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HolobiomicsLab

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1. ▌
   Mass Spectrum Basepeak Extraction 2 · holobiomicslab

   Use when when you have Thermo Fisher Scientific .raw files from Orbitrap instruments and need to build a quantitative summary of MS1 acquisition intensity dynamics across a run—specifically, the m/z and intensity of the most intense peak in each MS1 scan.
   6 installs
2. ▌
   Mass Tolerance Window Calibration 2 · holobiomicslab

   Use when when implementing adduct detection in LC-MS metabolomics workflows, after defining theoretical adduct mass offsets (e.g., [M+NH4]+ at +17.0266 Da, [M+K]+ at +38.9815 Da), and before assigning adduct labels to a feature table.
   6 installs
3. ▌
   Mb Vip Feature Importance Ranking 3 · holobiomicslab

   Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify which features drive model performance and warrant further statistical validation or biological interpretation.
   6 installs
4. ▌
   Metabcombiner Object Construction 2 · holobiomicslab

   Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to identify overlapping <m/z, retention time> features across them.
   7 installs
5. ▌
   Metabolite Feature Anova Analysis 2 · holobiomicslab

   Use when you have normalized abundance data from LC-MS/MS for multiple samples classified into three or more discrete groups (e.
   5 installs
6. ▌
   Metabolite Ratio Batch Correction 3 · holobiomicslab

   Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with measured ion areas for compounds and assigned internal standards.
   6 installs
7. ▌
   Metabolite Signal Drift Detection 3 · holobiomicslab

   Use when when you have multi-batch metabolomics data (SummarizedExperiment object with raw or log-transformed assays) and need to assess whether specific metabolites exhibit systematic signal drift across experimental run order or strong batch effects that would justify hierarchical normalisation.
   5 installs
8. ▌
   Metabolite Target List Formatting 2 · holobiomicslab

   Use when you have a raw LC–MS compound metadata file (xlsx or csv) with heterogeneous column names and column order, and you need to prepare it for targeted peak detection in TARDIS.
   6 installs
9. ▌
   Metabolomic Signal Quantification 2 · holobiomicslab

   Use when you have raw untargeted LC/MS data in open mzML or mzXML format and need to extract a quantified feature matrix (m/z and retention time coordinates with sample intensities) without prior knowledge of optimal signal detection parameters, batch effects, or quality control samples.
   5 installs
10. ▌
    Metabolomics Data Format Handling 4 · holobiomicslab

    Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into MetaboAnalystR 4.0 for unified LC-MS1 feature detection and MS/MS spectra processing.
    7 installs
11. ▌
    Metabolomics Data Quality Metrics 3 · holobiomicslab

    Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high technical variability or signal degradation before proceeding to statistical analysis or interpretation of.
    5 installs
12. ▌
    Metadata Structure Transformation 3 · holobiomicslab

    Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be deposited into a structured online repository like Metabolomics Workbench, but the raw format does not conform to the.
    7 installs
13. ▌
    Missing Peak Imputation Fillpeaks 2 · holobiomicslab

    Use when apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection failures.
    5 installs
14. ▌
    Molecular Fingerprint Computation 2 · holobiomicslab

    Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a fingerprint representation optimized for biosynthetic-class prediction, structural clustering, or bioinformatic feature.
    6 installs
15. ▌
    Ms Instrument Type Classification 4 · holobiomicslab

    Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS Imaging) is covered by at least one processing module.
    6 installs
16. ▌
    Ms2 Fingerprint Vector Generation 2 · holobiomicslab

    Use when you have LC-MS/MS data in mzML, mzXML, or MGF format from one or more metabolomics samples and need to compare samples that may have poor overlap in detected features, strong retention time shifts between runs, or were acquired on different LC methods or MS technologies (e.
    6 installs
17. ▌
    Scan Filter File Organization 2 · 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).
    5 installs
18. ▌
    File System Audit And Validation 2 · 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.
    4 installs
19. ▌
    Fticr Mass Calibration Edgeshift 3 · holobiomicslab

    Use when you have FTICR-MS direct injection (mzML) data with identified chromatographic peaks and need to correct systematic m/z bias.
    6 installs
20. ▌
    Mass Track Consensus Computation 3 · holobiomicslab

    Use when after mass tracks have been aligned across all samples (either via pairwise alignment for ≤10 samples or nearest-neighbor clustering for larger cohorts), and you need to generate a single representative m/z per aligned bin for downstream feature extraction and annotation.
    7 installs
21. ▌
    Neural Network Input Preparation 2 · holobiomicslab

    Use when when you have annotated representative LCMS samples (raw mzML files + labeled feature tables in mzmine CSV format) and need to convert them into balanced or unbalanced peak matrix batches with fixed dimensions for neural network training.
    8 installs
22. ▌
    Proforma 2 0 Peptidoform Parsing 2 · holobiomicslab

    Use when you have a ProForma 2.0 peptidoform string (e.
    7 installs
23. ▌
    Scan Index Parsing And Filtering 2 · holobiomicslab

    Use when you have a Thermo Orbitrap .raw file and need to (1) verify that a targeted acquisition method (e.g., PRM) maintains consistent scan spacing across all cycles; (2) extract only scans matching a specific precursor ion and fragmentation method;
    5 installs
24. ▌
    Annotation Table Quality Control 2 · 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.
    4 installs
25. ▌
    API Response Latency Measurement 2 · holobiomicslab

    Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.
    5 installs
26. ▌
    Backend Performance Benchmarking 2 · holobiomicslab

    Use when when you have execution time data for visualization scripts across multiple backends (matplotlib, Bokeh, Plotly) and need to determine which backend offers the fastest median performance for specific mass spectrometry plot types (chromatogram, mobilogram, peakmap, peakmap-marginals.
    6 installs
27. ▌
    Batch Spectral Record Processing 2 · 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.
    5 installs
28. ▌
    Calibration Residual Calculation 2 · holobiomicslab

    Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a given PPM tolerance window.
    7 installs
29. ▌
    Chemical Identifier Verification 3 · 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.
    7 installs
30. ▌
    Chemical Phylogenetic Comparison 3 · 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.
    5 installs
31. ▌
    Clustered Peak Output Formatting 2 · holobiomicslab

    Use when after peak clustering has been completed in pyINETA (i.
    5 installs
32. ▌
    Data Summarization And Tabulation 2 · holobiomicslab

    Use when after obtaining structural clusters from the MAMSI framework using different parameter configurations (e.
    6 installs
33. ▌
    Fragment Peak Chemical Annotation 2 · holobiomicslab

    Use when you have MS/MS spectra with assigned precursor formulas and need to annotate the chemical composition of individual fragment peaks for metabolite structure elucidation or fragmentation pathway analysis. Apply this skill when you want to avoid external fragmentation tree computation (e.
    4 installs
34. ▌
    Mass2motif Parameter Optimization 2 · holobiomicslab

    Use when when you have a preprocessed bag-of-fragments corpus from tandem mass spectrometry spectra and need to train an MS2LDA model to discover Mass2Motifs.
    7 installs
35. ▌
    Neighbourhood Density Computation 2 · holobiomicslab

    Use when after library-matching has produced ranked candidate spectra with MS2Deepscore embeddings.
    6 installs
36. ▌
    Peak Quality Label Stratification 2 · holobiomicslab

    Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
    6 installs
37. ▌
    Rippp Structure Database Matching 2 · holobiomicslab

    Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or mzData format from LC-MS/MS analysis; (2) a set of predicted RiPP precursor peptides derived from genomic biosynthetic gene cluster mining (via antiSMASH, BOA, or raw FASTA);
    5 installs
38. ▌
    Spectral Dimensionality Reduction 2 · holobiomicslab

    Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
    5 installs
39. ▌
    Workflow Output Validation And QA 2 · holobiomicslab

    Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.
    9 installs
40. ▌
    Adduct Specific Model Fine Tuning 3 · holobiomicslab

    Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
    7 installs
41. ▌
    Backend Merging And Concatenation 2 · holobiomicslab

    Use when when you have two or more MsBackend objects (e.g., multiple MsBackendMemory, MsBackendDataFrame, or MsBackendMzR instances) containing distinct sets of MS spectra and you need to consolidate them into a single backend for downstream analysis, parallel processing, or export.
    5 installs
42. ▌
    C Sharp Wrapper Invocation From R 3 · holobiomicslab

    Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings are unavailable or impractical. Use this when the target assembly requires Windows/.
    6 installs
43. ▌
    Carbon Oxidation State Assessment 3 · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peak data, when you need to classify metabolites by their redox state to predict bioavailability or lability, or when generating thermodynamic indices for chemodiversity analysis and environmental metabolomic interpretation.
    9 installs
44. ▌
    Chemical Shift Reference Matching 2 · holobiomicslab

    Use when when preparing an input spectral peak list for NMRformer or similar Transformer-based peak assignment models, and you have observed peaks whose chemical shifts do not align with known metabolite signatures.
    7 installs
45. ▌
    Compound Class Annotation Parsing 3 · holobiomicslab

    Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
    4 installs
46. ▌
    De Novo Precursor Mass Annotation 3 · holobiomicslab

    Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting without access to spectral libraries.
    5 installs
47. ▌
    Derivatizing Matrix Configuration 4 · holobiomicslab

    Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for metabolite annotation, and the matrix is not yet configured in your Met-ID installation.
    6 installs
48. ▌
    Chromatographic Peak Detection Msw 4 · holobiomicslab

    Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time dimensions. Use this skill when you must isolate individual ion signals before applying calibration corrections (e.
    5 installs
49. ▌
    Cnn Inference On Metabolomics Data 2 · holobiomicslab

    Use when you have LC-MS feature tables (with m/z and retention time columns) paired with raw .mzXML or .mzML files, and you need to automatically validate which detected features correspond to genuine chromatographic peaks versus false positives or noise.
    5 installs
50. ▌
    Compound Identification From Ms Ms 2 · holobiomicslab

    Use when you have LC-MS/MS data in mgf format and a custom spectral database prepared with CFM-id (or an in-built database), and you need to identify unknown compounds by comparing their experimental fragmentation patterns against predicted or reference spectra with quantified match scores.
    4 installs
51. ▌
    Condition Effect Matrix Generation 2 · holobiomicslab

    Use when you need to create a synthetic feature table with known, ground-truth condition effects for method validation when: (1) testing normalization or batch-correction algorithms that must not confound condition signal with batch noise;
    4 installs
52. ▌
    Feature Abundance Pattern Matching 3 · holobiomicslab

    Use when after initial retention-time-based feature grouping when you have groups of multiple features at similar m/z and retention time but need to determine which features actually arise from the same compound.
    6 installs
53. ▌
    Feature Pairing Confidence Scoring 2 · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) and need to establish reliable correspondence between features across datasets.
    4 installs
54. ▌
    Fragment Level Spectrum Prediction 2 · holobiomicslab

    Use when when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict its tandem mass spectrum for structural elucidation or mass spectrometry validation.
    6 installs
55. ▌
    In Silico Fragmentation Prediction 3 · holobiomicslab

    Use when you have candidate metabolite structures (from database lookup or enumeration) and experimental MS/MS spectra (mzML, mzXML format), and need to rank candidates by how well their predicted fragments match observed peaks.
    7 installs
56. ▌
    Inadequate Spectral Interpretation 2 · holobiomicslab

    Use when you have clustered peak networks from INADEQUATE NMR spectra (output from the Clustering module) and need to assign metabolite identities by comparing them to known spectral signatures.
    3 installs
57. ▌
    Ion Mobility Heatmap Visualization 3 · holobiomicslab

    Use when you have raw LC-IMS-MS data (Agilent, Thermo, Bruker, or mzML format) and need to visualize and export the spatial distribution of a specific ion species (or ion family) across both ion mobility and retention time dimensions.
    6 installs
58. ▌
    Lcms Peak Alignment And Annotation 2 · holobiomicslab

    Use when you have an XCMS-processed feature set (XCMSet object) from replicate LC/MS runs comparing labeled (e.g., 13C-glucose) and unlabeled (e.g., 12C-glucose) conditions, and need to identify which features show isotope incorporation (fold-change ≥1.5, p-value <0.
    6 installs
59. ▌
    Mass Spectrometry Data Integration 2 · holobiomicslab

    Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to correct for systematic shifts in mass-to-charge, drift time, or retention time caused by instrumental drift, column aging.
    5 installs
60. ▌
    Mass Spectrum Embedding Generation 2 · holobiomicslab

    Use when you have cleaned MS/MS spectra (in formats like .mgf, .msp, .
    5 installs
61. ▌
    Model Metadata Schema Verification 3 · holobiomicslab

    Use when before submitting peak data or other inputs to a machine learning classification API for the first time, after a model update, or if you encounter unexpected prediction errors. It is essential when the underlying model's input names or structure may change and require code updates.
    5 installs
62. ▌
    Modularity Optimization Clustering 2 · holobiomicslab

    Use when after MS-DIAL peak character estimation has grouped LC-MS features into preliminary clusters based on peak shape and chromatographic similarity, and you need to select a single representative parental feature from each cluster to reduce redundancy before MS-FINDER annotation.
    5 installs
63. ▌
    Motifdb Reference Library Querying 2 · holobiomicslab

    Use when after Mass2Motifs have been inferred from tandem MS/MS spectra via LDA topic modeling and you need to assign putative substructure annotations to those motifs.
    6 installs
64. ▌
    Metabolite Candidate Matching 2 · holobiomicslab

    Use when you have: (1) a set of predicted candidate metabolites with known mass-to-charge ratios and chemical properties derived from a parent drug formula; (2) raw mass spectrometry data in mzML format from a sample suspected to contain those metabolites;
    5 installs
65. ▌
    Metabolite Formula Prediction 2 · holobiomicslab

    Use when when you have a known drug's chemical formula and need to generate a comprehensive list of predicted metabolite formulas to match against experimental mzML mass spectrometry data.
    4 installs
66. ▌
    Ms Backend API Implementation 3 · 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.
    5 installs
67. ▌
    Ms Dial Version Compatibility 3 · 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.
    5 installs
68. ▌
    Parameter Tuning Metabolomics 2 · 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.
    4 installs
69. ▌
    Ppm Error Tolerance Filtering 3 · 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.
    4 installs
70. ▌
    Pseudo Data Pair Construction 2 · 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.
    5 installs
71. ▌
    Runtime Performance Profiling 3 · 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.
    5 installs
72. ▌
    Sirius Zodiac Score Filtering 2 · 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.
    7 installs
73. ▌
    Spectral Peak Data Extraction 2 · 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.
    5 installs
74. ▌
    Spectrum Tokenization For Nlp 2 · holobiomicslab

    Use when when you have raw mass spectra from experimental libraries (e.
    6 installs
75. ▌
    Structured Data Serialization 2 · 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.
    5 installs
76. ▌
    Tabular Data Field Comparison 3 · 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.
    6 installs
77. ▌
    Tic Peak Isolation Validation 2 · 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.
    7 installs
78. ▌
    Msi Peak Intensity Extraction 2 · 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.
    8 installs
79. ▌
    Roi Definition And Extraction 2 · 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.
    5 installs
80. ▌
    Autotuner Object Manipulation 2 · holobiomicslab

    Use when after AutoTuner has completed EICparams extraction and parameter estimation on raw untargeted metabolomics data (mzML, mzXML, or CDF format), and you need to pass those estimates into XCMS or MZmine2 for full dataset processing.
    5 installs
81. ▌
    Bruker Solarix Format Parsing 2 · holobiomicslab

    Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d) and need to programmatically access the transient time-domain signal and metadata for zero-filling, apodization windowing (e.g., Hanning), or mass calibration.
    7 installs
82. ▌
    Chemical Structure Validation 2 · holobiomicslab

    Use when after compound database dereplication with SIRIUS or MetFrag has produced candidate annotations (CSV or JSON format), and you need to filter implausible structures, compute standardized molecular descriptors, and rank candidates by confidence before reporting final metabolite.
    7 installs
83. ▌
    Configuration File Generation 3 · holobiomicslab

    Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5 and need version-specific parameter defaults (e.g., column names and scaling factors that differ between versions).
    6 installs
84. ▌
    Elemental Composition Parsing 2 · holobiomicslab

    Use when when you have FT-ICR MS peak data with assigned molecular formulas (e.g., from CoreMS, Formularity, or similar formula assignment tools) and need to compute thermodynamic indices (DBE, GFE, AImod, NOSC) or classify peaks by elemental composition.
    6 installs
85. ▌
    Entry Point Script Validation 2 · holobiomicslab

    Use when after installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows.
    5 installs
86. ▌
    Isotopic Envelope Calculation 2 · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution for comparison against experimental MS peaks, validation of mass calibration, or simulation of expected peptide signals in a mass spectrometry assay.
    5 installs
87. ▌
    Iterative Fitting Convergence 2 · holobiomicslab

    Use when you have 1D mass spectrometry signal data (e.
    4 installs
88. ▌
    Lexical Analysis Tokenization 3 · 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.
    8 installs
89. ▌
    Mass Spectrometry Data Import 3 · holobiomicslab

    Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.
    5 installs
90. ▌
    Mass2motif Annotation Mapping 3 · holobiomicslab

    Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
    4 installs
91. ▌
    Targeted Metabolite Extraction 3 · holobiomicslab

    Use when you have centroided LC-MS data (.mzML format) and a curated list of targeted metabolites or lipids (with m/z, retention time, and polarity) that you want to quantify and quality-assess across multiple analytical runs, and you need both per-run AUC values and averaged QC metrics for each.
    5 installs
92. ▌
    Xcms Data Import Preprocessing 4 · holobiomicslab

    Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass calibration (e.
    6 installs
93. ▌
    Ccs Library Format Parsing 3 · holobiomicslab

    Use when when you have received or cloned a CCS reference library (such as the DTCCSN2 library for U13C labeled lipids) bundled with lipidomics software and need to verify its integrity, understand its lipid class composition, or extract metadata before using it for CCS bias calculation or.
    6 installs
94. ▌
    Graph Tensor Serialization 3 · holobiomicslab

    Use when after constructing feature tensors encoding atom adjacency matrices, bond types, and chemical properties from canonical SMILES—and before feeding graphs into a GNN training loop—to enable reproducible, portable, and memory-efficient storage of graph objects that will be loaded in batches.
    5 installs
95. ▌
    Hdf5 Feature Table Loading 3 · holobiomicslab

    Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for multi-dimensional alignment, CCS calibration, or isotope detection.
    5 installs
96. ▌
    Arrow Columnar Data Decoding 2 · holobiomicslab

    Use when when reading mzPeak files or other Parquet-backed mass spectrometry archives where spectral m/z and intensity arrays are stored in columnar layouts (point or chunked format) and you need to reconstruct them into Python NumPy arrays, pandas DataFrames, or equivalent in-memory structures for.
    6 installs
97. ▌
    Backend Routing And Dispatch 3 · holobiomicslab

    Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their preferred rendering engine (matplotlib, bokeh, or plotly) at call time without modifying the core plotting logic.
    6 installs
98. ▌
    Biobase Object Serialization 2 · holobiomicslab

    Use when when you have raw peak table data from mass spectrometry or other metabolomic instruments in either a standardized tabular format or one of 12 common software tool outputs (e.
    5 installs
99. ▌
    Bruker Transient Data Import 2 · holobiomicslab

    Use when you have Bruker Solarix raw transient data (.d folders containing ser or fid files) from an FT-ICR instrument and need to load it into a Python environment for noise thresholding, peak picking, mass calibration, or molecular formula assignment.
    5 installs
100. ▌
     Configuration Object Pattern 3 · holobiomicslab

     Use when when designing a library that needs to support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and you want to avoid reimplementing parameter validation, storage, and dispatch logic for each backend.
     6 installs