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HolobiomicsLab

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1. ▌
   Molecular Structure Alignment · holobiomicslab

   Use when when you have two or more lipid structures represented as labeled molecular graphs and need to compute pairwise structural distances to cluster lipidomes, identify similar lipid species, or rank lipids by structural relatedness.
   2 installs
2. ▌
   Msi Peak Intensity Extraction · holobiomicslab

   Use when you have MSI intensity data exported from commercial software (MSiReader, SCiLS) or Cardinal processing pipelines as plain-text CSV files or Cardinal MSProcessedImagingExperiment/MSContinuousImagingExperiment objects, and you need to prepare it for mass-difference tabulation and adduct.
   0 installs
3. ▌
   Network Topology Edge Parsing · holobiomicslab

   Use when you have a metabolic or biological network encoded as pairwise directed interactions (e.
   0 installs
4. ▌
   Parameter Tuning Metabolomics · holobiomicslab

   Use when you have at least 3 raw mass spectrometry samples in open formats (mzML, mzXML, CDF) from untargeted metabolomics experiments and need to configure parameters for XCMS, MZmine2, or similar processing software.
   0 installs
5. ▌
   Peak Border Center Estimation · holobiomicslab

   Use when you have LC-HRMS chromatograms in retention time × m/z matrix format and need to automatically localize chromatographic peak positions and extents prior to matching against a reference peak library or generating CNN training instances.
   2 installs
6. ▌
   Per Lipid Class Normalization · holobiomicslab

   Use when you have IM-MS lipidomic data from samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract), measured CCS values stratified by lipid class and adduct type, and access to the DTCCS_N2 reference library for U13C lipids.
   0 installs
7. ▌
   Per Root Metabolite Profiling · holobiomicslab

   Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root linear-axis metabolite profiling outputs to validate reported genotype-level results (e.
   0 installs
8. ▌
   Pip Package Manager Operation · holobiomicslab

   Use when when you have cloned or downloaded a Python project repository and need to install all declared dependencies to make the package importable and functional. Use this skill at the start of any local setup workflow when a requirements.
   2 installs
9. ▌
   Preference System Integration · holobiomicslab

   Use when when a GUI widget (e.g., isotopes display, compound list, or analysis parameter panel) must show or hide content according to user selections stored in application preferences, and the current implementation either shows all content regardless of preference or lacks a preference-reading.
   0 installs
10. ▌
    Pseudo Data Pair Construction · holobiomicslab

    Use when when you have a raw list of SMILES strings but lack sufficient real mass spectrometry reference data (typically <300 spectra) to train a generative model for unknown chemical identification.
    0 installs
11. ▌
    Psm Score Sorting And Ranking · holobiomicslab

    Use when when you have grouped PSMs by spectrum identifier and need to (1) establish input candidate PSMs for rescoring by selecting top-ranked PSMs based on search engine score, or (2) re-rank PSMs after rescoring completes to select final output PSMs for FDR calculation and result writing.
    2 installs
12. ▌
    Query Language Grammar Design · holobiomicslab

    Use when when you need to enable non-programmer mass spectrometry users to express complex spectral search patterns (e.g., isotope patterns, precursor mass constraints, scan-type filters) without writing procedural code.
    2 installs
13. ▌
    R Bioconductor Omics Workflow · holobiomicslab

    Use when you have a raw or partially processed multi-class or time-series metabolomic peak table (in standardized or software-specific format) and need to determine which combination of imputation, QC sample normalization, transformation, and metabolite/sample-based normalization methods will.
    2 installs
14. ▌
    R Function Workflow Execution · holobiomicslab

    Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE barocycler-based concurrent multiomics method and need to perform integrative preprocessing (spectral normalization and alignment across samples) followed by multivariate analysis to identify differential lipids.
    2 installs
15. ▌
    Random Walk Graph Propagation · holobiomicslab

    Use when you have: (1) a set of spectral library matches (seed identities) mapped to molecular structures, (2) a candidate structure graph derived from in silico fragmentation (e.
    2 installs
16. ▌
    Resource Capacity Calculation · holobiomicslab

    Use when when configuring an OpenMS Streamlit application for online deployment with Redis and RQ worker processes, you need to determine how many worker processes can safely run in parallel within a Docker container's memory constraint.
    0 installs
17. ▌
    Robust Regression Gam Fitting · holobiomicslab

    Use when metabolomics intensity data exhibits systematic signal drift across sample runs (especially within batches), QC samples are available to anchor normalization, and you require robustness against outlier compounds or aberrant sample intensities.
    0 installs
18. ▌
    Roi Definition And Extraction · holobiomicslab

    Use when when you have loaded imzML MSI data into napari and need to focus analysis on a specific anatomical or morphological region rather than the entire image.
    2 installs
19. ▌
    Run Order Diagnostic Plotting · holobiomicslab

    Use when you have metabolomics data structured as a SummarizedExperiment with run-order metadata and need to diagnose whether signal intensity or abundance varies systematically with sample acquisition order (intra-batch drift) or batch assignment (inter-batch effects).
    0 installs
20. ▌
    Sample Matrix Effect Handling · holobiomicslab

    Use when you have measured metabolites or lipids from archival blood samples (e.
    2 installs
21. ▌
    Saturated Peak Reconstruction · holobiomicslab

    Use when processing IM-MS data files (Agilent .d or UIMF format) that contain high-abundance ions suspected of signal saturation, particularly in untargeted or discovery proteomics/metabolomics workflows where dynamic range compression would obscure quantitative relationships.
    0 installs
22. ▌
    Scan Filter File Organization · holobiomicslab

    Use when when converting mzML files to imzML format and the source mzML contains multiple scan filters (e.g., different MS/MS isolation windows, ionization modes, or mass ranges acquired in a single imaging experiment).
    0 installs
23. ▌
    Sirius Zodiac Score Filtering · holobiomicslab

    Use when after running SIRIUS on a mass spectrometry feature set and obtaining compound_identification.tsv output containing Zodiac and Cosmic confidence scores, apply this filter to eliminate low-confidence SIRIUS annotations before downstream prioritization or chemical class analysis.
    0 installs
24. ▌
    Slurm Gpu Resource Allocation · holobiomicslab

    Use when you have a machine learning training workflow (e.g., k-fold cross-validation) where each fold is independent, can run in parallel, and requires exactly one GPU per fold.
    0 installs
25. ▌
    Smarts Reaction Rule Encoding · holobiomicslab

    Use when when you have a set of known chemical reactions (e.g., from MetaCyc or KEGG) that you want to generalize into reusable transformation rules for predicting novel reactions on new compound sets.
    0 installs
26. ▌
    Species Identifier Annotation · holobiomicslab

    Use when you have a parsed lipid species table output from LipidSearch or LIQUID containing lipid names or identifiers and their quantitative measurements, but lack standardized taxonomic annotation (e.g., Glycerophospholipids, Phosphatidylcholines).
    0 installs
27. ▌
    Spectral Database Compilation · holobiomicslab

    Use when you have generated predicted fragment spectra for a set of compounds using CFM-ID or similar in-silico prediction tools and need to organize these results into a persistent, queryable database that mirrors the schema of an existing online spectral reference (such as the predicted-fragments.
    2 installs
28. ▌
    Spectral Peak Data Extraction · holobiomicslab

    Use when when you need to retrieve m/z–intensity pairs from a MsBackend-backed Spectra object for visualization, comparison, or processing; particularly when the backend stores peak data separately (e.
    2 installs
29. ▌
    Spectral Peak Feature Hashing · holobiomicslab

    Use when when you have a large collection of query high-resolution mass spectra that must be rapidly matched against a spectral library containing modified and unmodified peptides, and you need to reduce computational overhead before approximate nearest neighbor indexing or GPU-accelerated.
    2 installs
30. ▌
    Spectrum Object Instantiation · holobiomicslab

    Use when after successfully parsing raw spectral data from one of the supported file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) into intermediate dictionaries containing m/z arrays, intensity arrays, and metadata key-value pairs.
    0 installs
31. ▌
    Spectrum Object Schema Design · holobiomicslab

    Use when when building a mass spectrometry data import pipeline that must ingest spectra from multiple file formats and produce a unified, queryable representation suitable for metadata validation, peak filtering, and similarity comparisons.
    2 installs
32. ▌
    Spectrum Tokenization For Nlp · holobiomicslab

    Use when when you have raw mass spectra from experimental libraries (e.
    0 installs
33. ▌
    Structured Data Serialization · holobiomicslab

    Use when when you have mwTab-formatted Mass Spectrometry or Nuclear Magnetic Resonance experimental data from the Metabolomics Workbench that must be converted to JSON for API integration, data sharing across systems, or validation against a defined JSON schema.
    1 install
34. ▌
    Study Size Weighted Averaging · holobiomicslab

    Use when you have metabolomics results from multiple independent studies (each with a fold-change, p-value, and sample size N) and need to produce a single quantitative meta-analysis fold-change estimate.
    1 install
35. ▌
    Tensorflow Hdf5 Serialization · holobiomicslab

    Use when when you have acquired Keras models (via get_models.sh or similar download) and need to deploy them locally through TensorFlow Serving within a Docker/docker-compose stack.
    0 installs
36. ▌
    Tensorflow Serving Deployment · holobiomicslab

    Use when you have trained Keras models that need to be served as microservices for real-time inference. Specifically: (1) models have been converted to HDF5 TensorFlow 2.3.0 format with properly named input layers ('input_2048', 'input_4096') and output layer ('output');
    0 installs
37. ▌
    Tic Peak Isolation Validation · holobiomicslab

    Use when you have raw mass spectrometry data (mzML, mzXML, or CDF format) from at least 3 samples and need to automatically identify candidate peak regions in the TIC chromatogram before extracting ion-level parameters for XCMS or MZmine2 processing.
    0 installs
38. ▌
    Workflow Context Preservation · holobiomicslab

    Use when when submitting OpenMS workflows to RQ (Redis Queue) in online Docker mode, you need to preserve the job ID and execution context for recovery after container restarts or worker failures. Apply this skill if: (1) you are using QueueManager.
    0 installs
39. ▌
    Ion Mobility 4d Annotation Workflow · holobiomicslab bundle

    Use when you have ion-mobility LC-IMS-MS/MS data (e.g. timsTOF / PASEF) and want CCS-aware annotations — 4D feature extraction with collision cross section, CCS calibration and filtering, CCS-aware library matching, and (optional) networking.
    2 installs
40. ▌
    Lipidomics Lcms Annotation Workflow · holobiomicslab bundle

    Use when you have untargeted lipidomics LC-MS/MS data (mzML) and want a class- and species-level annotated lipid feature table — preprocessing, normalization, lipid identification by MS/MS, retention/adduct rule validation, differential analysis, and a fused master table.
    0 installs
41. ▌
    Nmr Metabolomics Profiling Workflow · holobiomicslab bundle

    Use when you have NMR metabolomics data (1D/2D spectra or FIDs) and want a quantified, identified metabolite profile — spectral preprocessing (phase/baseline/referencing, binning), metabolite identification by chemical shift, quantification, and group statistics.
    0 installs
42. ▌
    Leiden Clustering Of Cells · holobiomicslab

    Use when after constructing a kNN graph (via pp.neighbors) on preprocessed, scaled, and PCA-reduced single-cell expression data.
    0 installs
43. ▌
    Transcript To Gene Mapping · holobiomicslab

    Use when you have transcript-level quantification files (salmon quant.sf.gz, kallisto, or Sailfish output) and need to perform gene-level differential expression analysis.
    0 installs
44. ▌
    Ce Ms Migration Time Measurement · holobiomicslab

    Use when when processing raw CE-MS data and need to establish a baseline migration time scale before transforming to effective mobility.
    0 installs
45. ▌
    Mass Spectrum Peak Normalization · holobiomicslab

    Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra have been acquired under different instrumental conditions, ionization efficiencies, or detector gains that produce.
    2 installs
46. ▌
    Model Inference And Tokenization · holobiomicslab

    Use when you have MS/MS spectra in .msp format and need to retrieve similar compounds or compute spectral similarities for compound identification. The input spectra should already be cleaned (malformed or invalid SMILES removed), and you have access to a pre-trained SpecEmbedding model checkpoint.
    0 installs
47. ▌
    Molecular Similarity Calculation · holobiomicslab

    Use when you have two or more molecular structures (represented as SMILES or spectral data) and need to rank transformation product candidates by structural plausibility, filter isomeric or duplicate TP predictions, or group features into components based on chemical relatedness.
    0 installs
48. ▌
    Singularity Container Deployment · holobiomicslab

    Use when you have a Nextflow workflow (e.g., Nextflow4MS-DIAL) that currently runs under Docker or bare metal, and you need to execute it on an HPC cluster that lacks Docker support or enforces Singularity as the container runtime.
    0 installs
49. ▌
    Batch Effect Matrix Construction · holobiomicslab

    Use when when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods. Use this skill when: (1) you want reproducible, ground-truth batch effects overlaid on condition-only variation;
    0 installs
50. ▌
    Chemical Identifier Verification · holobiomicslab

    Use when when you have a list of chemically known compounds and need to validate that an MS processing pipeline (e.g., mzExacto) correctly retrieves their characteristic m/z, retention time, match factor, and area values from GC-MS data.
    0 installs
51. ▌
    Chemical Mass Tolerance Matching · holobiomicslab

    Use when when you have a metabolomics peak list (m/z values with optional retention times) from LC-MS or GC-MS and want to filter a computationally expanded chemical library to only compounds whose calculated masses (accounting for ionization adducts) fall within a defined tolerance of observed.
    6 installs
52. ▌
    Fticr Mass Calibration Edgeshift · holobiomicslab

    Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.
    0 installs
53. ▌
    Gc Ims Peak Alignment Evaluation · holobiomicslab

    Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using hierarchical clustering.
    0 installs
54. ▌
    Gcxgc Preprocessed Data Handling · holobiomicslab

    Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a reference using 2D correlation optimized warping) and need to consolidate them into a single analytical object for.
    0 installs
55. ▌
    Ion Mobility Dimension Detection · holobiomicslab

    Use when when processing raw mass spectrometry data files of unknown or mixed provenance, and you need to automatically route IMS inputs to their corresponding analysis pipeline.
    0 installs
56. ▌
    Log Transformation Preprocessing · holobiomicslab

    Use when apply log transformation when peak intensity distributions are right-skewed with heteroscedastic variance (intensity-dependent noise), particularly in QC-based batch correction workflows where variance stabilization improves the effectiveness of subsequent Pareto scaling normalization.
    0 installs
57. ▌
    Mass Spectrometry Data Alignment · holobiomicslab

    Use when you have two LC-MS feature tables (each containing m/z, retention time, and intensity columns) from the same or related biological samples and need to identify which features in dataset A correspond to which features in dataset B.
    0 installs
58. ▌
    Mass Spectrum Peak List Handling · holobiomicslab

    Use when you have raw or preprocessed electron ionization (EI) mass spectral data that must be stored in, retrieved from, or validated against the MSP file format (used by NIST MS Search and similar spectral library tools).
    2 installs
59. ▌
    Match Factor Threshold Filtering · holobiomicslab

    Use when you have a GC-MS dataset with Match.Factor scores for each detected compound (output from Agilent Unknowns Analysis or equivalent), and you want to reduce the number of query chemicals passed to computationally intensive cheminformatics functions (categorate, mzExacto, or exactoThese).
    0 installs
60. ▌
    Metabolite Spectral Data Merging · holobiomicslab

    Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of in-house standards in separate MSP files) and need to combine them with consistent metadata (SMILES, InChIKey, molecular.
    0 installs
61. ▌
    Metabolomics Matrix Manipulation · holobiomicslab

    Use when you have a raw metabolomics abundance table (e.g., LC/MS or GC/MS peak intensities or concentrations) with non-normal distributions and missing values, and you need to prepare it for Gibbs sampler or other model-based imputation.
    0 installs
62. ▌
    Qc Sample Batch Drift Correction · holobiomicslab

    Use when you have a QC-annotated feature table (samples × features with QC sample identifiers) from LC-MS untargeted metabolomic profiling and observe systematic signal drift across the run sequence or between batch blocks.
    1 install
63. ▌
    Spectral Prediction Model Fusion · holobiomicslab

    Use when you have pre-trained MLP and GNN spectral prediction models evaluated on the same ESI/LC-MS test dataset, and you seek to improve average rank performance beyond either baseline model alone.
    0 installs
64. ▌
    Annotation Complexity Comparison · holobiomicslab

    Use when you have MS imaging or LC-MS data with pre-annotated m/z values that include multiple isomer or metabolite names per m/z (stored as semicolon-delimited or multi-record strings), and you want to measure whether a refinement step (e.
    0 installs
65. ▌
    Annotation Table Quality Control · holobiomicslab

    Use when after obtaining in silico annotations from SIRIUS (Zodiac/Cosmic scores) or ISDB (cosine/shared peaks metrics), before using the annotation table for Feature Component calculation, chemical class assignment, or metabolite discovery prioritization.
    2 installs
66. ▌
    Batch Effect Correction Workflow · holobiomicslab

    Use when you have a feature table generated from LC-MS/MS non-targeted metabolomics data that spans multiple sample preparation batches, instrumental runs, or experimental conditions.
    0 installs
67. ▌
    Batch Spectral Record Processing · holobiomicslab

    Use when you have acquired MS/MS spectra in .msp format (e.g., from MassBank or experimental acquisition) and need to transform them into a structured library format compatible with automated annotation tools.
    0 installs
68. ▌
    Ccs Prediction Model Application · holobiomicslab

    Use when you have structural input data (SMILES or molecular geometry files) for N-Me derived unsaturated sterol lipids and need to generate a predicted CCS dataset indexed by lipid identifier and structural isomer class.
    1 install
69. ▌
    Centered Log Ratio Normalization · holobiomicslab

    Use when apply CLR normalization when you have count-based microbiome or metabolome compositional data (e.g., 16S rRNA gene abundances, LC-MS/MS metabolite abundances) that will be used as input to multivariate predictive models (neural networks, regression, correlation analysis).
    0 installs
70. ▌
    Chemical Phylogenetic Comparison · holobiomicslab

    Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1 features to each other based on predicted molecular substructures and chemical properties rather than arbitrary.
    0 installs
71. ▌
    Chemical Space Structure Ranking · holobiomicslab

    Use when you have an unknown compound's mass spectrum (m/z peaks and intensities in .
    0 installs
72. ▌
    Chromatographic Alignment Tuning · holobiomicslab

    Use when when processing a cohort of centroided mzML LC-MS files with high sample-to-sample retention time and m/z drift, and you need reproducible alignment of detected peaks across all samples before gap-filling and feature consolidation.
    2 installs
73. ▌
    Color Palette Application Greens · holobiomicslab

    Use when when rendering a treemap of qc_summary() output showing ion counts and percentages by filter status (passed/failed), and you need a perceptually uniform, colorblind-friendly palette that clearly distinguishes filter categories while using sequential intensity to reinforce the magnitude of.
    0 installs
74. ▌
    Conditional Logic Implementation · holobiomicslab

    Use when you have a user-submitted spectrum with domain-context metadata (e.
    0 installs
75. ▌
    Cross Sample Metabolite Matching · holobiomicslab

    Use when after feature extraction (MS1 peak picking, MS2 recognition, or targeted list extraction) from multiple individual samples and before annotation.
    0 installs
76. ▌
    Deep Learning Feature Extraction · holobiomicslab

    Use when you have preprocessed and normalized LC-MS metabolomics data from multiple disease groups (e.g., healthy, disease-A, disease-B) and need to identify which m/z features or their patterns discriminate between phenotypes.
    0 installs
77. ▌
    Detection Network Output Parsing · holobiomicslab

    Use when you have raw LC-MS data in mzML format with regions of interest (ROI) already identified, and a trained detection model (e.g., checkpoint0029.pth) has produced bounding box predictions with confidence scores.
    0 installs
78. ▌
    Dmodx Orthogonal Distance Metric · holobiomicslab

    Use when apply DModX when you have a normalized LC-MS feature matrix (post-normalization, Step 7 in OUKS) and need to identify samples whose metabolomic profiles are systematically displaced from the learned PCA subspace—indicating potential technical artifacts, extreme biological phenotypes, or.
    2 installs
79. ▌
    Embedding Similarity Computation · holobiomicslab

    Use when when you have pre-computed embeddings (from MSBERT, Spec2Vec, or other deep learning models) for a query spectrum dataset and a reference library, and need to measure how well the embedding space ranks correct library matches.
    0 installs
80. ▌
    Ensemble Variance Quantification · holobiomicslab

    Use when when you have retention order predictions from multiple independently trained models (e.g., ROASMI_1 through ROASMI_5) for the same set of compounds and need to estimate prediction confidence or identify compounds with high model disagreement.
    2 installs
81. ▌
    False Positive Mitigation Tuning · holobiomicslab

    Use when after running Paramounter's peak-height optimization on XCMS CentWave-extracted metabolomic features, if the downstream analysis or feature validation reveals an unacceptable rate of false positives, or if the extraction workflow is experiencing software crashes or timeout failures due to.
    2 installs
82. ▌
    Feature Annotation Consolidation · holobiomicslab

    Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to consolidate redundant or related ion signals into compound-level feature groups before downstream statistical or.
    2 installs
83. ▌
    Feature Detection Rate Filtering · holobiomicslab

    Use when after constructing a MetaboSet object with LC-MS peak abundances, sample metadata (pData with QC labels), and feature metadata (fData), and after marking missing values as NA.
    0 installs
84. ▌
    Feature Group Isotope Annotation · holobiomicslab

    Use when you have a feature table from nontargeted LC-MS peak detection (containing m/z, retention time, and intensity values) and need to disambiguate whether detected features represent the same molecular entity under different ionization/modification states or are true independent signals.
    0 installs
85. ▌
    Feature Intensity Quantification · holobiomicslab

    Use when after features have been identified in LC-MS data via peak picking, MS2 recognition, or targeted-list matching, and you need to measure their signal magnitude (peak height or area) across samples for quantitative comparison, normalization, or statistical testing in metabolomics studies.
    0 installs
86. ▌
    Feature Node Identifier Matching · holobiomicslab

    Use when you have created a feature-based GNPS molecular network and a corresponding MS2LDA experiment, and you need to propagate substructural motif annotations from the MS2LDA output back to the network nodes by matching feature IDs.
    0 installs
87. ▌
    Feature Table Moniker Management · holobiomicslab

    Use when when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to track which version of the table is being used at each step.
    0 installs
88. ▌
    File System Audit And Validation · holobiomicslab

    Use when after invoking the saveAnnotations function on a MetaboAnnotatoR annotations object to confirm that all four expected output file types (global results file, ranked results file, per-feature ranked spectra PDFs, and pseudo-MS/MS MGF file) have been written to the output directory without.
    0 installs
89. ▌
    Fragment Ion Difference Counting · holobiomicslab

    Use when when preparing tandem MS/MS data for spectral alignment and similarity comparison, particularly when you have loaded raw fragmentation spectra and need to extract and quantify mass difference patterns that capture the fragmentation process.
    0 installs
90. ▌
    Fragment Ion Scoring And Ranking · holobiomicslab

    Use when when you have an experimental MS/MS spectrum (centroid mode) and need to convert it into a scored fragment library entry, or when you must rank candidate fragments by confidence before performing spectrum-to-spectrum matching in metabolite annotation workflows.
    0 installs
91. ▌
    Fragment Ion Type Interpretation · holobiomicslab

    Use when you have an tandem MS spectrum with unidentified peaks and a known or hypothesized peptide sequence (in ProForma 2.0 format, including post-translational modifications).
    0 installs
92. ▌
    Fragmentation Pattern Annotation · holobiomicslab

    Use when when you have an experimental MS/MS spectrum (query spectrum as m/z–intensity pairs) and need to identify the compound by comparing its fragmentation pattern to a spectral library.
    0 installs
93. ▌
    Genomic Metabolomic Link Ranking · holobiomicslab

    Use when you have paired genomic (BGCs clustered into GCFs via BiG-SCAPE) and metabolomic data (MS2 spectra grouped into MFs), with strain/sample co-occurrence patterns and predicted BGC–spectrum IOKR scores, and you need to prioritise which GCF–MF pairs are most likely to represent true natural.
    0 installs
94. ▌
    Ion Count Percentage Calculation · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to an mpactr object and generating a qc_summary() data.
    0 installs
95. ▌
    Ion Filter Status Categorization · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to a peak table, when you need to quantify how many ions passed or failed each filter and summarize the overall filtering impact by status distribution.
    0 installs
96. ▌
    Ion Type Assignment Verification · holobiomicslab

    Use when after calling MsmsSpectrum.annotate_proforma() to assign fragment ions to a mass spectrum, verify that each annotated peak has the correct ion_type ('b' or 'y'), charge state, and m/z deviation from the theoretical mass computed for that peptidoform.
    0 installs
97. ▌
    Isotopologue Signature Detection · holobiomicslab

    Use when you have preprocessed, statistically significant LC-MS features (from multiple assays or a single assay) and need to group features that represent the same metabolite in different isotopic labeling states.
    2 installs
98. ▌
    JSON Parsing Motifset Extraction · holobiomicslab

    Use when you have completed the MS2LDA LDA modeling phase and possess motifset.json or motifset_optimized.json files containing inferred Mass2Motifs.
    0 installs
99. ▌
    Kendrick Mass Defect Calculation · holobiomicslab

    Use when you have a feature list from LC- or GC-HRMS analysis (with m/z, retention time, and exact mass columns) and you want to detect homologous series of PFAS compounds that repeat by CF₂ mass increments (typically ≈34 Da).
    0 installs
100. ▌
     Lantibiotic Structure Annotation · holobiomicslab

     Use when you have (1) genomic data from a Streptomyces or other RiPP-producing organism in raw FASTA format or annotated GenBank format, (2) high-resolution LC-MS/MS spectra in centroided MGF, mzML, mzXML, or mzData format, and (3) a known or predicted lantibiotic core peptide sequence you wish to.
     0 installs