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HolobiomicsLab

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1. ▌
   Model Generalization Assessment Across Molecular Size Re 2 · holobiomicslab

   Use when a deep learning model for molecular structure prediction (e.g., NMR2Struct) has been trained and evaluated on a limited molecular size range (e.
   9 installs
2. ▌
   Training Data Inventory Construction From Spectral Libra 2 · holobiomicslab

   Use when you are preparing to apply Probability Product Kernel–based scoring to MS2 spectra for genomic–metabolomic linking, and you need to establish a reference set of ion peaks that represent robust spectral diversity without overfitting to any single study.
   9 installs
3. ▌
   Interactive Mass Spectrometry Plot Generation And Annota 3 · holobiomicslab

   Use when when you have extracted ion chromatograms (XICs), ion mobilograms (IMs), or mass spectra from diaPASEF or other DIA workflows and need to visualize them interactively to inspect peak boundaries, compare MS1 vs MS2 traces, validate feature identifications, or communicate results.
   12 installs
4. ▌
   Microbiome Metabolome Data Preprocessing Clr Transformat 3 · holobiomicslab

   Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream regression or neural network modeling of microbe-metabolite relationships.
   9 installs
5. ▌
   Natural Product Database Querying Norine Coconut Npatsas 2 · holobiomicslab

   Use when you have a chemical structure (as SMILES string or identifier) and need to discover matching records across specialized natural product databases.
   7 installs
6. ▌
   Backend Compatibility Verification Visualization Library 3 · holobiomicslab

   Use when you have mass spectrometry data loaded into a pandas DataFrame with m/z, retention time, and intensity columns, and need to confirm that pyOpenMS-Viz can produce visualizations (spectra, chromatograms, or peak maps) using a specific plotting backend (matplotlib, Bokeh, or Plotly) on real.
   9 installs
7. ▌
   Kernel Regression Learning From Spectral Fingerprint Pai 3 · holobiomicslab

   Use when when you have a training set of MS2 spectra with known chemical structures (e.
   10 installs
8. ▌
   Metabolite Compound List Mapping With Adduct Assignment 2 · holobiomicslab

   Use when when you have mzML files from targeted or untargeted metabolomics experiments run in multiple ionization modes (e.g., KO_NEG, KO_POS, STD_NEG, STD_POS, WT_NEG, WT_POS) and a CSV list of reference compounds (e.
   10 installs
9. ▌
   Retention Time And Mass Sorting Of Chromatographic Peaks 3 · holobiomicslab

   Use when you have raw GC-MS output from Agilent Unknowns Analysis (a .CSV with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
   9 installs
10. ▌
    Targeted Peak Detection Screening And Validation 2 · holobiomicslab

    Use when you have centroided mzML LC–MS data, a curated list of target compounds (with theoretical m/z, expected retention time, and polarity), and you need to confirm target presence and extract quantitative metrics (area under curve, max intensity, signal-to-noise ratio, peak correlation, point.
    12 installs
11. ▌
    Graph Neural Network Architecture Implementation 2 · holobiomicslab

    Use when you have a baseline GNN model trained on a molecular property prediction task (e.
    9 installs
12. ▌
    High Resolution Mass Spectrometry Interpretation 3 · holobiomicslab

    Use when you have centroided LC- or GC-HRMS data (in mzML format, ideally from data-dependent acquisition) and need to identify potential PFAS candidates from a large feature list.
    10 installs
13. ▌
    Mass Spectrometry Dataset Handling Preprocessing 2 · holobiomicslab

    Use when you have raw or semi-processed MS/MS spectra in MSP format (e.g., from GNPS, Orbitrap instruments) and need to feed them into MSBERT or similar transformer-based embedding models for library matching, clustering, or similarity scoring.
    15 installs
14. ▌
    Mass Spectrometry Instrument Resolution Modeling 2 · holobiomicslab

    Use when when correcting LC-MS fractional abundances of measured isotopologues (FAM) from isotope labeling experiments where instrument resolution (e.
    8 installs
15. ▌
    Neural Network Based Molecular Formula Inference 3 · holobiomicslab

    Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo setting where spectrum database matching is unavailable or undesirable.
    13 installs
16. ▌
    Peak Intensity Chromatographic Property Analysis 2 · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering) containing m/z, retention time, and peak intensity metrics, and you need to group LC-MS features into clusters to reduce redundancy before parental signal extraction.
    7 installs
17. ▌
    Python Module Integration And Pipeline Extension 2 · holobiomicslab

    Use when you have developed new scoring logic (e.g., average inchikey score, neighbourhood score) for an MS/MS spectral analogue search tool and need to embed these components into an existing production pipeline that uses a random forest to combine multiple features for candidate re-ranking.
    7 installs
18. ▌
    Instrument Platform Compatibility Mapping 3 · holobiomicslab

    Use when when adopting a mass spectrometry data processing tool (e.g., LipidMatch) and needing to verify whether your specific instrument platform (vendor + model) and acquisition mode combination (targeted, ddMS2-topN, AIF, direct infusion, imaging) have been formally validated.
    16 installs
19. ▌
    Docker Container Runtime Execution And Monitoring 2 · holobiomicslab

    Use when you have a vendor mass spectrometry raw file (e.g., .raw format) that requires conversion to Aird format using AirdPro CLI, and you are running on macOS or Linux.
    8 installs
20. ▌
    Bag Of Words Document Representation Generation 3 · holobiomicslab

    Use when you have raw MS/MS spectral data in standard mass spectrometry formats and need to prepare it for unsupervised substructure discovery via topic modeling.
    8 installs
21. ▌
    Biochemical Relation Integration For Annotation 2 · holobiomicslab

    Use when when you have LC/MS feature data (m/z, retention time, intensity) that must be annotated against a metabolic database and you have access to (or can construct) knowledge about biochemical reaction networks, expected isotope patterns, and instrument-specific adduct formation rules.
    8 installs
22. ▌
    Blank Sample Background Interference Estimation 3 · holobiomicslab

    Use when after MS1 feature detection and accurate mass annotation, when you have identified a set of blank injections (negative controls) run in the same analytical sequence segment as your biological or study samples.
    6 installs
23. ▌
    Containerized Application Deployment Validation 2 · holobiomicslab

    Use when when deploying containerized versions of a multi-variant application (e.g., CLI, development, Linux, and Windows flavors) and you need to verify that each built image meets documented size constraints before registry push or production release.
    11 installs
24. ▌
    Isotope Pattern Annotation In Feature Detection 2 · holobiomicslab

    Use when when performing feature detection on centroided DDA mzML files from LC- or GC-HRMS and you need to confirm the elemental composition or differentiate between candidate features—particularly for PFAS screening where isotopic signatures (chlorine, bromine, fluorine) are diagnostic.
    13 installs
25. ▌
    Mass Spectrometry Preprocessing Quality Control 2 · holobiomicslab

    Use when immediately after importing raw peak tables and metadata from MS preprocessing software (e.g., Progenesis, MS-DIAL, Bruker Metaboscape).
    10 installs
26. ▌
    Metabolite Feature Normalization Across Batches 2 · holobiomicslab

    Use when after data merging and cleanup (blank removal) and before univariate or multivariate statistical analysis, when your merged feature table (samples as columns, metabolite features as rows) contains samples processed in different MS batches or instrumental runs that may introduce systematic.
    11 installs
27. ▌
    Ms Ms Spectrum Statistical Significance Testing 2 · holobiomicslab

    Use when you have aligned fragment ion pairs from two MS/MS spectra (via maximum weight matching or other methods) and need to assign p-values or Z-scores to each matched pair to distinguish true biological/chemical relationships from random noise.
    11 installs
28. ▌
    Mass Spectrometry Data Visualization Pandas 3 · holobiomicslab

    Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV) loaded into a Pandas DataFrame with columns for m/z, retention time, ion mobility, or intensity values, and you need to render spectrum plots, chromatograms, mobilograms, or 2D peak maps.
    7 installs
29. ▌
    S4 Class Extension For Backend Implementation 3 · holobiomicslab

    Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly into workflows that use the Spectra package.
    11 installs
30. ▌
    Singular Value Decomposition Pathway Analysis 2 · holobiomicslab

    Use when when you have a peak intensity matrix (rows = metabolite features, columns = samples) with corresponding compound annotations (peak ID → KEGG/ChEBI ID mapping), and you need to rank pathways or metabolite set groupings (KEGG pathways, Reactome pathways, GNPS Molecular Families, MS2LDA.
    11 installs
31. ▌
    Mass Spectrum Preprocessing And Normalization 2 · holobiomicslab

    Use when when you have raw MS/MS spectra in MGF or mzML/mzXML formats and need to feed them into Casanovo or similar transformer-based de novo sequencing models.
    14 installs
32. ▌
    Spectral Annotation And Overlay Visualization 3 · holobiomicslab

    Use when after correlation testing has validated putative parent–adduct ion pairs (e.g., via corrPairsMSI() on a massdiff object annotated with adductMatch results), use this skill to annotate and visualize the mass spectrum plot to confirm that identified pairs exhibit expected overlap—e.
    9 installs
33. ▌
    Embedding Space Visualization And Interpretation 2 · holobiomicslab

    Use when after training or loading a pre-trained deep learning model that produces high-dimensional embeddings (e.g., 200-dimensional vectors from MS2DeepScore). Use this skill when you have a set of spectra with known chemical class annotations (e.
    13 installs
34. ▌
    Ft Icr Ms Data Preprocessing And Quality Control 2 · holobiomicslab

    Use when when you have raw or processed FT-ICR MS peak-abundance .
    12 installs
35. ▌
    Spectral Similarity Prediction Neural Networks 2 · holobiomicslab

    Use when when you have paired MS/MS spectra with known structural similarity labels (Tanimoto scores from molecular fingerprints) and need to predict structural similarity for new spectrum pairs faster than fingerprint-based methods, or when you want to assess model prediction confidence per.
    10 installs
36. ▌
    Multivariate Statistical Analysis Metabolomics 2 · holobiomicslab

    Use when when you have preprocessed non-targeted LC-MS/MS feature tables (post-merging, cleanup, blank removal, and batch correction) and seek to uncover multivariate patterns across samples, discriminate between experimental groups, or reduce dimensionality of high-dimensional metabolomic data.
    10 installs
37. ▌
    Peak Map Rendering Retention Time Mz Intensity 4 · holobiomicslab

    Use when when you have loaded mass spectrometry data (from mzML or Bruker .
    11 installs
38. ▌
    Probabilistic Topic Modeling Mass Spectrometry 3 · holobiomicslab

    Use when you have preprocessed tandem mass spectrometry spectra converted into a bag-of-fragments representation (with fragments and neutral losses extracted and noise filtered) and your goal is to discover recurring fragmentation patterns or substructures across a large spectral dataset without.
    10 installs
39. ▌
    Resolution Effect Correction Unlabeled Samples 2 · holobiomicslab

    Use when when you have paired LC-MS data from both labeled (isotope-tracer dosed) and unlabeled (control) samples of the same analytes, and you want to correct FAM to true MDV while accounting for resolution effects from the mass spectrometer (especially relevant for high-resolution instruments.
    12 installs
40. ▌
    Ribosomally Synthesized Peptide Identification 3 · holobiomicslab

    Use when you have LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and corresponding genomic sequence data (raw FASTA nucleotide sequences or genome mining tool outputs like antiSMASH .final.
    11 installs
41. ▌
    Spectral Batch Submission To Networking Server 3 · holobiomicslab

    Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and perform structured chemical similarity analysis.
    13 installs
42. ▌
    Spectral Peak Frequency Threshold Optimization 2 · holobiomicslab

    Use when you have MS/MS spectra with fragment frequency annotations (from consensus spectrum generation) and need to decide which fragments to retain versus remove. Trigger conditions: (1) you have replicate MS/MS spectra for the same feature with per-fragment recurrence frequencies calculated;
    12 installs
43. ▌
    Statistical Hypothesis Testing Mean Comparison 3 · holobiomicslab

    Use when you have computed raw or standardised correlation scores (or other link-ranking metrics) for all possible GCF-MF pairs in a dataset and want to verify that validated links (those with known strain co-occurrence or experimental confirmation) are significantly enriched at higher score values.
    12 installs
44. ▌
    Transformer Attention Mechanism Implementation 2 · holobiomicslab

    Use when you have a sequence-to-structure prediction task where: (1) inputs are token sequences or embeddings representing molecular fragments or spectral data; (2) outputs are structured molecular representations (adjacency matrices for connectivity, formula vectors);
    9 installs
45. ▌
    Converter Pipeline Integration And Execution 3 · holobiomicslab

    Use when when you have a .msp mass spectra file with incomplete or missing chemical metadata fields (SMILES, InChI, CAS number, formula, InChIKey, IUPAC name) and need to populate those fields by querying multiple external chemical identifier services and local cheminformatics tools in parallel.
    12 installs
46. ▌
    Mass Spectrometry Intensity Drift Correction 2 · holobiomicslab

    Use when mS quantification data exhibits intensity drift—a systematic decline or variation in detector response across the run sequence. Intensity drift is particularly common in long measurement sessions and compromises the accuracy of feature-by-sample intensity matrices.
    12 installs
47. ▌
    Metabolite Database Identifier Normalization 2 · holobiomicslab

    Use when you have metabolomics metadata in mwTab or tabular format with column headers and values that may contain database identifiers (e.g., HMDB IDs, PubChem CIDs, KEGG compound IDs) in heterogeneous or non-canonical formats (mixed case, optional prefixes, variable naming conventions).
    12 installs
48. ▌
    Spectral Array Extraction And Reconstruction 2 · holobiomicslab

    Use when your input is an mzPeak archive (ZIP of Parquet files) and you need to recover spectrum signal data (m/z values and intensities) for downstream analysis, visualization, or format conversion. Use this skill when working with profile or centroid mode spectra stored in `spectra_data.
    8 installs
49. ▌
    Chemical Structure Transformation Documentation 2 · holobiomicslab

    Use when when you have access to source code or algorithmic documentation of a metabolite generation pipeline (such as MAGMa's job subproject) and need to understand, validate, or reconstruct the transformations that convert a parent compound into enumerated metabolite candidates.
    10 installs
50. ▌
    Molecular Network Construction For Metabolomics 3 · holobiomicslab

    Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown metabolites.
    11 installs
51. ▌
    Statistical Significance Testing P Value Calculation 2 · holobiomicslab

    Use when after standardizing link scores (strain correlation and IOKR) across all potential GCF-MF pairs in a metabologenomics dataset, perform significance testing to determine whether validated links show statistically distinguishable score distributions from the background.
    14 installs
52. ▌
    Molecular Dataset Partitioning And Preprocessing 3 · holobiomicslab

    Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and you need to format them for GNN training and held-out test evaluation with consistent standardization.
    11 installs
53. ▌
    Mass Spectrometry Visualization Backend Comparison 3 · holobiomicslab

    Use when you have a mass spectrometry visualization library that claims to support multiple plotting backends and need to verify that: (1) all backends produce functionally equivalent outputs, (2) execution times are consistent with reported benchmarks, and (3) the library scales appropriately.
    12 installs
54. ▌
    Deep Learning Model Inference And Ensemble Prediction 2 · holobiomicslab

    Use when you have a trained deep learning model and want to quantify prediction uncertainty for each input pair or decision point. Use this when you need to identify low-confidence predictions (high IQR) and filter them out to reduce error in specific score ranges (e.
    10 installs
55. ▌
    Metabolomics Data Integration With Metabolic Networks 3 · holobiomicslab

    Use when you have measured intracellular metabolite concentrations (e.g., via LC–MS/MS) across multiple cell lines or samples and want to predict which metabolic reactions are substrate-limited versus transcriptionally regulated.
    10 installs
56. ▌
    Python Package Installation And Dependency Management 3 · holobiomicslab

    Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that depends on specific versions of auxiliary packages (like spectrum-utils==0.3.5).
    7 installs
57. ▌
    Statistical Significance Estimation Mass Spectrometry 2 · holobiomicslab

    Use when after aligning fragment ions between two tandem mass spectra (query and reference) using maximum weight matching and you need to assign confidence scores to the matched ion pairs.
    14 installs
58. ▌
    Feature Metadata Extraction From Clustering Objects 2 · holobiomicslab

    Use when after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
    12 installs
59. ▌
    Metabolomic Dataset Preprocessing And Normalization 2 · holobiomicslab

    Use when you have raw or minimally processed FT-ICR MS peak tables in Formularity .
    12 installs
60. ▌
    Semantic Role Assignment For Mass Spectrometry Data 2 · holobiomicslab

    Use when you have uploaded a delimited data file (comma-, semicolon-, or tab-separated) with a header row into Punc'data and need to ensure that each column is correctly mapped to its semantic role (m/z, intensity, formula, or other mass spectrometry attributes) before proceeding to analysis.
    11 installs
61. ▌
    Method Equivalence Verification Across API Invocations 2 · holobiomicslab

    Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode diagnostic outputs (e.g., EIC plots, peak detection metrics) are identical regardless of which invocation pattern is used.
    8 installs
62. ▌
    Input Output Kernel Regression For Metabolite Matching 3 · holobiomicslab

    Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links using metabolite structure information rather than genomic or strain-based features alone.
    9 installs
63. ▌
    Software Dependency Management And Environment Setup 2 · holobiomicslab

    Use when you are preparing to run the MetaboDirect pipeline for the first time on a new machine, or you need to reproduce a published benchmark or analysis on a different OS (Windows, Linux, MacOS) and want to guarantee that all six pipeline steps (data pre-processing, diagnostics, exploration.
    13 installs
64. ▌
    Chromatographic Peak Detection Retention Time Alignment 2 · holobiomicslab

    Use when you have multiple high-resolution mzML files from LC-MS/MS experiments (e.
    9 installs
65. ▌
    Empirical Compound Construction From Feature Clustering 3 · holobiomicslab

    Use when after feature detection and quality control have produced a feature table in TSV format from Asari or equivalent preprocessing.
    11 installs
66. ▌
    Nested Data Structure Construction For Chemical Metadata 2 · holobiomicslab

    Use when you have loaded raw Agilent Unknowns Analysis CSV output with required columns (Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
    6 installs
67. ▌
    Mass Spectrometry Imaging Data Interpretation 2 · holobiomicslab

    Use when when you have preprocessed MALDI-MSI data (in msimat format) and want to determine whether abundant peaks are actually molecular adducts of simpler parent ions rather than distinct metabolites.
    7 installs
68. ▌
    Mass To Charge Retention Time Feature Mapping 2 · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA) mzML files from LC- or GC-HRMS measurements and need to convert continuous raw mass spectrometric signals into discrete, quantifiable chromatographic features (m/z, RT, intensity, charge, isotope) before PFAS-specific prioritization or.
    12 installs
69. ▌
    Metabolite Quantification Accuracy Assessment 3 · holobiomicslab

    Use when you have executed mzExacto() on a preprocessed GC-MS dataset and need to verify that the returned dataframe correctly matches query chemicals to their m/z peaks, retention times, and quantitative measurements (area values).
    9 installs
70. ▌
    Peak Annotation Quantification And Comparison 3 · holobiomicslab

    Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
    9 installs
71. ▌
    Peaklist Metabolite Assignment Prioritization 3 · holobiomicslab

    Use when you have extracted m/z and retention time (m/z-RT) information for peaks from untargeted LC/HRMS data (using tools like IDSL.IPA) and need to assign molecular formula identities to those peaks.
    12 installs
72. ▌
    Pfas Characteristic Mass Difference Detection 4 · holobiomicslab

    Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
    13 installs
73. ▌
    Root Mean Squared Error Regression Evaluation 3 · holobiomicslab

    Use when you have a trained regression model (e.g., a neural network or similar predictor) and a held-out test set with ground-truth continuous labels, and you need to measure whether the model's predictions match the true values.
    8 installs
74. ▌
    Source Code Analysis For Algorithm Extraction 2 · holobiomicslab

    Use when when you need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the software performs in silico generation, enumeration, or filtering of candidate molecular structures and the published paper or.
    12 installs
75. ▌
    Structural Similarity Ground Truth Validation 3 · holobiomicslab

    Use when you have a spectral library with structural ground truth (InChIKey or SMILES annotations for ≥50% of spectra) and want to benchmark whether a new or existing spectral similarity scorer ranks structurally related compounds higher than unrelated ones.
    12 installs
76. ▌
    Vendor Mass Spectrometry File Format Handling 3 · holobiomicslab

    Use when you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird format for batch processing, cloud deployment, or integration with downstream analysis tools.
    12 installs
77. ▌
    Neural Network Model Deployment In Python 2 · holobiomicslab

    Use when you have a trained conformer-based peak-picking model (in ONNX format) and need to apply it to chromatographic or ion-mobility mass spectrometry data (TransitionGroup objects) to detect peak boundaries and apex positions, generating TransitionGroupFeature records for downstream analysis or.
    11 installs
78. ▌
    Cross Language Implementation Compatibility 3 · holobiomicslab

    Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.
    13 installs
79. ▌
    Dataframe Construction From Backend Sources 3 · holobiomicslab

    Use when when implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
    9 installs
80. ▌
    Mass Spectrometry Data Structure Conversion 2 · holobiomicslab

    Use when when you have received metabolomics mass-spectrometry data in vendor-native or open formats (.raw, .d, mzXML) and need to ingest it into SMART for preprocessing, peak detection, or statistical analysis.
    12 installs
81. ▌
    Ms2 Spectrum Extraction And Consensus Building 3 · holobiomicslab

    Use when when you have DDA LC-MS/MS data (mzML format) with identified chromatographic peaks at a specific m/z (e.g., 304.1131) and multiple MS2 spectra fragmented from that precursor, and you need to produce a single high-confidence MS2 spectrum for comparison against reference databases (e.
    6 installs
82. ▌
    File Format Conversion Peak Picking To Lipidmatch 3 · holobiomicslab

    Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest it into LipidMatch for lipid identification.
    12 installs
83. ▌
    Hierarchical Clustering Dendrogram Interpretation 3 · holobiomicslab

    Use when you have a pre-computed hierarchical dendrogram from correlation-based clustering of LC-MS features (with fixed linkage criterion and distance metric) and need to decide whether a single constant-threshold cut or data-driven silhouette optimization better resolves the underlying cluster.
    12 installs
84. ▌
    Tandem Mass Spectrometry Fragmentation Simulation 3 · holobiomicslab

    Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to evaluate without access to real mass spectrometry hardware.
    7 installs
85. ▌
    Tandem Mass Spectrometry Mirror Plot Construction 3 · holobiomicslab

    Use when when you have raw LC-MS or LC-IMS-MS data in instrument format (Agilent .d, Thermo .raw, Bruker .
    11 installs
86. ▌
    Molecular Fingerprint Extraction And Vectorization 2 · holobiomicslab

    Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
    12 installs
87. ▌
    Molecular Structure Prediction Out Of Distribution 2 · holobiomicslab

    Use when your goal is to assess whether a pretrained NMR2Struct model trained on molecules ≤19 heavy atoms can generalize to larger, more complex molecules, or whether accuracy degrades significantly.
    9 installs
88. ▌
    Scalability Extrapolation And Throughput Estimation 4 · holobiomicslab

    Use when you have a new or modified LC-MS data processing tool and need to determine whether it can handle production-scale sample cohorts (50–100+ samples) on modest hardware (single-core CPU, ≤16 GB RAM).
    7 installs
89. ▌
    Benchmarking And Comparative Performance Evaluation 3 · holobiomicslab

    Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains over established baselines. Use it specifically when you have access to ground-truth annotations (e.
    11 installs
90. ▌
    Constraint Based Model Sampling And Flux Prediction 3 · holobiomicslab

    Use when you have constraint-based metabolic models with integrated multi-omics constraints (transcriptomics via Reaction Activity Scores, extracellular flux ratios via YSI bioanalyzer or LC-MS, nutrient availability bounds), and you need to determine whether differential enzyme expression.
    11 installs
91. ▌
    Mz Retention Time Tolerance Parameter Configuration 3 · holobiomicslab

    Use when when invoking Asari to process centroid mzML files for the first time in a PCPFM experiment, or when RT and m/z accuracy characteristics of your LC-MS instrument differ from the pipeline defaults (e.
    8 installs
92. ▌
    Post Translational Modification Pattern Recognition 3 · holobiomicslab

    Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and genomically-predicted precursor peptide sequences, and you need to identify which predicted RiPPs are actually expressed and modified in the sample.
    11 installs
93. ▌
    Permanova Statistical Testing Multivariate Groups 3 · holobiomicslab

    Use when you have normalized peak intensities or abundance matrices from mass spectrometry (e.
    8 installs
94. ▌
    Tandem Mass Spectrum Preprocessing And Normalization 2 · holobiomicslab

    Use when you have acquired raw MS/MS spectra (in MGF or mzML format) from a mass spectrometry instrument or public repository (e.g., MassIVE, MetaboLights, GNPS) that will be used for de novo chemical formula ranking or adduct assignment.
    6 installs
95. ▌
    Targeted Metabolite Detection Parameter Optimization 2 · holobiomicslab

    Use when when you have centroided .mzML LC–MS runs and a target list (compound ID, theoretical m/z, expected RT, polarity) but are uncertain whether your m/z and RT windows are wide enough to capture all targets without false positives.
    8 installs
96. ▌
    Data Dependent Acquisition Controller Implementation 3 · holobiomicslab

    Use when you have a conceptual MS/MS fragmentation strategy (e.
    8 installs
97. ▌
    Metabolite Abundance Normalization Across Conditions 3 · holobiomicslab

    Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or conditions, and you need to create a normalized, cell-line-level metabolite dataset before computing Reaction Propensity.
    9 installs
98. ▌
    Metabolomics Quantification Table Processing 2 · holobiomicslab

    Use when you have a quantification table (rows = metabolite features, columns = samples with abundance values), corresponding metadata table (sample annotations, groupings), and spectral data files, and you need to produce a unified JSON dashboard artifact that can be loaded into an interactive.
    7 installs
99. ▌
    Sequential Tool Integration And Data Routing 3 · holobiomicslab

    Use when when you have raw LC-HRMS metabolomics data in .mzML or .
    15 installs
100. ▌
     Spectral Scoring And Significance Assessment 3 · holobiomicslab

     Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) against a chemical structure database of known natural products, and you need to: (1) identify which pipeline(s).
     11 installs