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HolobiomicsLab

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1. ▌
   Noise Level Parameter Tuning · holobiomicslab

   Use when when you have an aligned GCIMS dataset and need to configure the findPeaks function with CWT algorithm to detect peaks across retention time and drift time dimensions.
   6 installs
2. ▌
   Pareto Scaling Normalization · holobiomicslab

   Use when you have peak intensity vectors from LC/GC-MS experiments with corresponding QC (quality control) sample measurements, and you need to correct for batch effects—especially when QC samples show systematic shifts in peak heights across analytical batches.
   11 installs
3. ▌
   Similarity Score Computation · holobiomicslab

   Use when when you have a query electron ionization mass spectrum (m/z and intensity pairs) and need to identify the most similar spectra from an MSP-formatted spectral library.
   6 installs
4. ▌
   Spectral Metadata Extraction · holobiomicslab

   Use when after loading an MSP spectral library file into memory using mssearchr's MSP parser, when you need to verify that each spectrum record contains complete and valid metadata (precursor m/z values, peak lists, header annotations) before writing the parsed spectra to a new MSP file or.
   5 installs
5. ▌
   Spectral Peak Shape Modeling · holobiomicslab

   Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each peak while accounting for chromatographic band broadening, peak tailing, and retention-time dispersion.
   12 installs
6. ▌
   Alignment Quality Assessment · holobiomicslab

   Use when after retention time and m/z-based clustering have been applied to group features across samples in a multi-sample metabolomics study.
   3 installs
7. ▌
   Analog Search Result Routing · holobiomicslab

   Use when after MS2Query has ranked and scored library matches against query spectra, when you need to apply different confidence thresholds, interpretation strategies, or downstream workflows depending on whether the result is an exact match (precursor m/z difference ≈ 0) or a chemical analog.
   4 installs
8. ▌
   Candidate Metabolite Ranking · holobiomicslab

   Use when when you have generated a set of predicted metabolite structures from BioTransformer's metabolism prediction engine and need to assign identity to observed compounds from LC-MS/MS, spectral, or chromatographic experiments.
   5 installs
9. ▌
   Chemical Formula Enumeration · holobiomicslab

   Use when you have an unknown MS/MS spectrum with a measured precursor m/z and want to generate a list of plausible chemical formula–adduct pairs to rank or filter downstream.
   7 installs
10. ▌
    CI CD Pipeline Orchestration · holobiomicslab

    Use when you need to automate testing and quality checks on code changes—specifically when pull requests or commits are made to a repository and you want to verify that builds succeed, test suites pass, and code quality metrics meet project standards before merging.
    6 installs
11. ▌
    Cloud Compatible File Output · holobiomicslab

    Use when after feature clustering and drift correction (Gravity and Blueshift outputs) are complete and you need to produce a final, validated feature table ready for storage, archival, or downstream analysis.
    6 installs
12. ▌
    Conditional Dispatch Routing · holobiomicslab

    Use when you have received a peak/feature table from an unknown or variable upstream peak-picking tool and need to ingest it into LipidMatch or a similar unified workflow. The input file format, column naming, or metadata structure is tool-specific (e.
    5 installs
13. ▌
    CSV To Dictionary Conversion · holobiomicslab

    Use when you have a CSV file containing molecule definitions (chemical formula, m/z, intensity, retention time, or other peak properties) and need to prepare it for SMITER's simulation workflow.
    7 installs
14. ▌
    Electronic Noise Ion Removal · holobiomicslab

    Use when working with raw MS/MS spectra that contain ions with repeated (identical) intensity values—a hallmark of electronic noise rather than true metabolite fragments.
    5 installs
15. ▌
    Energy Based Formula Scoring · holobiomicslab

    Use when you have an unknown MS/MS spectrum (precursor m/z and fragment peak list) and a set of candidate molecular formulae, and you need to rank them by likelihood without access to a spectrum database or precomputed fragmentation trees.
    6 installs
16. ▌
    Energy Based Model Inference · holobiomicslab

    Use when when you have an unknown MS/MS spectrum (m/z and intensity pairs) and need to assign a chemical formula and ionization adduct to the precursor mass, particularly when spectrum database lookups are unavailable or when you want to exploit learned patterns in fragmentation rather than.
    6 installs
17. ▌
    Exact Mass Database Matching · holobiomicslab

    Use when after feature detection and alignment on raw MS data, when you have a list of unknown feature m/z values and need to assign them to known xenobiotic metabolites or their predicted biotransformation products.
    8 installs
18. ▌
    False Discovery Rate Control · holobiomicslab

    Use when you have generated candidate peptide-spectrum matches from a spectral library search (especially open modification searches using cascade strategies) and need to assign statistical confidence to those matches. Use it whenever the scoring metric (e.
    6 installs
19. ▌
    Feature Annotation Filtering · holobiomicslab

    Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among thousands of detected features.
    7 installs
20. ▌
    Filter Output Interpretation · holobiomicslab

    Use when after applying a filter function (filter_mispicked_ions(), filter_group(), filter_cv(), filter_insource_ions()) to an mpactr object, use this skill to inspect and document which features were retained versus removed.
    7 installs
21. ▌
    Fragmentation Motif Learning · holobiomicslab

    Use when you have preprocessed mass spectrometry fragmentation data (neutral losses and fragment masses extracted and noise-filtered) and want to discover hidden structural motifs across a spectral dataset in an unsupervised manner.
    4 installs
22. ▌
    Gnps Library Format Assembly · holobiomicslab

    Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, molecular weight, annotation fields) that must be combined into a single structured library entry suitable for spectral library.
    7 installs
23. ▌
    Gnps Workflow Identification · holobiomicslab

    Use when you have downloaded a GNPS molecular networking job archive and need to extract its contents (spectra.mgf, molecular_families.tsv, annotations.tsv, file_mappings) but do not know which GNPS workflow version produced it, preventing correct file naming and downstream computational analysis.
    7 installs
24. ▌
    Heatmap Visualization Design · holobiomicslab

    Use when after training a DeepMSProfiler model and generating per-sample predictions: when you need to display Pearson or Spearman correlation coefficients between individual metabolite signals and disease class labels in a matrix form suitable for publication or exploratory review of.
    4 installs
25. ▌
    Homologous Series Clustering · holobiomicslab

    Use when you have a feature list (m/z, retention time, intensity) from HRMS data and want to identify potential PFAS homologous series for prioritization.
    5 installs
26. ▌
    Installation Troubleshooting · holobiomicslab

    Use when when setting up matchms for the first time in a new environment, after upgrading Python or conda, when switching between package managers (pip vs conda), or when distributing matchms to end users to confirm functionality across supported installation channels.
    4 installs
27. ▌
    Instrumental Drift Detection · holobiomicslab

    Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex Multiquant software (v3.0.
    8 installs
28. ▌
    Intensity Frequency Analysis · holobiomicslab

    Use when you have an MS/MS peak list and need to remove electronic noise—specifically when you observe suspiciously identical intensity values repeated across multiple peaks in a single spectrum, which is characteristic of instrument-generated artifacts rather than genuine analyte signals.
    7 installs
29. ▌
    Knime Workflow Orchestration · holobiomicslab

    Use when you have raw LC-MS data (mzML, NetCDF) from multiple runs that require sequential feature detection, alignment, quantification, and optional filtering (e.g., blank exclusion, QC reproducibility, retention-time outlier removal) before spatial mapping or annotation.
    9 installs
30. ▌
    Library Integration Workflow · holobiomicslab

    Use when you have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library, and you want to include them as matching candidates in your UHPLC-HRMS/MS fragment m/z matching workflow without modifying.
    5 installs
31. ▌
    Linux Command Line Execution · holobiomicslab

    Use when you have vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent .
    7 installs
32. ▌
    Lipid A Structure Annotation · holobiomicslab

    Use when when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to identify and annotate lipid A structures at scale.
    6 installs
33. ▌
    Lipid Identification Scoring · holobiomicslab

    Use when after peak picking (MZmine, XCMS, MS-DIAL, or Compound Discoverer output) and candidate retrieval, when you have experimental fragment m/z values and multiple candidate lipid species from the in-silico library.
    3 installs
34. ▌
    Lipid Species Identification · holobiomicslab

    Use when you have centroid-mode LC–MS AIF chromatograms processed by xcms and RamClustR (or equivalent), a feature table with m/z and retention time coordinates, and you need to resolve individual lipid species identities with confidence scores and fragmentation evidence.
    8 installs
35. ▌
    M Z Alignment Across Samples · holobiomicslab

    Use when you have extracted mass tracks (EICs) from multiple LC-MS samples at 0.001 amu resolution and need to construct a sample-agnostic m/z reference frame.
    9 installs
36. ▌
    Mass Feature To Node Mapping · holobiomicslab

    Use when you have an untargeted metabolomics feature table with m/z values, retention times, and intensity measurements, a metabolic network representation with compound nodes and chemical formulas, and you want to infer functional pathway activity directly from features without performing.
    8 installs
37. ▌
    Massql Query Language Syntax · holobiomicslab

    Use when you need to search for specific mass spectrometry patterns (e.g., precursor ion m/z, product ion presence, retention time windows, intensity constraints, neutral loss patterns) across one or more mzML files.
    5 installs
38. ▌
    Matplotlib Heatmap Rendering · holobiomicslab

    Use when when you have a confusion matrix (predicted vs. ground-truth labels) or similarity matrix (pairwise scores between spectra) and need to communicate classification accuracy or chemical similarity patterns through a visual heatmap.
    6 installs
39. ▌
    Metabolite Candidate Ranking · holobiomicslab

    Use when you have an untargeted mass spectrometry spectrum (MS/MS data) and a set of candidate molecules from PubChem or similar databases, and you need to rank candidates by likelihood of being the true molecular annotation.
    7 installs
40. ▌
    Metabolite Ion Consolidation · holobiomicslab

    Use when after chromatographic peak detection in LC-MS data, when you have hundreds or thousands of features and need to consolidate ions presumed to originate from the same metabolite.
    6 installs
41. ▌
    Metabolomic Feature Matching · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) from separate metabolomic experiments or replicates, and you need to establish which features in dataset A correspond to which features in dataset B to enable comparative or longitudinal analysis.
    8 installs
42. ▌
    Metabolomics Data Formatting · holobiomicslab

    Use when after running feature clustering (Gravity) or drift correction (Blueshift) on LCMS data, when you have a processed feature table and need to standardize its structure, validate metadata completeness, enforce missing-value thresholds, and generate a QC report documenting pass/fail status.
    8 installs
43. ▌
    Metabolomics Tool Deployment · holobiomicslab

    Use when you have a Galaxy installation (specifically Galaxy Master branch commit c429777c93680dcee449fe410f5360afbe673758 or compatible) and need to add metabolomics analysis capabilities including tools for XCMS integration, mass spectrometry file reading (via MSFileReader), and metabolite.
    8 installs
44. ▌
    Metadata Field Normalization · holobiomicslab

    Use when immediately after importing raw mass spectrometry data from mzML, mzXML, msp, MGF, or JSON formats into matchms.
    6 installs
45. ▌
    Molecular Formula Assignment · holobiomicslab

    Use when you have acquired MS/MS spectra (in MGF format with required fields: TITLE, PRECURSOR_MZ, PRECURSOR_TYPE, COLLISION_ENERGY) from known or unknown compounds and need to predict their molecular formulas with ranked candidates and confidence scores.
    8 installs
46. ▌
    Molecular Formula Validation · holobiomicslab

    Use when when you have a feature list from HRMS with tentatively assigned molecular formulas (from in silico tools or databases) and need to assess formula plausibility before applying downstream PFAS-specific filters.
    6 installs
47. ▌
    Ms Feature Tree Construction · holobiomicslab

    Use when you have untargeted LC-MS/MS metabolomic data (peak-detected .mzXML/.mzML/.mzDATA files processed through MZmine2) and need to relate MS1 features by chemical similarity rather than sequence homology.
    7 installs
48. ▌
    Ms Ms Spectrum Preprocessing · holobiomicslab

    Use when you have raw or semi-processed MS/MS spectral data from bottom-up tandem mass spectrometry experiments (data-dependent acquisition) that you intend to input to de novo peptide sequencing tools like Casanovo.
    6 installs
49. ▌
    Multi Class Label Assignment · holobiomicslab

    Use when you have raw LC-MS metabolomics data from multiple disease groups and need to classify new or existing samples into discrete disease categories.
    5 installs
50. ▌
    Multi Omics Data Integration · holobiomicslab

    Use when when you have matched transcriptomics (RNA-seq read counts), intracellular metabolomics (LC-MS abundance data), and extracellular flux measurements (YSI bioanalyzer or similar) from multiple biological samples or cell lines, and you need to determine whether differences in metabolic enzyme.
    9 installs
51. ▌
    Multiblock Pls Model Fitting · holobiomicslab

    Use when you have split multi-assay LC-MS intensity data into training (90%) and test (10%) subsets with assay-specific column prefixes, and you need to fit a discriminant or regression model that respects the block structure (separate assays) while jointly predicting a phenotypic outcome (e.
    5 installs
52. ▌
    Mzml Spectral Format Parsing · holobiomicslab

    Use when you have mzML-format raw data files (from any mass spectrometry vendor or conversion tool) and need to ingest them into MS-DIAL version 5 or later for untargeted metabolomics or lipidomics analysis.
    6 installs
53. ▌
    Network Node Label Spreading · holobiomicslab

    Use when you have an untargeted metabolomics dataset with a two-layer network topology already constructed (one layer representing biochemical knowledge/pathways, the other representing data-driven MS2 similarity), seed metabolites with reliable annotations from database matching or curation, and.
    6 installs
54. ▌
    Pairwise Spectral Comparison · holobiomicslab

    Use when you have a collection of preprocessed mass spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to quantify similarity relationships across all pairs—for instance, to identify redundant spectra in a library, cluster related compounds, or perform spectral library searches.
    9 installs
55. ▌
    Pairwise Spectrum Comparison · holobiomicslab

    Use when you have a collection of cleaned mass spectrometry spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to identify spectral similarities, find related compounds, or generate a comprehensive similarity matrix for downstream analysis such as spectral library matching or clustering.
    5 installs
56. ▌
    Peak Filtering Noise Removal · holobiomicslab

    Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library matching.
    7 installs
57. ▌
    Peak Intensity Normalization · holobiomicslab

    Use when you have raw MS/MS spectral peak lists with absolute intensity values and need to compare spectra using entropy similarity, dot product, or other distance metrics.
    8 installs
58. ▌
    Peak Recovery Post Filtering · holobiomicslab

    Use when after applying cluster-based filtering with quasi-molecular adduct constraints and frequency thresholds on LC-MS feature candidates, when some peaks have been entirely removed from the candidate pool and you want to prevent loss of true metabolites that failed to meet filtering criteria.
    6 installs
59. ▌
    Phylogenetic Tree Validation · holobiomicslab

    Use when after generating a Chemical Feature Tree from q2-qemistree (or any tree artifact) and before using it for alpha-diversity or beta-diversity phylogenetic analyses.
    8 installs
60. ▌
    Polarity Mode Filtering Lcms · holobiomicslab

    Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run acquired in a specific polarity mode.
    5 installs
61. ▌
    Precursor Product Mz Parsing · holobiomicslab

    Use when you have raw MRM sample files from a LC-MS/MS instrument and need to systematically recover all precursor m/z and product m/z pairs for each transition. Use this as an initial parsing step before quantitation, method optimization, or transition verification workflows.
    6 installs
62. ▌
    Proforma Peptidoform Parsing · holobiomicslab

    Use when when you have a ProForma 2.0–formatted peptide string with PSI-MOD or UniMod modification labels and need to extract the underlying amino acid sequence and modification positions before performing theoretical fragment ion calculation or spectrum peak matching.
    6 installs
63. ▌
    Project Metadata Integration · holobiomicslab

    Use when a paired omics project record contains a genome identifier (e.g., GenBank accession) but lacks the corresponding organism name field, and you need to populate that metadata field to enable full text search, sample tracking, or project validation before archival to Zenodo.
    8 installs
64. ▌
    Pytorch Model Implementation · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (m/z and intensity arrays) and need to map it to a fixed-size latent vector for use in an encoder–decoder architecture. Specifically applicable when the downstream task requires a molecular structure reconstruction (e.
    8 installs
65. ▌
    Qc Sample Quality Assessment · holobiomicslab

    Use when after drift correction and before imputation when you have LC-MS data with designated QC samples and you need to remove features with poor reproducibility across QC replicates.
    10 installs
66. ▌
    Retention Time Peak Flagging · holobiomicslab

    Use when after applying peak detection algorithms to identify local maxima in feature signals across retention time or m/z dimensions, but before exporting or filtering the peak list for further analysis.
    6 installs
67. ▌
    Retention Time Peak Matching · holobiomicslab

    Use when after drift correction and quality flagging, when you have a feature abundance matrix with associated metadata (Feature_ID, m/z, retention time) and need to identify which features likely represent the same underlying metabolite or adduct series before statistical analysis or metabolite.
    7 installs
68. ▌
    Sample Missingness Filtering · holobiomicslab

    Use when when you have loaded (un)targeted metabolite data into a Metaboprep object and need to exclude samples with excessive missing values before quality control or statistical analysis. This is typically applied early in the QC pipeline when sample-level data completeness is a concern (e.
    6 installs
69. ▌
    Session Object Serialization · holobiomicslab

    Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data object containing t-SNE embeddings (based on ms2deepscore similarity scores) and associated spectral metadata.
    8 installs
70. ▌
    Siamese Architecture Scoring · holobiomicslab

    Use when after a TCN-based formula prediction model has generated initial formula candidates from MS/MS spectra, apply this skill to rescore and refine those candidates when you need to improve ranking accuracy.
    9 installs
71. ▌
    Similarity Matrix Generation · holobiomicslab

    Use when you have a collection of cleaned spectra in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compute all pairwise similarity scores to identify related or duplicate spectra, support spectral library searching, or enable network-based analysis.
    4 installs
72. ▌
    Spectral Data Format Parsing · holobiomicslab

    Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for downstream spectral analysis, fragmentation tree computation, or metabolite identification.
    5 installs
73. ▌
    Spectral Entropy Calculation · holobiomicslab

    Use when when you have preprocessed MS/MS spectral peak data (m/z and intensity pairs) and need to compute a complexity metric for individual spectra prior to similarity comparisons, or when benchmarking compound identification performance against dot product–based methods.
    5 installs
74. ▌
    Spectral Fragment Assignment · holobiomicslab

    Use when when you have an experimental tandem mass spectrum (peaks with m/z and intensity values) and wish to identify which fragments or chemical subformulae each peak corresponds to.
    5 installs
75. ▌
    Spectral Mz Window Filtering · holobiomicslab

    Use when when you have resolved mzML or mzXML spectrum files and need to isolate signals for a target m/z value (e.g., 870.954) across all retention times or a specific scan.
    5 installs
76. ▌
    Spectral Similarity Grouping · holobiomicslab

    Use when when you have computed a sparse pairwise distance matrix from nearest neighbor indexes of high-resolution MS/MS spectra and need to partition them into clusters such that spectra within each cluster correspond to similar fragmentation patterns (e.g., same peptide or metabolite).
    4 installs
77. ▌
    Spectral Workflow Validation · holobiomicslab

    Use when after implementing or modifying a cross-language integration layer that wraps Python mass spectrometry functions (e.g., spectral matching, peak detection, normalization from matchms or spectrum_utils) as R-callable functions within Spectra workflows.
    5 installs
78. ▌
    Spectrum Metadata Extraction · holobiomicslab

    Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including scan information, precursor m/z and charge, and ion selection parameters—into a queryable, vendor-agnostic tabular schema.
    10 installs
79. ▌
    Sterol Isomer Classification · holobiomicslab

    Use when you have LC-IM-MS/MS raw data from sterol-containing tissue samples and need to assign detected peaks to specific structural isomers (e.g., distinct double bond positions or saturation patterns in C27–C29 sterols).
    8 installs
80. ▌
    Tandem Mass Spectrum Parsing · holobiomicslab

    Use when when you have raw or instrument-native tandem mass spectrometry data (MS/MS) in formats such as mzML, mzXML, or proprietary binary formats, and you need to align, match, or compare spectra using methods like SIMILE that require structured access to precursor m/z, fragment m/z values, and.
    6 installs
81. ▌
    Tandem Ms Feature Assessment · holobiomicslab

    Use when after importing raw peak tables from tandem MS/MS preprocessing software (e.
    7 installs
82. ▌
    Targeted Peak Extraction Ms1 · holobiomicslab

    Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify.
    5 installs
83. ▌
    Two Layer Topology Traversal · holobiomicslab

    Use when you have an untargeted metabolomics dataset with partial metabolite annotations (from database matching or prior curation) and need to extend annotation coverage to unannotated metabolites.
    8 installs
84. ▌
    Model Metadata Extraction · holobiomicslab

    Use when when you need to programmatically interface with a TensorFlow Serving model instance and must discover or validate the expected input names (e.
    6 installs
85. ▌
    Multitask Model Inference · holobiomicslab

    Use when you have a trained multitask model checkpoint and preprocessed spectral inputs (1D NMR spectra, 1H-only, 13C-only, or combined 1H+13C), and you need to generate simultaneous predictions of molecular formula and connectivity structure to quantify modality contributions, compare single vs..
    4 installs
86. ▌
    Nmr Peak Table Generation · holobiomicslab

    Use when you have raw 1D NMR spectra (in NMRPipe or similar format) from biological samples (urine, worm, or other metabolomics experiments) and need to extract a structured peak table with chemical shifts and intensities for downstream metabolite identification or quantification.
    5 installs
87. ▌
    Nmr Spectra Preprocessing · holobiomicslab

    Use when when you have raw 1D NMR spectroscopic data (urine, worm, or other biological samples) in a format supported by NMRBox/NMRPipe and need to generate peak tables with automatic phasing, baseline correction, and spectral deconvolution without manual intervention.
    8 installs
88. ▌
    Optimal Transport Scoring · holobiomicslab

    Use when when you have an observed NMR mixture spectrum and one or more candidate reconstructed spectra (each formed by combining single-compound reference spectra from a library), and you need a scalar similarity score to rank or select the approximation.
    8 installs
89. ▌
    CI Workflow Execution · holobiomicslab

    Use when you have a GitHub repository with published CI workflow badges (e.g., unit test or package test badges in the README) and need to independently verify that the workflows execute successfully, reproduce the pass/fail status, and collect structured test results.
    5 installs
90. ▌
    JSON Response Parsing · holobiomicslab

    Use when you receive a JSON response from a REST API endpoint (e.g., TensorFlow Serving /model/metadata) and need to extract and validate specific fields such as model input names, signatures, or outputs.
    4 installs
91. ▌
    Module Import Testing · holobiomicslab

    Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional after upstream updates. Use it as a gate before finalizing a release to catch installation or import breakage early.
    8 installs
92. ▌
    Qcpool Cv Calculation · holobiomicslab

    Use when you have Sciex Multiquant txt exports containing signal intensities from QCpool samples injected at regular intervals (e.g., every 10–20 samples) during one or more analytical sequences in a metabolomics or lipidomics study.
    5 installs
93. ▌
    Batch Timing Analysis · holobiomicslab

    Use when when evaluating whether a new or candidate mass spectrometry processing library (e.g., spectrum_utils) offers faster spectrum processing throughput than established alternatives (e.
    8 installs
94. ▌
    CSV Format Validation · holobiomicslab

    Use when when you have a .csv file intended as input to CypReact containing SMILES strings and need to verify it meets the required comma-separated format specification and that each SMILES string is syntactically valid before processing molecules through CYP isoform testing.
    5 installs
95. ▌
    Isotopic Peak Removal · holobiomicslab

    Use when after loading raw FT-ICR MS peak lists with assigned molecular formulas when you have detected peaks across multiple m/z values that correspond to isotopic variants of the same parent compound.
    6 installs
96. ▌
    Job Tuple Enumeration · holobiomicslab

    Use when when initializing MSMetaEnhancer or extending it with new converters, you need to discover all available (source_attribute, target_attribute, converter_name) conversion triples to build a complete job registry.
    8 installs
97. ▌
    JSON Metadata Parsing · holobiomicslab

    Use when you have a repository of JSON-formatted scientific annotations (e.g., MIBiG curation data) and need to systematically extract structured metadata fields (such as cluster.
    5 installs
98. ▌
    Msi Data Table Export · holobiomicslab

    Use when after calculating mean intensity values across all spectra in an MSI dataset (or within a manually selected ROI), and you need to store the resulting m/z–intensity table in a portable format for downstream ROI analysis, database annotation, or external statistical pipelines.
    3 installs
99. ▌
    R Matrix Manipulation · holobiomicslab

    Use when when working with three-part metabolomics data structures (featuredata matrix, metabolitedata and sampledata dataframes) and you need to: (1) identify subsets of metabolites by their annotation (e.
    8 installs
100. ▌
     R Package Integration · holobiomicslab

     Use when when you have a functional R package with core statistical or computational logic that needs to be made accessible to non-R users, or when you want to streamline a multi-step analytical workflow (e.
     6 installs