (by name or SMILES) and a reference library organized into named groups (e.
    0 installs
81. ▌
    Target List Coordinate Mapping 3 · holobiomicslab

    Use when you have a CSV-formatted target list with m/z, retention time, or ion mobility identifiers and need to locate and extract peak abundances from raw MS data files (Agilent .d, Thermo .raw, Bruker .d, mzML) acquired across LC-MS, LC-IMS-MS, DDA, DIA, or direct infusion modes.
    0 installs
82. ▌
    Test Suite Pass Fail Reporting 2 · holobiomicslab

    Use when when you need to verify that a research software package (e.g., MassQL) maintains functional correctness over time, assess the reliability of a tool before integration into a workflow, or document test coverage and failure modes for reproducibility.
    1 install
83. ▌
    Thermo Raw File Format Parsing 3 · holobiomicslab

    Use when you have acquired multidimensional mass spectrometry data (MS1, MS/MS, or data-independent acquisition) from a Thermo instrument saved in the proprietary '.
    0 installs
84. ▌
    Time Domain Signal Apodization 2 · holobiomicslab

    Use when working with raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d format) prior to noise thresholding and mass-domain calibration.
    0 installs
85. ▌
    Url Format Constraint Checking 2 · holobiomicslab

    Use when ingesting or validating project JSON documents against a schema (such as app/public/schema.json in the Pairing Omics Data Platform) that designates certain fields as URL type (e.
    0 installs
86. ▌
    Webworker File Access Enabling 2 · 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
87. ▌
    Whitespace Character Detection 2 · holobiomicslab

    Use when validating project JSON documents against the platform's schema (app/public/schema.json) and you need to ensure all URL-type fields conform to URL syntax rules. Specifically, use it when the schema designates certain fields as URL type (e.
    0 installs
88. ▌
    Workflow Routing Configuration 3 · holobiomicslab

    Use when when you have raw mass spectrometry data files from multiple acquisition modalities (LC-MS, GC-MS, ion mobility, or imaging) and need to automatically route each to the correct downstream analysis module without manual intervention.
    0 installs
89. ▌
    Projected Area Computation 2 · 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
90. ▌
    Twim Ms Data Preprocessing 2 · 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
91. ▌
    Dotnet Framework Development 2 · holobiomicslab

    Use when you need to compile and test a .NET-based metabolomics or bioinformatics desktop application (e.g., MS-DIAL version 5 series) from source code, or you are implementing new parsing or data-processing modules that must integrate with WPF UI frameworks and ReactiveExtensions patterns.
    0 installs
92. ▌
    Feature Pair Mass Refinement 2 · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across direct-injection MS experiments.
    0 installs
93. ▌
    Integration Test Development 2 · holobiomicslab

    Use when when you have implemented or modified a data ingestion module (e.g., mzML parser) and need to verify that file deserialization produces correct internal representations.
    0 installs
94. ▌
    Spectra Mgf Format Loading 2 · holobiomicslab

    Use when when you have downloaded a GNPS molecular networking archive (GNPS1 or GNPS2 workflow output) and need to reconstruct spectral records for integration with genomic data (BGCs, antiSMASH results) or for computing molecular family links and spectral similarity scores.
    0 installs
95. ▌
    Spectral Database Matching 3 · holobiomicslab

    Use when when you have MS2 .mzML format data files from untargeted metabolomics or proteomics experiments and need to perform an initial annotation step by matching experimental spectra against known reference libraries (GNPS, HMDB, MassBank) with a defined precursor mass tolerance (e.g., 15 ppm).
    0 installs
96. ▌
    Spectral Format Conversion 2 · holobiomicslab

    Use when when raw spectral data exists in one mass spectrometry file format but downstream analysis requires a different format; when integrating spectra from multiple sources or instruments that produce heterogeneous file formats;
    0 installs
97. ▌
    Spectral Output Formatting 2 · holobiomicslab

    Use when after generating tandem mass spectrum predictions from a neural model (ICEBERG, SCARF, or baseline), and before attempting retrieval ranking, metric computation, or validation against experimental spectra.
    0 installs
98. ▌
    Spectral Window Extraction 3 · holobiomicslab

    Use when you have loaded multidimensional MS data (from MZA HDF5 files or other formats) and need to examine a specific m/z region—for example, to visualize a known lipid or metabolite mass range, perform peak detection within a narrow window, or reduce computational overhead by working on a subset.
    0 installs
99. ▌
    Spectrum Metadata Handling 2 · holobiomicslab

    Use when when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries, MassBank, MetaboLights, Metabolomics Workbench, MS2LDA, or ProteoXchange) and need to extract its raw spectral data.
    0 installs
100. ▌
     Spectrum Subset Extraction 2 · holobiomicslab

     Use when after duplicate filtering of MZmine-exported MGF and CSV files, when you have combined spectra from multiple samples in a single MGF and need to segregate them by sample identifier before fragment annotation or adduct assignment.
     0 installs