← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

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

1. ▌
   Lipid Mass Spectral Matching · holobiomicslab

   Use when you have peak-picked LC-HRMS/MS or direct infusion MS/MS data (m/z, retention time, intensity) from Q-Exactive, Agilent, Bruker, or SCIEX instruments and need to annotate experimental fragment patterns to known lipid structures.
   0 installs
2. ▌
   Mass Shift Tolerance Scoring · holobiomicslab

   Use when when searching for peptide spectra with unknown or open modifications (i.e., any mass shift within a broad tolerance range rather than a fixed set of known modifications).
   0 installs
3. ▌
   Mass Spectrum Peak Detection · holobiomicslab

   Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct infusion MS (DI-MS), ASAP-MS, or other high-throughput ambient ionization methods, and need to identify which m/z signals represent true peaks of interest rather than noise or baseline drift.
   2 installs
4. ▌
   Mass Spectrum Plot Rendering · holobiomicslab

   Use when after importing and preprocessing mass spectrometry data (in .raw, .
   0 installs
5. ▌
   Matlab Data Structure Design · holobiomicslab

   Use when you have multiple CDF files containing mass spectrometry imaging data (spectra, m/z arrays, and spatial coordinates) that need to be ingested into MATLAB for the DIMPLE pipeline or similar linear-axis mass spectrometry imaging analysis.
   0 installs
6. ▌
   Maven Pom Version Extraction · holobiomicslab

   Use when preparing a software release and you need to verify that all Maven modules declare identical version numbers before creating a release branch.
   1 install
7. ▌
   Mean Centering Normalization · holobiomicslab

   Use when apply mean-centering when you have a feature intensity table (samples × compounds) from metabolomics analysis and you need to standardize feature intensities by removing the average signal before multivariate analysis (e.g., PCA) or downstream statistical modeling.
   0 installs
8. ▌
   Metabolic Ion Peak Filtering · holobiomicslab

   Use when you have a raw or extracted peak feature table (CSV or tabular format) containing mass-to-charge ratios, retention times, and intensity values across multiple samples from different experimental groups, and you need to identify which peaks show statistically significant differential.
   0 installs
9. ▌
   Metabolomics Data Processing · holobiomicslab

   Use when when you have raw or partially processed metabolomics data (feature tables with sample metadata) and need to apply quality-control metrics, normalization, statistical inference, or advanced classification/variable selection without relying on a Galaxy instance.
   0 installs
10. ▌
    Metabolomics Data Validation · holobiomicslab

    Use when you have raw or semi-processed m/z peak lists (positive and negative ion mode) and a sample metadata table, and you need to confirm they meet MetaboShiny's structural and semantic requirements before loading them into the normalization pipeline.
    0 installs
11. ▌
    Mnar Data Quality Assessment · holobiomicslab

    Use when when you have applied multiple left-censored missing value imputation methods to metabolomics data and need to compare their performance quantitatively.
    2 installs
12. ▌
    Module Loader Implementation · holobiomicslab

    Use when you have mass spectrometry imaging data in multiple vendor or open-source formats and need to programmatically route each file to its correct processing handler based on file extension, avoiding hardcoded conditional chains and enabling extensible format support.
    2 installs
13. ▌
    Molecular Structure Decoding · holobiomicslab

    Use when after running spectrum-conditioned diffusion generation that produces latent molecular representations, when you need to convert continuous or abstract model outputs into discrete chemical formats suitable for structure matching, library comparison, or chemical database lookup.
    0 installs
14. ▌
    Molecular Structure Encoding · holobiomicslab

    Use when you have molecular structures (SMILES strings or molecular graphs) that need to be input to a transformer model for property prediction (e.g., Collision Cross Section), and the model requires tokenized or embedded representations rather than raw chemical notation.
    0 installs
15. ▌
    Msbackend API Implementation · holobiomicslab

    Use when you need to create a new backend to integrate MS data from a novel file format, database, or in-memory storage system into the Spectra ecosystem. Use this skill when existing backends (MsBackendMemory, MsBackendMzR, MsBackendSql, etc.) do not support your data source or storage paradigm.
    0 installs
16. ▌
    Network Stability Assessment · holobiomicslab

    Use when you have constructed a network object (from correlation data, adjacency matrices, or edge lists) and need to evaluate which nodes are most critical to network integrity, how the network responds to the removal of highly connected nodes, or whether the network exhibits robust or fragile.
    0 installs
17. ▌
    Node Pair Edge Deduplication · holobiomicslab

    Use when your input network contains multiple edge types (Biochemical, Structural, Mass Spectral, Correlation) linking the same node pairs, and you want to export or visualize a single-edge-per-pair network to avoid visual clutter and ambiguous interpretations.
    0 installs
18. ▌
    Numeric List Slot Management · holobiomicslab

    Use when when extending the MsBackend virtual class to create a custom backend for mass spectrometry data, and you need to store peak m/z and intensity values as variable-length numeric vectors indexed by spectrum.
    0 installs
19. ▌
    Oldens Method Implementation · holobiomicslab

    Use when you have trained multi-layer perceptron neural networks on paired microbiome-metabolome data and need to extract interpretable feature attribution scores from the learned weights to identify microbe-metabolite interaction relationships.
    0 installs
20. ▌
    Package Metadata Compilation · holobiomicslab

    Use when when a package README or publication claims to install a large, fixed number of tools (e.g., 'approximately 89 tools') but does not enumerate them explicitly.
    3 installs
21. ▌
    Peak Labeling And Annotation · holobiomicslab

    Use when immediately after automatic peak detection on a raw or processed MS spectrum when you have a list of candidate peaks with m/z and intensity values but lack systematic identifiers, confidence estimates, or ranked ordering.
    0 installs
22. ▌
    Perl Entry Point Development · holobiomicslab

    Use when you are building a standalone Perl application for Windows that uses Prima for GUI rendering and depends on external binaries (e.g., Gnuplot 5.4.2) that must be verified before the user can interact with the main interface.
    0 installs
23. ▌
    Protocol Metadata Extraction · holobiomicslab

    Use when you have experimental protocol information scattered across multiple rows in a spreadsheet or table (e.
    0 installs
24. ▌
    Protonation State Assignment · holobiomicslab

    Use when you have SMILES-encoded molecular structures and need to model their behavior under electrospray ionization (ESI) or other ionization methods in mass spectrometry.
    0 installs
25. ▌
    Pytest Output Interpretation · holobiomicslab

    Use when after running `pytest tests/` on a Python package (especially one with dev extras installed), you need to determine if the full test suite passed, identify which tests failed, and extract error messages or stack traces for debugging.
    0 installs
26. ▌
    Python Code Style Validation · holobiomicslab

    Use when preparing Python code for contribution to a project that documents style requirements (black and/or flake8), during pre-commit validation in a CI/CD pipeline, or when reviewing pull requests to enforce uniform code standards across the repository.
    2 installs
27. ▌
    Python Dependency Management · holobiomicslab

    Use when when initializing a new Python project environment, reproducing a published analysis, or building documentation that requires external dependencies. Specifically apply this skill when you have a requirements.txt file listing pinned versions and need to ensure all downstream tools (e.
    2 installs
28. ▌
    Random Missing Value Masking · holobiomicslab

    Use when preparing ion image data for contrastive learning in mass spectrometry imaging (MSI), specifically when you need to augment single ion images into pairs of variants for encoder training in COL mode (co-localized ions) or as a base component of ISO mode (isotope ions).
    0 installs
29. ▌
    Raw File Routing And Queuing · holobiomicslab

    Use when you have collected raw MS files via an uploader tool and need to automatically forward them to a data processor for proteomics analysis, ensuring format compatibility and maintaining linkage to the original upload session and user project.
    0 installs
30. ▌
    Reference Database Screening · holobiomicslab

    Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, use this skill to match those predictions against a curated reference database of known molecular embeddings.
    0 installs
31. ▌
    Reference Quality Validation · holobiomicslab

    Use when when you have curated structure-organism pairs with associated reference metadata and need to verify that each pair's literature citations are present, non-conflicting, and complete before publishing them as a high-confidence validated dataset.
    2 installs
32. ▌
    Repository Environment Setup · holobiomicslab

    Use when when you have received a GitHub repository URL for a computational workflow (e.g., ENPKG full workflow) and need to prepare your local machine to execute the workflow.
    0 installs
33. ▌
    Search Engine Output Parsing · holobiomicslab

    Use when you have PSM output files from one or more search engines (e.g., MaxQuant msms.txt, MSGFPlus .mzid, Sage .sage.
    0 installs
34. ▌
    Simulation Result Validation · holobiomicslab

    Use when you have obtained a repository containing simulation scripts (e.g., Type I error or power analysis scripts) and need to verify that executing those scripts produces the same summary statistics and findings reported in the associated publication or documentation.
    0 installs
35. ▌
    Smiles Structure Preparation · holobiomicslab

    Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
    2 installs
36. ▌
    Spatial Filtering Ion Images · holobiomicslab

    Use when preparing raw ion image data from mass spectrometry imaging for deep learning-based representation learning.
    2 installs
37. ▌
    Spectral Baseline Correction · holobiomicslab

    Use when you have loaded raw MSI spectral data (imzML format) in profile or centroid mode and need to remove background noise and baseline artifacts before intensity normalization or ROI analysis.
    2 installs
38. ▌
    Spectral Metadata Validation · holobiomicslab

    Use when processing heterogeneous mass spectral datasets from multiple open libraries (e.g., MassBank, UNPD, GMD) where structural identifiers, precursor m/z, and adduct information are frequently incomplete or inconsistent across records.
    0 installs
39. ▌
    Spectral Noise Reduction Msi · holobiomicslab

    Use when you have imported raw MSI spectral data in imzML format and observe high background noise or low signal-to-noise ratio that would obscure biochemical annotations or ROI analysis.
    2 installs
40. ▌
    Spectrum Metadata Validation · holobiomicslab

    Use when after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats using matchms, when you need to ensure that metadata fields (e.
    0 installs
41. ▌
    Tabular Data Standardization · holobiomicslab

    Use when when you have received raw MRM lipidomics export files in vendor-specific formats (TSV, CSV) with inconsistent column naming, unparsed lipid identifiers (e.g., 'PC(36:1)' as a single string), and unknown data quality issues.
    2 installs
42. ▌
    Taxonomy Metadata Extraction · holobiomicslab

    Use when you have executed a spectrum search against one or more domain-specific MASSTs (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, or foodMASST) and need to systematically extract taxonomic lineages (kingdom, phylum, class, order, family, genus, species, strain) and sample metadata.
    2 installs
43. ▌
    Test Coverage For Edge Cases · holobiomicslab

    Use when integrating a new metadata validation step into a conversion pipeline that fetches structured chemical identifiers (SMILES, InChI, CAS numbers, IUPAC names) from external services.
    2 installs
44. ▌
    Tic Peak Boundary Estimation · holobiomicslab

    Use when after sliding-window analysis has identified candidate TIC peaks but before parameter extraction from Extracted Ion Chromatograms (EICs).
    0 installs
45. ▌
    Tool Parameter Configuration · holobiomicslab

    Use when you have selected a specific SECIMTools module (e.
    0 installs
46. ▌
    Tool XML Wrapper Integration · holobiomicslab

    Use when you have standalone metabolomics analysis tools (Python scripts, R packages, MATLAB compiled applications) that you want to expose through Galaxy's UI and make composable into reproducible workflows.
    0 installs
47. ▌
    Vendor Export Schema Mapping · holobiomicslab

    Use when raw MRM lipidomics data arrives in vendor-specific export formats (e.g., Sciex, Waters, Thermo TSV/CSV) with inconsistent or proprietary column naming, numeric encoding, and lipid nomenclature.
    2 installs
48. ▌
    Virtual Environment Creation · holobiomicslab

    Use when before installing ENPKG dependencies for the first time, or when setting up the workflow on a new machine or user account. Trigger when you have cloned enpkg_full or enpkg_workflow and need to install runtime and optional development dependencies in isolation.
    0 installs
49. ▌
    Compound Class Annotation Workflow · holobiomicslab bundle

    Use when you want chemical-class-level annotations for untargeted LC-MS/MS features rather than exact structures — determine molecular formulas with SIRIUS, compute CSI:FingerID fingerprints, and predict compound classes with CANOPUS and NPClassifier (superclass / class / pathway), producing a class-annotated feature table for chemical-inventory and enrichment analysis.
    0 installs
50. ▌
    Ce Ms Eof Marker Identification · holobiomicslab

    Use when when processing CE-MS test files and you need to identify and extract the migration time of the EOF marker (e.g., Paracetamol) to normalize compound migration times across runs.
    0 installs
51. ▌
    Metadata Annotation Integration · holobiomicslab

    Use when you have chemical annotations (GNPS spectral library matches) assigned to MS/MS samples and a validated ReDU sample-information template (TSV) with categorical metadata (e.g., sample type, extraction method, ionization source).
    0 installs
52. ▌
    Ms2 Data Preprocessing Pipeline · holobiomicslab

    Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that may contain multiple MS2 spectra per feature and require reduction or standardization before library matching.
    0 installs
53. ▌
    Roi Detection Mass Spectrometry · holobiomicslab

    Use when you have raw or converted mass spectrometry data (CE-MS or LC-MS in mzXML or mzML format) and need to identify candidate metabolite regions before feature extraction.
    0 installs
54. ▌
    Spectral Retrieval Ranking Task · holobiomicslab

    Use when when you have pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by similarity to each query for compound identification or structural similarity retrieval.
    0 installs
55. ▌
    Axis Label Format Customization · holobiomicslab

    Use when when designing injection plate layouts in InjectionDesign and needing to display sample positions with clear, domain-appropriate labels on the y-axis (e.g., row identifiers, well coordinates, or sample indices).
    0 installs
56. ▌
    Centroided Ms Feature Detection · holobiomicslab

    Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass, chromatographic, and intensity dimensions as input to PFAS prioritization, suspect screening, or other MS-based analyses.
    0 installs
57. ▌
    Chemical Identifier Unification · holobiomicslab

    Use when when you have raw GC-MS output (CSV with columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    0 installs
58. ▌
    Chromatogram Netcdf File Import · holobiomicslab

    Use when you have raw GCxGC-MS chromatogram data in NetCDF (CDF) format from an instrument and need to load it into R for preprocessing (smoothing, baseline correction, peak alignment) and multivariate analysis.
    0 installs
59. ▌
    Chromatographic Peak Resolution · holobiomicslab

    Use when when you have loaded raw GC-MS data in netCDF or mzML format and visual or statistical inspection reveals overlapping chromatographic peaks (i.e., multiple m/z ions co-eluting at the same retention time window).
    1 install
60. ▌
    Deconvolved Spectrum Comparison · holobiomicslab

    Use when after auto-deconvolution of GC-MS data has produced a table of deconvolved mass spectra, and you need to organize these spectra into clusters or detect which compounds co-elute or share similar fragmentation patterns.
    0 installs
61. ▌
    Drug Database Record Extraction · holobiomicslab

    Use when when you have obtained a DrugBank release file (requiring access credentials) and need to integrate drug chemical structure, name, and identifier information into a metadata cleanup or chemical enrichment pipeline.
    0 installs
62. ▌
    Dysregulation Score Computation · holobiomicslab

    Use when you have per-sample metabolite abundance data (e.g., from LC-MS or GC-MS) and a metabolite-to-pathway assignment table, and need to generate a sample-by-pathway dysregulation matrix for downstream classification, prognosis prediction, or pathway-level phenotype association.
    0 installs
63. ▌
    Gc Ms Spectral Library Matching · holobiomicslab

    Use when when you have GC-MS data with detected peaks that require structural annotation, retention index calibration has been applied (typically using FAMES standards), and you need to assign compound identities with confidence scores.
    0 installs
64. ▌
    Mass Spectral Data Augmentation · holobiomicslab

    Use when when you have limited real GC-MS overlapped peak data but need thousands of labeled examples to train a deep learning model for mass spectral deconvolution.
    0 installs
65. ▌
    Mass Spectral Matrix Prediction · holobiomicslab

    Use when you have raw GC-MS data with overlapped peaks in a specific retention time region and need to resolve the individual pure mass spectra of all components present in that region.
    0 installs
66. ▌
    Molecular Network Graph Parsing · holobiomicslab

    Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for further metabolite assignment, comparative network analysis, or visualization.
    0 installs
67. ▌
    Ms Peak Table Format Validation · holobiomicslab

    Use when immediately after loading a raw GC-MS CSV file and before executing the spreadOut() function. Use it when you have received peak table data from an instrument vendor (e.
    0 installs
68. ▌
    Peak Detection Cwt Optimization · holobiomicslab

    Use when when you have a pre-aligned GCIMSDataset and need to systematically identify and annotate chromatographic peaks across multiple samples.
    0 installs
69. ▌
    Qc Type Color Marker Assignment · holobiomicslab

    Use when configuring a new injection-plate design template in InjectionDesign if you have multiple QC types to position on a plate and need to visually distinguish them in the final worksheet.
    0 installs
70. ▌
    Raw Chromatography Data Parsing · holobiomicslab

    Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral analysis.
    0 installs
71. ▌
    Spectral Peak Clustering Gc Ims · holobiomicslab

    Use when after peak detection on individual GC-IMS samples, when you need to assign consistent cluster IDs to peaks detected across multiple samples to enable cross-sample comparison and quantification.
    0 installs
72. ▌
    Xcms Parameter Optimization Msw · holobiomicslab

    Use when when you have direct-injection or low-complexity mass spectrometry data (mzML files) and need to detect chromatographic peaks using wavelet-based methods instead of centWave, especially when standard retention-time-dependent peak detection is not suitable or when you need to tune.
    0 installs
73. ▌
    Algorithm Interface Abstraction · holobiomicslab

    Use when you have multiple independent peak-picking algorithms available and need to allow end-users to select among them for the same analytical task (peak detection in untargeted LC-MS data) without coupling the rest of your pipeline to each algorithm's API.
    0 installs
74. ▌
    Background Ion Blank Comparison · holobiomicslab

    Use when after generating an initial LC-MS feature table (from Asari or similar peak detection) and before normalization or statistical analysis, especially when blank samples (e.g., solvent-only or buffer-only runs) were acquired alongside study samples.
    0 installs
75. ▌
    Batch Generation And Validation · holobiomicslab

    Use when you have raw mzML files and a feature table (CSV) from LCMS data processed by tools like mzMine, and you need to create train/test/validation batches with specific matrix dimensions (120 × 2) and verified margin/peak signal separation before training or evaluating a neural network.
    2 installs
76. ▌
    Blank Intensity Ratio Filtering · holobiomicslab

    Use when apply this filter after feature detection and before downstream statistical analysis when your experimental design includes blank samples (e.
    0 installs
77. ▌
    Candidate Metabolite Prediction · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in positive or negative ion mode and need to identify candidate metabolites from a structure database.
    0 installs
78. ▌
    Chemical Annotation Integration · holobiomicslab

    Use when after training a tandem mass spectrometry embedding model (such as MSBERT) on a reference spectral library (e.g., GNPS), apply this skill to confirm that the high-dimensional embedding vectors project into interpretable chemical space.
    0 installs
79. ▌
    Chemical Formula Representation · holobiomicslab

    Use when you need to feed chemical formulas into a neural network-based formula scorer (such as MIST-CF) that must learn data-dependent representations of formula structure and composition.
    0 installs
80. ▌
    Chemical Metadata Harmonization · holobiomicslab

    Use when when aggregating MS/MS spectra from multiple public repositories (GNPS, MassBank, Mona) or in-house sources with inconsistent metadata naming conventions, missing or malformed adduct annotations, or incomplete chemical structure annotations (SMILES/InChI/InChIKey).
    0 installs
81. ▌
    Compound Identification Scoring · holobiomicslab

    Use when you have preprocessed MS/MS spectra (noise-filtered, normalized) and need to compute pairwise similarity or distance scores for compound library matching, when your goal is to rank candidate compounds by spectral match quality and maximize correct identification rate above dot-product.
    0 installs
82. ▌
    Configuration File Modification · holobiomicslab

    Use when when you need to expand or contract a mass spectrometry dataset by adding or removing allowed instrument types (e.
    0 installs
83. ▌
    Contrastive Loss Implementation · holobiomicslab

    Use when training embeddings from MS/MS spectra and you need to simultaneously enforce: (1) discrimination between spectra with different structural properties via contrastive learning on peak information and metadata embeddings, and (2) accurate reconstruction of embeddings from peak features via.
    0 installs
84. ▌
    Metabolite To Gene Mapping · holobiomicslab

    Use when you have metabolomic data (e.g., from LC-MS or GC-MS comparing patient to controls) showing differential abundant metabolites (DAMs), candidate genes from exome sequencing or variant calling, and access to a protein–protein or gene–gene interaction network (e.g., STRING).
    0 installs
85. ▌
    R S4 Object Accessor Usage · holobiomicslab

    Use when you have constructed or received a SummarizedExperiment object (or similar S4 class) containing MS feature tables, counts matrices, or sample-level metadata, and need to retrieve specific slots (e.
    1 install
86. ▌
    Sample Metadata Extraction · holobiomicslab

    Use when when you have an Excel file uploaded by a user following the InjectionDesign template schema and need to convert it into a modifiable, structured sample list that preserves up to three classification dimensions and QC type assignments for LC/GC-MS multi-omics experiments.
    0 installs
87. ▌
    Transformer Model Training · holobiomicslab

    Use when you have a dataset of augmented simulated overlapped GC-MS peaks and need to train a Transformer model to automatically deconvolve them into pure component mass spectra.
    0 installs
88. ▌
    Arrow Tabular Data Reading · holobiomicslab

    Use when when you have Parquet-encoded tabular data (e.
    0 installs
89. ▌
    Candidate Ranking By Score · holobiomicslab

    Use when you have a query mass spectrum and a set of candidate molecular structures, and you need to prioritize candidates by their likelihood of matching the query. Typical triggers include: (1) you have computed or extracted spectral features (e.
    0 installs
90. ▌
    Cluster Assignment Mapping · holobiomicslab

    Use when after density-based clustering (e.g., DBSCAN) has been performed on a sparse pairwise distance matrix derived from MS/MS spectra nearest neighbor indexes.
    0 installs
91. ▌
    Composite Spectra Analysis · holobiomicslab

    Use when your untargeted LC/HRMS dataset contains Data-Independent Acquisition data (MS^E, AIF, or SWATH-MS) or MS1-only composite spectra where multiple precursor ions fragment simultaneously, and you need to deconvolve overlapping fragmentation spectra to enable accurate chemical structure.
    0 installs
92. ▌
    Compound Candidate Ranking · holobiomicslab

    Use when after compound database dereplication has produced candidate annotations (from SIRIUS or MetFrag) and you need to select the most reliable candidates for final annotation.
    0 installs
93. ▌
    Compound Database Matching · holobiomicslab

    Use when you have MS2 .mzML spectral data from untargeted metabolomics and need to assign chemical identities to detected precursor ions.
    0 installs
94. ▌
    Compound Identifier Lookup · holobiomicslab

    Use when you have an experimental MS/MS spectrum (m/z and intensity pairs in mzML/mzXML format from DDA or targeted acquisition on Thermo, Waters, or Bruker instruments) and need to identify the unknown compound by comparing it against a reference database.
    0 installs
95. ▌
    Container Image Management · holobiomicslab

    Use when your LC-HRMS metabolomics data (.mzML or .abf files) must be processed reproducibly across multiple machines (local workstations, HPCs, cloud) without manual tool installation, or when you need to enforce identical computational environments for peer review and long-term archival.
    0 installs
96. ▌
    Cross Omics Strain Mapping · holobiomicslab

    Use when when you have paired genomics (AntiSMASH BGC annotations) and metabolomics (GNPS spectra and molecular families) data from the same microbial strains and need to identify which biosynthetic pathways produce which observed natural products.
    0 installs
97. ▌
    Custom Data Schema Mapping · holobiomicslab

    Use when a practitioner has pre-computed features from an external feature-finding procedure (e.g., vendor software, alternative open-source tools) and wishes to incorporate them into PFΔScreen's PFAS prioritization pipeline without re-detecting features from raw mzML data.
    0 installs
98. ▌
    De Novo Peptide Sequencing · holobiomicslab

    Use when you have annotated MS/MS spectra in MGF format and need to identify peptide sequences that may not exist in reference protein databases—such as in immunopeptidomics, metaproteomics, paleoproteomics, venomics, or monoclonal antibody assembly workflows.
    0 installs
99. ▌
    Dependency Version Parsing · holobiomicslab

    Use when before launching a multi-tool computational workflow (e.g., QCxMS2 mass spectra calculations) that depends on external programs with version-sensitive APIs or features. Apply this skill when: (1) the workflow has explicit minimum version requirements for one or more dependencies;
    0 installs
100. ▌
     Distance Matrix Clustering · holobiomicslab

     Use when you have a sparse pairwise distance matrix derived from nearest neighbor indexing of MS/MS spectra (or similar high-dimensional objects) and need to partition spectra into groups based on local density and neighborhood connectivity.
     0 installs