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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Data Quality Gating · holobiomicslab

   Use when after curating and integrating structure-organism pairs from heterogeneous sources when you need to enforce quality thresholds before publishing or analyzing a reference dataset.
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   Manifest Generation · holobiomicslab

   Use when you maintain a local repository of biological sequences (such as MIBiG) and need to produce a searchable inventory that links local files to their metadata and external database availability status.
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   Msi Data Import CSV · 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.
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   Msi Peak Annotation · 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.
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5. ▌
   Script File Mapping · holobiomicslab

   Use when you have edited core algorithm scripts in the Core-Match GitHub repository and need to integrate those changes into a locally installed LipidMatch-4.2 distribution (downloaded from innovativeomics.com). The trigger is the presence of modified .
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6. ▌
   Sdf File Processing · holobiomicslab

   Use when you have molecular structures (from databases, design tools, or literature) that need to be analyzed for CYP reactivity or metabolic properties, and you must convert them into a format compatible with the CypReact command-line tool.
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7. ▌
   Tsv File Generation · holobiomicslab

   Use when after completing a BiG-SLiCE v2 clustering analysis on an input folder of BGCs, when you need to retrieve the computed BGC and GCF cluster membership tables in a portable, widely-compatible tabular format rather than querying the SQLite database directly.
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8. ▌
   Wpf Gui Compilation · holobiomicslab

   Use when when you have cloned the MsdialWorkbench repository and need to produce an executable WPF GUI application (MsdialGuiApp) for Windows.
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9. ▌
   Metabolomics Workflow Router · holobiomicslab

   Use when a user has a whole metabolomics analysis GOAL (e.g. "annotate my untargeted LC-MS/MS data", "find biomarkers", "where else has this molecule been seen") rather than a single step — select the right end-to-end composite workflow super-skill, then run its stages, grounding each against its source papers.
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10. ▌
    Gtf File Parsing · holobiomicslab

    Use when you have a GTF-formatted genome annotation file and need to generate alternative splicing events (exon skipping, intron retention, alternative splice sites, mutually exclusive exons) or transcript-isoform inclusion levels (PSIs).
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11. ▌
    Candidate Rank Scoring · holobiomicslab

    Use when after compound database dereplication has generated per-spectrum candidate lists (e.
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12. ▌
    Chemical Class Mapping · 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.
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13. ▌
    Genome Sequence Mining · 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.
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14. ▌
    JSON Record Enrichment · 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).
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15. ▌
    Lc Ms Data Calibration · 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.
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16. ▌
    Mass Delta Computation · 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.
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17. ▌
    Mass Error Calculation · 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.
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18. ▌
    Ms Dial Output Parsing · 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.
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19. ▌
    Ms Ms Raw Data Loading · holobiomicslab

    Use when when you have raw LC-MS/MS instrument output files (e.g., .mzML, .
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20. ▌
    Ms Ms Spectrum Parsing · 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.
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21. ▌
    Ms1 Feature Extraction · 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.
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22. ▌
    Mzml Format Generation · holobiomicslab

    Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
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23. ▌
    Mzml Format Validation · holobiomicslab

    Use when after downloading an mzML file from a remote repository (e.g., MetaboLights, MassIVE, GNPS) via USI resolution, before attempting to parse it into a spectrum container or visualization dashboard.
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24. ▌
    Peak M Z Recalibration · holobiomicslab

    Use when after peak detection when you have a table of detected peaks with m/z values and need to improve mass accuracy for downstream annotation.
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25. ▌
    Spectrum Peak Matching · 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.
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26. ▌
    Subformula Enumeration · 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.
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27. ▌
    HTTP API Endpoint Design · holobiomicslab

    Use when when you need to expose a multi-step spectral processing workflow (parse → extract → render → annotate → compress) as a web service endpoint that accepts jcamp/RAW/mzML spectral files and must return coordinated output artifacts (modified JCAMP files, peak tables, and PNG images) in a.
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28. ▌
    Mwtab To JSON Conversion · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and data blocks that need to be converted to JSON for integration with REST APIs, web applications, or downstream tools that expect JSON input.
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29. ▌
    Python Environment Setup · holobiomicslab

    Use when when you have cloned a scientific Python repository (e.g., ROIAL-NMR) and need to verify that the documented dependencies can be installed and the main entrypoint is invokable without errors. Use this skill before attempting to run the application's core analysis workflows.
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30. ▌
    Spectral Image Rendering · holobiomicslab

    Use when when you have parsed and validated spectral data (jcamp, RAW, or mzML format) from NMR/IR/MS instruments and need to create visual representations with peak annotations for inspection, annotation, or publication.
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31. ▌
    Spectral Peak Validation · holobiomicslab

    Use when before feeding a peak list into the NMRformer model or other transformer-based spectral assignment frameworks.
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32. ▌
    Bedpe Format Handling · holobiomicslab

    Use when your ChIP-Seq input is paired-end sequencing data stored in BEDPE format (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.gz), and you need to estimate fragment length and call peaks while respecting the paired nature of the reads rather than treating them as independent single-end alignments.
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33. ▌
    R Package Champ Usage · holobiomicslab

    Use when when you have raw methylation array data (450K or EPIC format) in .idat files or as a beta-valued matrix and need to conduct a complete analysis pipeline including data import, quality filtering, normalization, batch effect correction, DMR detection, or gene set enrichment.
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34. ▌
    Status Value Parsing · holobiomicslab

    Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.
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35. ▌
    Unit Test Validation · 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.
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36. ▌
    C Module Integration · holobiomicslab

    Use when you have raw mass spectrometry data in mzML or mzXML format and need to compress it using a format-agnostic compressor that expects a standardized spectral data contract.
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37. ▌
    Feature Pair Ranking · holobiomicslab

    Use when you have two feature matrices from different modalities (e.
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38. ▌
    M Z Array Processing · 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.
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39. ▌
    Static Code Analysis · holobiomicslab

    Use when when preparing to submit a pull request to a collaborative Python project (like BiG-SCAPE) that mandates PEP8 compliance, or when establishing quality gates for a codebase that has adopted linters as part of its contribution guidelines.
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40. ▌
    Wikidata Integration · holobiomicslab

    Use when when building or maintaining a local natural-product reference database that requires current Wikidata entries, or when preparing metadata for mass-spectrometry queries that need enriched compound annotations (e.g., alternative names, chemical classifications, source organisms).
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41. ▌
    Ms Ms Spectrum Matching · 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.
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42. ▌
    Assay Matrix Formatting · 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()).
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43. ▌
    Module Coverage Mapping · 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.
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44. ▌
    Msp File Format Parsing · 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.
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45. ▌
    Smiles Notation Parsing · 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.
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46. ▌
    Xcms Workflow Execution · 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.
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47. ▌
    Cosine Distance Scoring · 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.
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48. ▌
    Dia File Format Parsing · 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.
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49. ▌
    Error Report Generation · 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.
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50. ▌
    Gnps Network Processing · 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.
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51. ▌
    Hdf5 File Io Operations · 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.
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52. ▌
    Lc Ms Output Validation · 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.
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53. ▌
    Lcms Feature Extraction · holobiomicslab

    Use when when you have raw LC-MS chromatographic data (mzML or vendor format) and need to identify and characterize all detectable peaks across the full retention time range for untargeted metabolomics or discovery workflows.
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54. ▌
    Lipid Class Enumeration · holobiomicslab

    Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine, triglyceride) and fatty acid composition ranges (e.g., C14–C22 with 0–6 degrees of unsaturation).
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55. ▌
    M Z Rt Feature Matching · holobiomicslab

    Use when you have extracted peaks from multiple LC/HRMS batches (n > 1) with their m/z and RT values, and you need to identify and align peaks representing the same compound across batches to build a consensus feature matrix.
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56. ▌
    Mass Accuracy Alignment · 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.
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57. ▌
    Mass Defect Calculation · 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.
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58. ▌
    Massql Query Generation · holobiomicslab

    Use when you have trained a shallow decision tree on ChemEcho feature vectors (representing unique peak or neutral loss formulas from tandem MS spectra) and need to deploy the learned splitting logic as a queryable, inspectable artifact.
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59. ▌
    Metabolite Set Analysis · 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.
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60. ▌
    Ms Finder Format Export · 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.
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61. ▌
    Ms1 Spectrum Simulation · 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.
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62. ▌
    Ms1 Spectrum Subsetting · 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.
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63. ▌
    Mse Reconstruction Loss · holobiomicslab

    Use when training embeddings from multi-modal spectral data (peak information + metadata) where you need to ensure both contrastive discriminability AND reconstruction fidelity. Specifically use it in transformer-based architectures that produce embeddings from heterogeneous inputs (e.
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64. ▌
    Mztab Format Generation · 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.
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65. ▌
    Neutral Loss Prediction · 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).
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66. ▌
    Peaklist Format Parsing · 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.
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67. ▌
    Pfas Feature Annotation · 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.
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68. ▌
    Query Result Tabulation · 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.
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69. ▌
    R Statistical Computing · 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.
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70. ▌
    Raw File Format Parsing · 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.
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71. ▌
    Realtime Alert Dispatch · 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.
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72. ▌
    Spectral Data Alignment · 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.
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73. ▌
    Spectral Data Filtering · 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.
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74. ▌
    Spectral Data Retrieval · holobiomicslab

    Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/... or mzspec:MSV000084951:AH22) and need to extract the corresponding mass spectrum peak list (m/z and intensity pairs) for downstream analysis, visualization, or cross-repository comparison.
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75. ▌
    Chemical Shift Annotation · holobiomicslab

    Use when when you have preprocessed 1H NMR spectral data with unidentified peaks and need to determine metabolite identity by exploiting the correlation structure of NMR signals.
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76. ▌
    Diffusion Model Inference · holobiomicslab

    Use when when you have multi-modal spectroscopic data (IR, Raman, UV-Vis, mass spectra, or NMR) and need to recover the underlying molecular structure without relying on finite spectral libraries or autoregressive SMILES generation.
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77. ▌
    File Integrity Validation · holobiomicslab

    Use when you have a raw NV (NMRViewJ) binary file and need to confirm it is well-formed before parsing or processing.
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