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HolobiomicsLab

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1. ▌
   Global Similarity Aggregation 2 · holobiomicslab

   Use when after computing pairwise cosine similarities between all spectra across two LC-MS/MS datasets when you need a single scalar summary of dataset-level resemblance rather than individual spectrum matches.
   0 installs
2. ▌
   Gnps Spectral Data Processing 2 · holobiomicslab

   Use when your input is raw or semi-processed MS/MS spectra fetched from GNPS or a compatible library (e.g., EMBL-MCF 2.0, NIST23) and you need to prepare them for neural-network-based formula prediction.
   0 installs
3. ▌
   Graph Based Identity Transfer 2 · holobiomicslab

   Use when when you have spectral library matches (seed identities with high confidence scores) mapped to initial candidate structures from in silico fragmentation, and you want to propagate those identities to related structures in the fragmentation candidate graph to improve annotation coverage.
   0 installs
4. ▌
   Hdf5 Hierarchical Data Access 3 · holobiomicslab

   Use when you have multidimensional MS data converted to MZA HDF5 format (from Agilent .d, Bruker .d with ion mobility, Thermo .
   0 installs
5. ▌
   In Silico Compound Annotation 2 · holobiomicslab

   Use when after feature filtering and clustering have been completed in MS-CleanR and you have a cleaned feature set with m/z, retention time, and MS/MS spectra data ready for structural assignment. Use it when you need to identify unknown compounds by querying multiple chemical databases (e.
   0 installs
6. ▌
   Injection Sequence Annotation 2 · holobiomicslab

   Use when you have a Sciex Multiquant TXT export file containing a metabolomics or lipidomics analytical sequence and need to locate QCpool samples that were injected at regular intervals, validate their spacing matches study design expectations, and compile structured metadata for downstream.
   0 installs
7. ▌
   Ion Target Quality Monitoring 2 · holobiomicslab

   Use when you have MS1 data from multiple samples and need to assess whether particular ion targets (e.g., internal standards, biomarkers, or metabolites of interest) maintain consistent quality across the cohort. Trigger on: (1) suspicion of sample-to-sample variability in ion signal;
   0 installs
8. ▌
   Irt Peptide Standard Matching 2 · holobiomicslab

   Use when you have a Thermo Fisher Scientific .raw file from an LC-MS run containing a spiked iRT peptide standard mix (e.
   0 installs
9. ▌
   JSON File Parsing And Loading 2 · holobiomicslab

   Use when after generating a structured JSON result file from a prior computational step (e.g., gensim LDA model output in myexp.ldaresult.json format) and needing to store it in PostgreSQL for web application access, visualization, or further analysis.
   0 installs
10. ▌
    Lc Ms Eic Plot Interpretation 2 · holobiomicslab

    Use when after executing TARDIS in screening_mode = TRUE on centroided .mzML files with a defined target compound list.
    0 installs
11. ▌
    Level 4 Annotation Assignment 3 · holobiomicslab

    Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
    0 installs
12. ▌
    Lexical Analysis Tokenization 2 · holobiomicslab

    Use when you have a mass-spectrometry query string written in MassQL (or similar domain-specific SQL-inspired syntax) that must be converted into structured form for execution. The input is raw, unparsed text containing SQL keywords, MS-specific operators (e.
    0 installs
13. ▌
    Lipid Structure Specification 2 · holobiomicslab

    Use when you have identified lipid species unique to your sample type (e.
    0 installs
14. ▌
    M Z Tolerance Window Matching 3 · holobiomicslab

    Use when when you have detected features with m/z, drift time, and retention time dimensions and need to associate peaks into isotopic groups (e.g., monoisotopes with C13 substitutions) or align features across multiple LC-IMS-MS/MS samples.
    0 installs
15. ▌
    Mass Range Window Restriction 2 · holobiomicslab

    Use when you have loaded an MsmsSpectrum object and need to focus analysis on a biologically or chemically relevant mass window.
    0 installs
16. ▌
    Mass Spectral Data Formatting 2 · holobiomicslab

    Use when when you have raw mass spectral data in .mgf, .msp, .mzML, or .lbm2 file formats and need to search against a spectral library using entropy similarity or Flash Entropy Search. Also apply this skill before building spectral library indices or computing entropy-based compound identification.
    0 installs
17. ▌
    Mass Spectrometry Data Import 2 · holobiomicslab

    Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.
    0 installs
18. ▌
    Mass Spectrum Tensor Encoding 2 · holobiomicslab

    Use when when you have parsed EI-MS spectrum data (m/z and intensity values) and need to feed it into a pre-trained MWFormer transformer model for direct molecular weight prediction.
    0 installs
19. ▌
    Mass2motif Annotation Mapping 2 · holobiomicslab

    Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
    0 installs
20. ▌
    Metabolite Cluster Evaluation 3 · holobiomicslab

    Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to cross-validate the two available scoring methods (findMain and RAMClustR internal scoring) to identify cases where they.
    0 installs
21. ▌
    Metabolite Feature Annotation 2 · holobiomicslab

    Use when after MS1 feature extraction from mzXML files when you have: (1) a feature table with m/z, retention time, and intensity values; (2) DDA (Data-Dependent Acquisition) mzXML files containing MS2 fragmentation spectra; and (3) a reference spectral library in MSP format.
    0 installs
22. ▌
    Metabolomic Feature Alignment 3 · holobiomicslab

    Use when you have two or more CSV feature tables from independent metabolomic experiments (each with RT, m/z, intensity, isotope, and adduct columns), and you need to merge them into a single aligned feature matrix for downstream batch effect removal, marker identification, or pathway analysis.
    0 installs
23. ▌
    Minimum Cost Flow Formulation 2 · holobiomicslab

    Use when you have an NMR mixture spectrum and a library of single-compound reference spectra, and you need to identify which compounds are present and their relative abundances.
    0 installs
24. ▌
    Mobility Scale Transformation 2 · holobiomicslab

    Use when analyzing CE-MS(/MS) data where electroosmotic flow fluctuations cause variable migration times for the same compounds across runs.
    0 installs
25. ▌
    Molecular Fragment Prediction 2 · holobiomicslab

    Use when when you have an experimental tandem mass spectrum (m/z peaks and intensities) and a chemical formula, and need to identify the true molecular structure from a candidate library (e.g., PubChem).
    0 installs
26. ▌
    Ms Backend API Implementation 2 · holobiomicslab

    Use when you have MS data in a new format or storage system (e.g., a custom database, HDF5 file, or proprietary raw file) and need to make it accessible to Spectra-based analysis workflows without forking the Spectra package itself.
    0 installs
27. ▌
    Ms Data Format Identification 3 · holobiomicslab

    Use when when receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline. Specifically, apply this skill when: (1) input files arrive without documented instrument type or chromatographic/mobility dimensionality;
    0 installs
28. ▌
    Ms Dial Version Compatibility 2 · holobiomicslab

    Use when you are preparing to run LipoCLEAN on MS-DIAL output and need to create or update a configuration file, or you have switched between MS-DIAL 4 and MS-DIAL 5 data and need to verify that your options file and trained model are compatible with the current version's column naming and scaling.
    0 installs
29. ▌
    Ms Ms Spectral Interpretation 2 · holobiomicslab

    Use when you have acquired MS/MS spectral data (in mzML, mzXML, or equivalent format) for unknown compounds and need to identify the most probable metabolite structure.
    0 installs
30. ▌
    Multi Tool Results Comparison 2 · holobiomicslab

    Use when you have feature identification outputs from two or more DIA-MS search tools (e.g., DIA-NN and OpenSwath result files) and need to assess their agreement on analyte detection, quantification, and scoring.
    0 installs
31. ▌
    Mzml Format Output Validation 2 · holobiomicslab

    Use when after executing smiter.synthetic_mzml.write_mzml to generate synthetic LC-MS/MS runs from nucleoside or peptide fragmentation models.
    0 installs
32. ▌
    Nmr Spectrum Phase Adjustment 2 · holobiomicslab

    Use when you have acquired raw 1D NMR spectra (FID or processed spectra in NMRPipe format) that exhibit phase distortion—where peaks are not in pure absorption mode—and you need to prepare the spectrum for automatic deconvolution into peak tables.
    0 installs
33. ▌
    Nmrbox Environment Management 2 · holobiomicslab

    Use when when you need to deploy SAND for 1D NMR spectrum deconvolution on a new machine or cluster, or when testing code changes before merging into production.
    0 installs
34. ▌
    Package Dependency Management 2 · holobiomicslab

    Use when you need to set up a cloned or downloaded scientific Python package for local development, testing, or execution. Specifically, use it when: (1) you have a package repository with a pyproject.toml or setup.py that declares dev dependencies;
    0 installs
35. ▌
    Parameter Search Space Design 2 · holobiomicslab

    Use when when beginning an untargeted LC-MS analysis and either (1) the dataset characteristics (sample complexity, instrument platform, or polarity) differ from previously optimized cohorts, (2) multiple peak-picking algorithms (Centwave, FeatureFinderMetabo, ADAP) are available and their relative.
    0 installs
36. ▌
    Ppm Error Tolerance Filtering 2 · holobiomicslab

    Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to chemodiversity analysis, transformation network generation, or multivariate statistics.
    0 installs
37. ▌
    Quantitation Table Generation 3 · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a defined list of m/z, retention time, or other identifiers for which you need to extract and quantify peak abundances across one or more samples.
    0 installs
38. ▌
    R Data Structure Manipulation 2 · holobiomicslab

    Use when when xcms has produced misaligned feature groups and you need to extract raw LC-MS profiles from source files into a structured format acceptable by ncGTW's realignment functions.
    0 installs
39. ▌
    Rawrr Spectral Data Retrieval 2 · holobiomicslab

    Use when you have Thermo Orbitrap .raw files and need to access raw spectral data (individual MS1 or MS2 scans, base-peak values, chromatogram traces, retention times, or scan-level metadata) for custom analysis, visualization, or integration into an R-based pipeline.
    0 installs
40. ▌
    Rdkit Molecular Featurization 2 · holobiomicslab

    Use when you have molecular structure data (SMILES strings or MOL files) from an in-house chemical database and need to prepare it as input for a graph neural network that predicts liquid chromatography retention times for small molecule identification.
    0 installs
41. ▌
    Run Order Dependency Modeling 2 · holobiomicslab

    Use when your feature table includes QC (quality control) sample replicates distributed throughout the analytical run sequence, and you observe systematic intensity variation correlated with sample injection order or batch identifier—typical indicators of instrumental drift in untargeted LC-MS.
    0 installs
42. ▌
    Runtime Performance Profiling 2 · holobiomicslab

    Use when when you need to empirically validate that one mass spectrometry data processing library achieves higher throughput than competing alternatives. Specifically: you have multiple candidate libraries (e.
    0 installs
43. ▌
    Signal Residual Deconvolution 3 · holobiomicslab

    Use when analyzing 1D signal arrays (e.g., extracted ion chromatograms, arrival time distributions, or MS1 spectra intensity profiles) where multiple peaks may overlap or where peak shape information (amplitude, position, width) is required beyond simple local-maximum detection.
    0 installs
44. ▌
    Smiles Sdf Parsing Validation 2 · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
    0 installs
45. ▌
    Spectra Object Manipulation R 2 · holobiomicslab

    Use when when you have extracted and concatenated MS/MS spectra from multiple replicates for a set of metabolomic features (stored in a preprocessed list), and need to apply intensity-based filtering (e.
    0 installs
46. ▌
    Spectral Data Standardization 2 · holobiomicslab

    Use when you have completed a GNPS1 (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING) or GNPS2 (classical_networking_workflow, feature_based_molecular_networking_workflow) molecular networking job and need to access its output files in a standardized format for.
    0 installs
47. ▌
    Spectral Graph Interpretation 3 · holobiomicslab

    Use when after submitting MS/MS data and feature tables to GNPS and receiving a molecular networking job result.
    0 installs
48. ▌
    Spectral Match Interpretation 2 · holobiomicslab

    Use when you have obtained search results from one or more domain-specific MASST web applications (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) for a query mass spectrum and need to consolidate, rank, and visualize those matches to infer the identity and biological source of.
    0 installs
49. ▌
    Spectral Noise Classification 2 · holobiomicslab

    Use when you have MS/MS spectra contaminated with noise ions and need to improve compound identification accuracy.
    0 installs
50. ▌
    Spectrum Embedding Clustering 2 · holobiomicslab

    Use when after embedding MS/MS spectra into 32-dimensional GLEAMS vectors, when you need to group spectra by the same peptide origin.
    0 installs
51. ▌
    Structural Similarity Scoring 2 · holobiomicslab

    Use when when you have a collection of mass spectra with annotated chemical structures (SMILES/InChI) and need to generate structural similarity labels to train or validate a model that predicts molecular similarity from spectral pairs.
    0 installs
52. ▌
    Structure Selection Filtering 2 · holobiomicslab

    Use when when you have an unknown metabolite's predicted structural similarity scores (from a deep learning model such as DeepMASS) against all known metabolites in a reference database, and need to identify which known metabolites are most likely structurally related to the unknown to guide.
    0 installs
53. ▌
    Synthetic Spectrum Generation 2 · holobiomicslab

    Use when when you need to create benchmark LC-MS/MS datasets with controlled, known composition for testing MS analysis algorithms, validating retention-time or fragmentation predictions, or predicting co-elution and co-fragmentation challenges before conducting real experiments.
    0 installs
54. ▌
    Tabular Data Field Comparison 2 · holobiomicslab

    Use when you have multiple independent implementations of the same data format reader (e.g., Rust, Python, R versions) and need to verify they produce identical or equivalent output.
    0 installs
55. ▌
    Tandem Mass Spectrum Decoding 2 · holobiomicslab

    Use when when you have raw predictions from a trained fragment generation or intensity prediction neural network model and need to convert those predictions into a standard spectrum file format (m/z–intensity pairs) for comparison against experimental spectra or for structural elucidation workflows.
    0 installs
56. ▌
    Taxonomy String Normalization 2 · holobiomicslab

    Use when when preparing a metadata table (TSV format with species, genus, and family columns) for natural product metabolomics analysis where the Literature Component score must query known compounds by taxon.
    0 installs
57. ▌
    Transfer Learning Fine Tuning 2 · holobiomicslab

    Use when you have collected liquid chromatography (LC) spectra and retention time labels for your in-house molecular database, and you want to leverage a pretrained GNN-RT model rather than train from scratch.
    0 installs
58. ▌
    Transition Group Peak Picking 2 · holobiomicslab

    Use when you have loaded extracted ion chromatogram (XIC) data from DIA mass spectrometry and need to identify peak boundaries for peptide precursor transitions.
    0 installs
59. ▌
    Web Service Health Monitoring 2 · holobiomicslab

    Use when your annotation pipeline depends on multiple external web converters and you need to diagnose why annotation jobs are failing, slow, or incomplete. Use it if you observe missing metadata fields in output .
    0 installs
60. ▌
    Abstract Syntax Tree Design 2 · holobiomicslab

    Use when when you have a domain-specific query language (such as MassQL for mass spectrometry) and need to convert query strings into structured representations that preserve domain constraints (e.g., mass tolerance, scan type, intensity thresholds).
    0 installs
61. ▌
    Byte Offset Seek Operations 2 · holobiomicslab

    Use when when you have an indexed gzip-compressed mzML file and need to retrieve individual spectra or chromatograms by index without sequential file reading or full decompression. Typical scenario: you want spectrum[42] from a 10 GB indexed mzML.gz file and need sub-second access time.
    0 installs
62. ▌
    Candidate Structure Ranking 2 · holobiomicslab

    Use when you have (1) a set of candidate structures generated by in silico fragmentation (e.g., MetFrag output), (2) one or more seed nodes with known spectral library matches or identity scores, and (3) a fragmentation relationship graph connecting candidates.
    0 installs
63. ▌
    Data Integrity Verification 2 · holobiomicslab

    Use when after applying matchms metadata cleaning tools to normalize field values and standardize naming conventions on imported spectra (mzML, mzXML, msp, MGF, or JSON formats).
    0 installs
64. ▌
    Embedding Vector Generation 2 · holobiomicslab

    Use when when you have tokenized mass spectra (peak-mass and peak-intensity pairs from experimental or in-silico libraries such as NIST 2017 or MassBank) and need to perform rapid similarity searches or spectrum matching at scale.
    0 installs
65. ▌
    Format Conversion Chemistry 2 · holobiomicslab

    Use when when you have retrieved a user database entry (sequence or structure data) from the MassSpecBlocks backend and need to enable mass spectra analysis in the open-source CycloBranch program, or when you need to export NRP sequences and building-block annotations for consumption by external.
    0 installs
66. ▌
    Ftms Transient Data Loading 2 · holobiomicslab

    Use when you have a Bruker Solarix FT-ICR transient file in .d format (e.g., ESI_NEG_SRFA.d containing ser and fid files in CompassXtract format) and need to programmatically load it into a Python environment for signal processing, calibration, and mass spectrum generation.
    0 installs
67. ▌
    Interactive Plot Generation 2 · holobiomicslab

    Use when you have loaded m/z and intensity arrays from an MZA file (via mzapy) and need to inspect a mass spectrum, extracted ion chromatogram (XIC), or arrival time distribution (ATD) visually, either for QC purposes, method development, or publication-ready output.
    0 installs
68. ▌
    Metadata Structure Checking 2 · holobiomicslab

    Use when after loading a metadata file but before merging it with positive and negative mode m/z peaklists. Apply this skill when you have a candidate metadata table (e.
    0 installs
69. ▌
    Multi Format Data Ingestion 2 · holobiomicslab

    Use when you have raw metabolomics data files in one or more of the supported formats (.raw from Thermo instruments, .d directories from Agilent, or mzXML open-format exports) and need to ingest them into SMART for preprocessing, visualization, or statistical analysis.
    0 installs
70. ▌
    Mzpeak Format Io Operations 2 · holobiomicslab

    Use when you have mass spectrometry run data (spectra, chromatograms, instrument metadata) that must be stored in or recovered from the mzPeak format, or when you need to validate that a mzPeak implementation correctly supports both read and write paths for round-trip fidelity.
    0 installs
71. ▌
    Pytorch Inference Execution 2 · holobiomicslab

    Use when you have a pretrained PyTorch model with released weights (e.g., JESTR on NPLIB1), a prepared dataset with input features (spectra m/z–intensity arrays, molecular graphs), a GPU environment with CUDA 11.
    0 installs
72. ▌
    R Data Frame Transformation 2 · holobiomicslab

    Use when when you have autoQ output containing peak area measurements for isotopologues in data frame format and need to prepare data for metBarPlot visualization or cross-sample comparison. Specifically, use this skill when val.to.
    0 installs
73. ▌
    R Data Object Serialization 2 · holobiomicslab

    Use when you have mzPeak files (Parquet-based archives containing mass spectrometry spectra and chromatogram data) that you want to analyze in R, and you need to convert the Arrow columnar representation into native R objects that can be passed to downstream analysis functions (e.
    0 installs
74. ▌
    Sequence To Feature Mapping 2 · holobiomicslab

    Use when when you have a list of polypeptide sequences (plain text, CSV, or FASTA format) and need to compute their monoisotopic mass and average mass for downstream mass spectrometry interpretation, database matching, or physico-chemical property annotation.
    0 installs
75. ▌
    Spectral Peak Normalization 2 · holobiomicslab

    Use when when preparing query spectra and library spectra for similarity-based matching via dot product scoring, particularly in open modification spectral library searches where you need to match modified query spectra to unmodified library counterparts without the results being biased by.
    0 installs
76. ▌
    Spectrum Embedding Indexing 2 · holobiomicslab

    Use when you have pre-computed Word2vec embeddings of mass spectra and need to retrieve the k most similar spectra from a library of hundreds of thousands to millions of candidates.
    0 installs
77. ▌
    Adduct Ion Mass Calculation 2 · holobiomicslab

    Use when when you have derivatized metabolite structures (SMILES or mol format) and need to predict their ionization products in MS imaging, particularly when the derivatizing matrix produces non-standard adducts (e.
    0 installs
78. ▌
    Annotation Object Manipulation 2 · holobiomicslab

    Use when after completing metabolite annotation of LC-MS AIF features using the annotateRC function, when you need to persist ranked candidate matches, inspect multiple candidate annotations per feature, visualize matched ions in ranked spectra, or export pseudo-MS/MS spectra for external analysis.
    0 installs
79. ▌
    Control Flow Diagram Synthesis 3 · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (such as mzmine) selectively routes data to different processing pipelines based on declared input type (LC, GC, IMS, or MS Imaging).
    0 installs
80. ▌
    Dimensionality Reduction T Sne 2 · holobiomicslab

    Use when you have computed high-dimensional embeddings (e.
    0 installs
81. ▌
    Feature List Format Validation 2 · holobiomicslab

    Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic detection, or wishes to augment/replace pyOpenMS results with pre-processed features.
    0 installs
82. ▌
    Fragment Ion Database Matching 2 · holobiomicslab

    Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment libraries (e.g., LipidPos for lipids).
    0 installs
83. ▌
    Ggplot2 Geom Treemap Rendering 2 · holobiomicslab

    Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).
    0 installs
84. ▌
    High Dimensional Data Indexing 2 · holobiomicslab

    Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest neighbors efficiently.
    0 installs
85. ▌
    Inter Scan Interval Validation 2 · holobiomicslab

    Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the scheduled method with correct temporal spacing.
    0 installs
86. ▌
    Iokr Fingerprint Space Ranking 2 · holobiomicslab

    Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a compound-class-agnostic method.
    0 installs
87. ▌
    Lc Ms Adduct Pattern Detection 2 · holobiomicslab

    Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may represent the same compound ionized as different adducts (e.g., [M+H]⁺ vs. [M+Na]⁺).
    0 installs
88. ▌
    Lda Model Training Convergence 2 · holobiomicslab

    Use when you have a preprocessed bag-of-fragments corpus derived from tandem mass spectrometry spectra and need to discover recurring fragmentation motifs without prior compound identification.
    0 installs
89. ▌
    Mass Spectral Feature Grouping 3 · holobiomicslab

    Use when you have untargeted metabolomics MS/MS spectra from multiple features and need to identify which features belong to the same molecular family or are related by biotransformation.
    0 installs
90. ▌
    Ms Dial Export Format Handling 2 · holobiomicslab

    Use when you have performed lipid identification in MS-DIAL and need to pass the results to LipoCLEAN or another downstream quality-filtering tool. The skill is required whenever you are preparing MS-DIAL output for consumption by external analysis pipelines that expect standardized export formats.
    0 installs
91. ▌
    Ms Ms Spectrum Peak Annotation 2 · holobiomicslab

    Use when you have an experimental MS/MS spectrum (e.g., from MassBank or local data) and need to identify significant fragment ions above noise, assign occurrence scores to peaks, and generate a CSV-formatted library entry for use in metabolite feature annotation pipelines.
    0 installs
92. ▌
    Ms2 Fingerprint Matrix Merging 2 · holobiomicslab

    Use when you have two MemoMatrix objects generated from separate sample cohorts (e.
    0 installs
93. ▌
    Nmr Modality Ablation Analysis 2 · holobiomicslab

    Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal contribution of each NMR modality or justify multimodal input design.
    0 installs
94. ▌
    Mgf File Parsing 2 · holobiomicslab

    Use when you have raw or MZmine-processed MGF files (containing MS/MS spectra with m/z values, intensities, and precursor masses) that need to be segmented by sample, deduplicated, or prepared for fragment annotation and adduct analysis in the MolNotator pipeline.
    0 installs
95. ▌
    Msp File Parsing 2 · holobiomicslab

    Use when you have a Mass Spectrum Point (MSP) file containing electron ionization mass spectral records with header fields and peak intensity pairs, and you need to load it into an R data structure for library searching, format validation, or round-trip conversion.
    0 installs
96. ▌
    Mzml File Parsing 2 · holobiomicslab

    Use when you have raw LC- or GC-HRMS data from vendor instruments (ESI or APCI ionization) that needs to be converted to a vendor-neutral format for non-target screening, or you already have mzML files that require loading into a Python environment for downstream feature detection and MS2 spectral.
    0 installs
97. ▌
    Ms2 Dereplication 2 · holobiomicslab

    Use when you have MS2 tandem mass spectrometry data in .mzML format and need to match unknown spectra against a reference library (GNPS, HMDB, MassBank) to identify which known compounds are present in your sample.
    0 installs
98. ▌
    Peak M Z Indexing 2 · holobiomicslab

    Use when when you have LC-MS-MS metabolomics data in MGF format and need to prepare it for unsupervised analysis (e.g., topic modeling with LDA).
    0 installs
99. ▌
    Msp To CSV Parsing 2 · holobiomicslab

    Use when you have a .msp format MS/MS spectrum library (e.g., from MassBank or similar public databases) and need to convert it into individual CSV entries indexed by positive or negative ionisation mode for use as a custom fragment library in MetaboAnnotatoR annotation pipelines.
    4 installs
100. ▌
     Peak Count Capping 2 · holobiomicslab

     Use when apply peak-count capping when preprocessing tandem mass spectrometry (MS/MS) spectra for peptide identification or spectral library matching, particularly when working with high-resolution spectra that may retain numerous low-intensity noise peaks after intensity filtering.
     0 installs