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HolobiomicsLab

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1. ▌
   API Data Retrieval 2 · holobiomicslab

   Use when you need to obtain all project JSON documents currently deposited in a data platform (such as the Paired Omics Data Platform) to validate their structure against a JSON Schema specification, or when you require a complete snapshot of published records for quality assurance, data migration.
   0 installs
2. ▌
   Jcamp File Parsing 2 · holobiomicslab

   Use when you receive uploaded spectral data in JCAMP format (jcamp) as input to the /api/v1/chemspectra/file/convert endpoint, or when you need to extract and validate metadata and peak information from an existing JCAMP file before converting to another format or performing spectral analysis.
   0 installs
3. ▌
   Mwtab File Parsing 2 · holobiomicslab

   Use when you have mwTab format files (Mass Spectrometry or Nuclear Magnetic Resonance experimental data from Metabolomics Workbench) that need to be loaded into Python for downstream analysis, validation, conversion to JSON, or programmatic manipulation of metadata and data sections.
   0 installs
4. ▌
   Topic Modeling Lda 2 · holobiomicslab

   Use when after generating a corpus/features JSON file from raw MS2 fragmentation spectra or similar document-term data, when the goal is unsupervised discovery of latent topics (e.g., metabolite families or spectral motifs) without ground-truth labels.
   2 installs
5. ▌
   Gcf Mf Link Scoring 2 · holobiomicslab

   Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from the same microbial strains and need to rank which GCF–MF pairs are likely to represent true biosynthetic relationships.
   0 installs
6. ▌
   Bgc Mf Link Scoring 2 · holobiomicslab

   Use when you have preprocessed GCF-MF link pairs from paired genomics–metabolomics datasets (antiSMASH-detected BGCs clustered into GCFs, and GNPS spectra grouped into MFs) and need to rank them by likelihood of representing true natural product–biosynthetic gene associations.
   0 installs
7. ▌
   File I O Automation 2 · holobiomicslab

   Use when you have MZmine-exported LC-MS/MS data (MGF spectra and CSV metadata files) in both positive and negative ionization modes and need to execute the full MolNotator pipeline from duplicate filtering through dereplication and network generation.
   0 installs
8. ▌
   Pyteomics API Usage 2 · holobiomicslab

   Use when when you have polypeptide sequences and need to compute their monoisotopic or average mass, isotopic distribution patterns, or other physico-chemical properties; or when you need to parse and manipulate MS/LC-MS data, FASTA databases, or search engine output in a Python workflow.
   0 installs
9. ▌
   R Package API Usage 3 · holobiomicslab

   Use when when you have metabolomics data (tab-delimited text or SummarizedExperiment object) and need to apply batch correction, outlier detection, internal standard recommendation, and quality filtering at scale or in non-interactive workflows.
   0 installs
10. ▌
    Tabular Data Export 2 · holobiomicslab

    Use when you have extracted MS1 or MS2 peak lists and scan headers from Thermo Fisher RAW files using MetaXtract and need to load them into pandas, NumPy, or external analysis tools.
    3 installs
11. ▌
    2d Tic Preprocessing 3 · holobiomicslab

    Use when when you have raw GCxGC-MS data imported from NetCDF into a 2D-TIC chromatogram object and need to remove chemical and instrumental noise (column bleeding, baseline drift, detector contamination) to reveal metabolite differences between sample groups for downstream multiway PCA or.
    0 installs
12. ▌
    Drift Time Filtering 3 · holobiomicslab

    Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time chemical noise, high-drift-time tail artifacts, or off-scale ion signals that would degrade subsequent alignment and peak.
    0 installs
13. ▌
    Lcms Raw Data Import 2 · holobiomicslab

    Use when you have raw LC/MS data in mzML or mzXML format and need to initiate untargeted metabolomics analysis.
    0 installs
14. ▌
    Ms Scan File Parsing 2 · holobiomicslab

    Use when you have acquired a Thermo mass spectrometry RAW file (or other proprietary instrument format) and need to extract MS1 and/or MS2 scans in an open, interoperable format (mzML, MGF, or Raxport-processed FT1/FT2 files) for TIC visualization, PSM scoring, or stable isotope labeling analysis.
    0 installs
15. ▌
    Ms2lda Motif Mapping 2 · holobiomicslab

    Use when you have a GNPS-generated molecular network (either classical or feature-based) and corresponding MS2LDA experiment output containing Mass2Motif-to-spectrum assignments, and you want to visualize which substructural motifs are shared across clusters or features and how they distribute.
    0 installs
16. ▌
    Sample Label Mapping 2 · holobiomicslab

    Use when you have a raw peak table (CSV format, from any of 12 supported LC-MS software tools or standardized format) and a separate label file that assigns each sample to an experimental class (e.
    4 installs
17. ▌
    Unit Test Validation 2 · holobiomicslab

    Use when when you need to confirm that a research tool or package maintains a functioning test suite, especially before adopting it for downstream analysis or before contributing modifications. Triggered by the presence of a CI workflow badge (e.
    0 installs
18. ▌
    Xcms Profile Parsing 2 · holobiomicslab

    Use when you have xcms-processed LC-MS data with detected feature groups (from xcms grouping), suspect retention time misalignment across samples due to long acquisition periods or large sample cohorts, and need to feed raw profiles into ncGTW's realignment algorithm.
    0 installs
19. ▌
    R Function Calling 2 · holobiomicslab

    Use when after AutoTuner has completed peak identification (TIC analysis), peak isolation, and EIC parameter extraction on at least 3 raw mass spectrometry samples (qTOF, orbitrap, or FTICR formats converted to mzML/mzXML/CDF), and you need to export the tuned parameters in a format ready for XCMS.
    0 installs
20. ▌
    Motif To Node Mapping 2 · holobiomicslab

    Use when you have a GNPS-generated classical or feature-based mass spectral molecular network (graphml or JSON format) and a corresponding MS2LDA experiment with Mass2Motif assignments on the same spectra, and you want to visualize and quantify which structural motifs are shared within and across.
    0 installs
21. ▌
    Newick Format Parsing 2 · holobiomicslab

    Use when you have a Chemical Feature Tree artifact (phylogeny) output from q2-qemistree's make-hierarchy method and need to verify its structural validity, count nodes (leaves and internal nodes), measure tree depth, and assess branching patterns before using it for alpha- or beta-diversity.
    0 installs
22. ▌
    Spectral JSON Parsing 2 · holobiomicslab

    Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
    0 installs
23. ▌
    CI Workflow Execution 2 · holobiomicslab

    Use when you have a GitHub repository with published CI workflow badges (e.g., unit test or package test badges in the README) and need to independently verify that the workflows execute successfully, reproduce the pass/fail status, and collect structured test results.
    0 installs
24. ▌
    Fragment Ion Matching 2 · holobiomicslab

    Use when you have two tandem mass spectra (query and reference) with precursor m/z and fragment ion peaks, and you need to identify which fragment ions correspond between them to assess spectral similarity, detect structural variants, or validate compound identifications.
    0 installs
25. ▌
    Hmdb Formula Sampling 2 · holobiomicslab

    Use when when you need to create in silico LC-MS/MS experiments with diverse chemical backgrounds for testing fragmentation strategies or acquisition controllers, and you want the chemical diversity to reflect real metabolomic samples. Use this when you have a target m/z range (e.
    0 installs
26. ▌
    Mass Defect Filtering 2 · holobiomicslab

    Use when after MS-Dial peak picking and feature table construction, when you observe a high proportion of features with anomalous m/z decimal values that are inconsistent with known metabolite ionization patterns.
    0 installs
27. ▌
    Module Import Testing 2 · holobiomicslab

    Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional after upstream updates. Use it as a gate before finalizing a release to catch installation or import breakage early.
    0 installs
28. ▌
    Ms Data Preprocessing 3 · holobiomicslab

    Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted metabolomics workflow (e.g., AriumMS) that requires standardized, interoperable file formats.
    0 installs
29. ▌
    Mz Decimal Extraction 2 · holobiomicslab

    Use when after loading a feature table with m/z values from MS-Dial output when you need to identify and remove features with anomalous decimal m/z values.
    0 installs
30. ▌
    Mzml File Import Xcms 3 · holobiomicslab

    Use when you have raw mzML files from a mass spectrometry instrument and need to begin a preprocessing workflow in xcms. This is the essential first step before any peak detection (centWave, MSWParam) or feature grouping can occur.
    0 installs
31. ▌
    Mzml Spectral Parsing 2 · holobiomicslab

    Use when when beginning a metabolomics annotation workflow with raw MS2 spectral data in .mzML format. This step is necessary when you have vendor-converted or standard .
    0 installs
32. ▌
    Peak Table Extraction 2 · holobiomicslab

    Use when you have raw or converted spectral data (jcamp, RAW, or mzML format) from NMR, IR, or MS instruments and need to identify individual peaks, extract their properties (chemical shift, m/z, intensity, width), and generate a structured peak table for annotation, comparison, or publication.
    0 installs
33. ▌
    Qcpool Cv Calculation 2 · holobiomicslab

    Use when you have Sciex Multiquant txt exports containing signal intensities from QCpool samples injected at regular intervals (e.g., every 10–20 samples) during one or more analytical sequences in a metabolomics or lipidomics study.
    0 installs
34. ▌
    Slack API Integration 2 · holobiomicslab

    Use when rapid QC-MS detects a QC failure (e.g., internal standard retention time drift, m/z deviation, or intensity anomaly) during an active LC-MS instrument run and users have configured Slack as a notification target.
    0 installs
35. ▌
    Tabular Data Cleaning 2 · holobiomicslab

    Use when you have a CSV or table-format spectral peak list (with chemical shift, intensity, and metadata columns) destined for NMRformer or similar peak-to-metabolite assignment models, and you need to exclude low-quality peaks that would otherwise harm prediction accuracy.
    2 installs
36. ▌
    Upset Plot Generation 2 · holobiomicslab

    Use when after loading and filtering search results from two or more DIA-MS analysis tools at a specified Q-value cutoff, when you need to summarize which analytes are identified by all tools, by specific subsets, or uniquely by individual tools.
    0 installs
37. ▌
    Usi Namespace Parsing 2 · holobiomicslab

    Use when when you need to retrieve mass spectrometry spectrum data from a metabolomics repository but only have a USI string (e.g., 'mzspec:GNPS:TASK-c95481f0c53d42e78a61bf899e9f9adb-spectra/specs_ms.mgf:scan:1943' or 'mzspec:MASSBANK::accession:SM858102').
    0 installs
38. ▌
    Wpf Gui Compilation 2 · holobiomicslab

    Use when when you have cloned the MsdialWorkbench repository and need to produce an executable WPF GUI application (MsdialGuiApp) for Windows.
    0 installs
39. ▌
    Msi Data Import CSV 2 · holobiomicslab

    Use when you have MSI intensity data exported from MSiReader or SCiLS software as a plain-text CSV file (with peaks as columns and pixels/spots as rows), and you need to import it into R to perform pairwise mass difference calculations and adduct identification.
    4 installs
40. ▌
    Msi Peak Annotation 2 · holobiomicslab

    Use when you have processed MSI data (peak matrix and spatial coordinates) from matrix-assisted laser desorption/ionization (MALDI) or silver-assisted laser desorption/ionization (AgLDI) experiments, and you need to computationally distinguish matrix ions from analyte ions before downstream feature.
    0 installs
41. ▌
    Genome Sequence Mining 2 · holobiomicslab

    Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format) from the same organism, and you want to identify novel RiPPs by linking gene cluster predictions to observed mass spectra.
    0 installs
42. ▌
    Ms Ms Spectrum Parsing 2 · holobiomicslab

    Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak lists (m/z and intensity pairs) along with metadata (precursor m/z, charge, ionization mode) to feed into MS2Query or.
    0 installs
43. ▌
    Candidate Rank Scoring 2 · holobiomicslab

    Use when after compound database dereplication has generated per-spectrum candidate lists (e.
    0 installs
44. ▌
    Chemical Class Mapping 2 · holobiomicslab

    Use when you have a GNPS molecular network (GML or GraphML format) and wish to annotate network nodes with chemical class labels to support metabolite family interpretation. Use it specifically when you need to overlay chemical classification schemes (e.
    0 installs
45. ▌
    Git Repository Cloning 2 · holobiomicslab

    Use when you need to obtain source code or computational workflows from a published repository, particularly when the article explicitly provides a GitHub URL and documents that the repository contains code required to regenerate published results (e.g., simulation outputs, figures, or tables).
    0 installs
46. ▌
    JSON Record Enrichment 2 · holobiomicslab

    Use when when a project JSON record contains a resolvable public identifier (genome accession, biosynthetic gene cluster ID, etc.) but lacks the corresponding human-readable or standardized metadata field (organism name, cluster description).
    0 installs
47. ▌
    JSON Schema Validation 3 · holobiomicslab

    Use when you have loaded an mwTab file into a structured MWTabFile object and need to verify it conforms to MS or NMR schema specifications before deposition, curation, or downstream analysis.
    0 installs
48. ▌
    Lc Ms Data Calibration 2 · holobiomicslab

    Use when when you have paired LC-MS measurements from labeled and unlabeled samples of the same analytes, and you need to isolate the true isotopic labeling contribution by removing confounding signal from naturally occurring isotopes and tracer isotopic impurity.
    0 installs
49. ▌
    Mass Delta Computation 2 · holobiomicslab

    Use when when you have parsed two or more MS/MS spectra (precursor m/z and fragment ion lists) and need to quantify all pairwise mass differences between fragment ions before alignment or similarity scoring.
    0 installs
50. ▌
    Mass Error Calculation 2 · holobiomicslab

    Use when when screening LC-HRMS datasets for suspect compounds: you have detected features with measured m/z values and a database of reference compounds with theoretical m/z values, and you need to rank candidate matches by mass accuracy before proceeding to retention time and fragmentation.
    0 installs
51. ▌
    Ms Dial Output Parsing 2 · holobiomicslab

    Use when you have completed peak picking in MS-DIAL (generating files like Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt) and need to load the resulting feature table into R for quality control, feature filtering, normalization, or metabolite annotation.
    0 installs
52. ▌
    Ms Ms Raw Data Loading 3 · holobiomicslab

    Use when when you have raw LC-MS/MS instrument output files (e.g., .mzML, .
    0 installs
53. ▌
    Ms1 Feature Extraction 2 · holobiomicslab

    Use when when you have an LC-HRMS feature table (with m/z values, retention times, and isotopic signatures) and a suspect compound database (with reference m/z, expected retention time windows, isotope ratios, and neutral loss fragments), and you need to rapidly prioritize which features are most.
    0 installs
54. ▌
    Mzml Format Generation 2 · holobiomicslab

    Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
    0 installs
55. ▌
    Nmr Peak Deconvolution 2 · holobiomicslab

    Use when when you have raw or processed 1D NMR spectra (FID or frequency-domain format) and need to extract individual peak identities and quantitative parameters in tabular form.
    0 installs
56. ▌
    R Cmd Check Validation 2 · holobiomicslab

    Use when after installing an R package from a non-CRAN repository (such as r-universe) to confirm the package build is sound, dependencies resolve correctly, and no warnings or errors are introduced. Use it as a gate before relying on the package for downstream analysis or distribution.
    0 installs
57. ▌
    Spectrum Peak Matching 2 · holobiomicslab

    Use when you have an experimental tandem mass spectrum (peaks with m/z values and intensities), a chemical formula, and a set of candidate molecular structures retrieved from a database like PubChem.
    0 installs
58. ▌
    Subformula Enumeration 2 · holobiomicslab

    Use when when performing chemical noise removal on MS/MS spectra and you need to validate whether each fragment ion m/z is consistent with loss of a subformula from the precursor ion.
    0 installs
59. ▌
    Toml Format Validation 2 · holobiomicslab

    Use when you are setting up a new LipoCLEAN analysis for MS-DIAL output and need to create a configuration file tailored to your MS-DIAL version (4 or 5).
    0 installs
60. ▌
    M Z Array Processing 2 · holobiomicslab

    Use when when you have imported MSI data (imzML or vendor format) loaded into the napari plugin environment and need to organize raw spectral m/z and intensity arrays prior to mean intensity calculation, ROI analysis, or database annotation.
    0 installs
61. ▌
    Cosine Distance Scoring 2 · holobiomicslab

    Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of spectra to identify similar compounds, search spectral libraries, or build a similarity network for spectral clustering or.
    0 installs
62. ▌
    Error Report Generation 2 · holobiomicslab

    Use when when a user uploads a JSON project document to the Pairing Omics Data Platform and you need to determine whether it satisfies the platform's data structure requirements, including all mandatory fields, proper data types, and constraint satisfaction for paired omics metadata (e.
    0 installs
63. ▌
    Gnps Network Processing 2 · holobiomicslab

    Use when you have generated a GNPS mass spectral molecular network (in classical or feature-based mode) and want to annotate network nodes with substructural motifs from MS2LDA or chemical class information.
    0 installs
64. ▌
    Hdf5 File Io Operations 3 · holobiomicslab

    Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS calibration), or when you need to export annotated feature tables with isotopologue metadata back to HDF5 for archival.
    0 installs
65. ▌
    Lc Ms Output Validation 2 · holobiomicslab

    Use when after executing a Nextflow-based LC-HRMS metabolomics workflow with Docker or Singularity containerization on .mzML LC-MS data, before proceeding to downstream statistical or visualization analyses.
    0 installs
66. ▌
    Mass Defect Calculation 2 · holobiomicslab

    Use when processing feature lists from LC- or GC-HRMS data (in mzML format or as custom feature tables with m/z and molecular formula columns) and you need to flag potential PFAS candidates.
    0 installs
67. ▌
    Metabolite Set Analysis 3 · holobiomicslab

    Use when you have a metabolite intensity matrix (rows=metabolites or peaks, columns=samples) paired with metabolite-to-pathway or metabolite-to-feature-group annotations, and you want to score activity levels across pathways or metabolite groupings in a way that tolerates missing peaks and.
    0 installs
68. ▌
    Module Coverage Mapping 3 · holobiomicslab

    Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation techniques.
    0 installs
69. ▌
    Msp File Format Parsing 3 · holobiomicslab

    Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign SMILES, retention indices, or combine multiple libraries into a single consolidated MSP file for MS-DIAL.
    0 installs
70. ▌
    Smiles Notation Parsing 2 · holobiomicslab

    Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields rather than a dedicated SMILES field, or when assigning SMILES from external structure databases (SDF files) to library.
    0 installs
71. ▌
    Xcms Workflow Execution 3 · holobiomicslab

    Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the cohort.
    6 installs
72. ▌
    API Contract Validation 2 · holobiomicslab

    Use when integrating with an external API (such as TensorFlow Serving) where changes to the response schema could break dependent code, or when model metadata must be extracted and verified before being used in downstream analysis steps.
    0 installs
73. ▌
    Assay Matrix Formatting 2 · holobiomicslab

    Use when after generating a feature table via mzrtsim() containing simulated peak abundances across samples with condition and batch effects, and you need to expose the abundance data through Bioconductor's SummarizedExperiment interface for use with standard accessor functions (assay(), colData()).
    0 installs
74. ▌
    Dia File Format Parsing 3 · holobiomicslab

    Use when you have raw DIA mass spectrometry files in timsTOF (.d), TripleTOF (.wiff), or Orbitrap (.raw) format and need to extract precursor ion chromatogram (PIC) data as input for quality metric computation or machine learning-based file quality prediction.
    0 installs
75. ▌
    Docker Image Management 2 · holobiomicslab

    Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined entry point or CLI interface.
    0 installs
76. ▌
    Entrypoint Verification 2 · holobiomicslab

    Use when when you have obtained a Python package from a repository (e.g., via git clone) and need to confirm that the documented Python version constraint and pinned dependency versions are sufficient to execute the package's main entry point (typically main.py or a console script).
    0 installs
77. ▌
    Mass Accuracy Alignment 3 · holobiomicslab

    Use when after parsing MRM transition tables (m/z values, retention times, transition parameters) from mzML data, before statistical analysis or visualization. Use this skill when you have detected but unannotated transitions and need to map them to lipid species with quantified confidence.
    0 installs
78. ▌
    Ms Finder Format Export 2 · holobiomicslab

    Use when after completing MS-CleanR filtering (blank subtraction, background removal, RSD/RMD thresholding) and feature clustering steps, when you have a consolidated set of representative features and need structural identification via MS/MS spectral matching.
    0 installs
79. ▌
    Ms Ms Spectrum Matching 3 · holobiomicslab

    Use when you have a cleaned and clustered set of LC-MS features (m/z, retention time, MS/MS spectra) from MS-CleanR output and need to assign putative compound identities by matching observed MS/MS fragmentation patterns against reference spectral libraries using HRR-based scoring.
    0 installs
80. ▌
    Ms1 Spectrum Simulation 2 · holobiomicslab

    Use when when you need to generate synthetic LC-MS/MS data to test fragmentation strategies, validate acquisition controllers, or benchmark peak-picking and spectral matching algorithms before deployment on real mass spectrometers.
    0 installs
81. ▌
    Ms1 Spectrum Subsetting 2 · holobiomicslab

    Use when after generating a scan index from a Thermo Fisher Orbitrap raw file using readIndex(), apply this skill when your analysis goal requires working exclusively with MS1 (precursor) scans rather than tandem MS (MS2/MS3) spectra.
    0 installs
82. ▌
    Multiquant File Parsing 2 · holobiomicslab

    Use when you have Sciex Multiquant text export files from one or more metabolomics or lipidomics analytical sequences and need to identify and locate QCpool (pooled quality control) samples that should have been injected at regular intervals, or when you must validate that the study design's.
    0 installs
83. ▌
    Mztab Format Generation 3 · holobiomicslab

    Use when after completing peak detection, MS1 feature picking, and accurate mass database search (e.g., against HMDB) on FIA-MS or LC-MS(/MS) data.
    0 installs
84. ▌
    Neutral Loss Prediction 2 · holobiomicslab

    Use when you have LC-HRMS features with fragmentation data (observed m/z shifts, mass deficits, or tandem MS spectra) and a suspect compound database with known or predictable neutral loss fragments (e.g., H₂O, CO₂, CH₄, or structure-specific losses).
    0 installs
85. ▌
    Nmr Spectral Processing 2 · holobiomicslab

    Use when you have raw NMR/IR/MS spectral data in vendor-specific (RAW), open (jcamp), or mass spectrometry (mzML) formats and need to parse, validate, and convert them to a standardized internal representation with extracted metadata and peak tables for visualization or further analysis in.
    0 installs
86. ▌
    Peaklist Format Parsing 2 · holobiomicslab

    Use when you have raw or semi-processed m/z peak detection output from LC-MS/MS instruments (typically from XCMS, MSnbase, or other peak-picking tools) in one of several known formats (MetaboAnalyst-like, MetaboShiny native, or Metabolights) and need to ingest them into MetaboShiny for compound.
    0 installs
87. ▌
    Pfas Feature Annotation 2 · holobiomicslab

    Use when when you have a feature list (m/z, retention time, intensity) from LC- or GC-HRMS non-target screening and need to identify PFAS-like homologous series characterized by CF₂ (14 Da) repeating units.
    0 installs
88. ▌
    Query Result Tabulation 2 · holobiomicslab

    Use when after executing MassQL queries against mzML mass spectrometry files when you need to organize heterogeneous scan-level results (MS1 and MS2 data) into consistent tabular schemas for batch analysis, statistical comparison across files/queries, or visual summary generation.
    0 installs
89. ▌
    R Statistical Computing 2 · holobiomicslab

    Use when you have a merged and batch-corrected non-targeted LC-MS/MS feature table with sample metadata and need to perform statistical testing to identify significant features, compare groups (e.g., disease vs. control), or explore multivariate patterns.
    0 installs
90. ▌
    Raw File Format Parsing 2 · holobiomicslab

    Use when you have native Thermo Fisher RAW files and need to recover file-level metadata (instrument details, run statistics), scan headers (retention time, total ion current, scan mode for MS1 or MS2), or peak lists (m/z and intensity arrays) in tabular or array form suitable for computational.
    0 installs
91. ▌
    Realtime Alert Dispatch 2 · holobiomicslab

    Use when a QC check fails during an active LC-MS instrument run and you need to immediately notify configured users (via Slack channel or email address) of the failure event, including timestamp, check type, and severity metadata.
    0 installs
92. ▌
    Spectral Data Alignment 2 · holobiomicslab

    Use when you have quantification tables (with feature IDs and abundance values), metadata tables (with sample annotations), and separate spectral data files (e.g., MS/MS spectra or fragmentation patterns), and you need to integrate them into a unified input for msFeaST.
    0 installs
93. ▌
    Spectral Data Filtering 2 · holobiomicslab

    Use when you have loaded a full set of MS scans (e.g., all MS1 scans from readAllScanMS1 in Aerith) and need to restrict analysis to a specific retention-time window (e.g., 9–10 min with 0.
    0 installs
94. ▌
    Spectral Peak Filtering 2 · holobiomicslab

    Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata validation, or export.
    0 installs
95. ▌
    Twim Ms Data Processing 2 · holobiomicslab

    Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign unidentified features to biomolecular classes (e.
    0 installs
96. ▌
    Batch Timing Analysis 2 · holobiomicslab

    Use when when evaluating whether a new or candidate mass spectrometry processing library (e.g., spectrum_utils) offers faster spectrum processing throughput than established alternatives (e.
    0 installs
97. ▌
    Isotopic Peak Removal 2 · holobiomicslab

    Use when after loading raw FT-ICR MS peak lists with assigned molecular formulas when you have detected peaks across multiple m/z values that correspond to isotopic variants of the same parent compound.
    0 installs
98. ▌
    Msi Data Table Export 2 · holobiomicslab

    Use when after calculating mean intensity values across all spectra in an MSI dataset (or within a manually selected ROI), and you need to store the resulting m/z–intensity table in a portable format for downstream ROI analysis, database annotation, or external statistical pipelines.
    0 installs
99. ▌
    Genome Identifier Lookup 2 · holobiomicslab

    Use when a paired omics project JSON document contains genome identifiers (e.g. IMG IDs, NCBI accessions) but lacks corresponding organism names.
    0 installs
100. ▌
     Hrms Data Format Parsing 2 · holobiomicslab

     Use when you have raw or processed HRMS/MS data from Q-Exactive, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF instruments in formats such as mzML, CSV peaklists, or vendor-specific formats, and you need to extract experimental fragment m/z values and their intensities for comparison against.
     4 installs