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HolobiomicsLab

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1. ▌
   Sirius Spectral Request Construction 3 · holobiomicslab

   Use when when you have processed LC-MS/MS data with precursor m/z, ionization mode, collision energy (if available), and fragment peak lists (m/z and intensity pairs), and need to query CSI:FingerID for molecular fingerprint predictions as part of an automated metabolite identification workflow.
   7 installs
2. ▌
   Software Support Matrix Construction 2 · holobiomicslab

   Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
   10 installs
3. ▌
   Spectral Library Matching Validation 2 · holobiomicslab

   Use when you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.
   10 installs
4. ▌
   Spectrum Peak Counting And Reporting 3 · holobiomicslab

   Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a selected noise-filtering strategy retains an expected number of peaks for downstream molecular formula assignment.
   10 installs
5. ▌
   Tandem Mass Spectra Peptide Matching 2 · holobiomicslab

   Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and wish to identify peptidic natural products or ribosomally synthesized and post-translationally modified peptides (RiPPs) against a known structure database or custom RiPP structure database.
   11 installs
6. ▌
   Vendor Format To Standard Conversion 2 · holobiomicslab

   Use when when ingesting raw LC-MS/MS output from a mass spectrometry instrument and you need to prepare it for metabolite identification, fragmentation tree computation, or molecular formula annotation.
   6 installs
7. ▌
   Annotation Pipeline Data Preparation 2 · holobiomicslab

   Use when when you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa.
   12 installs
8. ▌
   Binary Classification Model Training 2 · holobiomicslab

   Use when you have curated a labeled dataset of MS/MS spectra annotated as 'relevant' (compounds of interest obtained from reference standards) or 'other' (reference standards or non-target compounds), and you need to build a classifier to automatically distinguish these two classes on unknown.
   10 installs
9. ▌
   Bipartite Network Node Edge Assembly 2 · holobiomicslab

   Use when after completing dereplication and cosine similarity clustering in the MolNotator workflow, when you have merged, dereplicated molecular and ion data (output from mode_merger and dereplicator steps) and need to assemble the final molecular network representation connecting predicted.
   8 installs
10. ▌
    Chemical Class Assignment Classyfire 3 · holobiomicslab

    Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes molecules by chemical taxonomy.
    10 installs
11. ▌
    Chromatogram Peak Boundary Detection 3 · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA-MS data) and need to identify precise peak boundaries and apex positions for feature extraction.
    9 installs
12. ▌
    Conditional Routing Logic Extraction 4 · holobiomicslab

    Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing pipelines.
    10 installs
13. ▌
    Corrected Intensity Table Validation 2 · holobiomicslab

    Use when after applying one or more intensity drift correction strategies (Internal Standard correction, statistical drift correction, custom or weighted bracketing) within QuantyFey and before exporting the corrected intensity table for final quantification.
    8 installs
14. ▌
    Cross Assay Feature Linkage Analysis 4 · holobiomicslab

    Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.
    7 installs
15. ▌
    De Novo Mass Spectrum Interpretation 3 · holobiomicslab

    Use when you have MS/MS spectra (centroided m/z and intensity pairs) and corresponding MS1 precursor masses but lack reference spectra or a priori formula information.
    10 installs
16. ▌
    Diversity Visualization By Treatment 2 · holobiomicslab

    Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
    6 installs
17. ▌
    Gc Ms Spectral Similarity Clustering 4 · holobiomicslab

    Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct a molecular network.
    8 installs
18. ▌
    Graph Based Molecular Representation 2 · holobiomicslab

    Use when when you have 1D NMR spectra (¹H and/or ¹³C) as input and need to predict complete molecular structure (both molecular formula and bond connectivity) for molecules with up to 19 heavy atoms.
    6 installs
19. ▌
    Extracted Ion Chromatogram Generation 3 · holobiomicslab

    Use when you have raw MS data (in Agilent .d, Thermo .raw, Bruker .
    8 installs
20. ▌
    Extracted Ion Chromatogram Processing 3 · holobiomicslab

    Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative identifications).
    7 installs
21. ▌
    Ion Type Classification And Filtering 2 · holobiomicslab

    Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification, and you need to identify which observed peaks correspond to specific fragment ion types (e.g., only b and y ions for backbone fragmentation, or immonium ions for amino acid identification).
    12 installs
22. ▌
    Lipid Retention Time Rule Application 2 · holobiomicslab

    Use when you have candidate lipid annotations from spectral library matching (e.g., XCMS + CAMERA output) with MS/MS scores, and you need to reduce false positives and predict previously unannotated lipids.
    9 installs
23. ▌
    Mass Charge Retention Time Validation 3 · holobiomicslab

    Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity designation, perform this validation step to confirm target visibility and refine m/z and RT window parameters before running.
    5 installs
24. ▌
    Mass Spectrometry Compound Extraction 3 · holobiomicslab

    Use when you have a preprocessed GC-MS dataset (from spreadOut) with standardized column names (Compound.Name, Component.RT, Base.Peak.MZ, Component.Area, Match.Factor) and a specific list of chemical compounds you want to extract and aggregate across multiple sample runs.
    10 installs
25. ▌
    Mass Spectrometry Data Column Mapping 2 · holobiomicslab

    Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer in its native export format and need to ingest it into LipidMatch for lipid identification.
    7 installs
26. ▌
    Mass Spectrometry Data Representation 3 · holobiomicslab

    Use when you need to store or retrieve mass spectrometry spectra (m/z and intensity pairs) from a novel data source or storage medium (e.
    8 installs
27. ▌
    Mass Spectrometry File Format Parsing 4 · holobiomicslab

    Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized bag-of-fragments representation for unsupervised topic modeling or substructure discovery workflows.
    12 installs
28. ▌
    Mass Spectrometry Peak Classification 3 · holobiomicslab

    Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false positives introduced by the peak-picking algorithm.
    8 installs
29. ▌
    Metabolite Tandem Ms Library Curation 3 · holobiomicslab

    Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural annotations (missing SMILES or molecular formula fields) and need to combine them into unified, polarity-specific msp files.
    8 installs
30. ▌
    Metabologenomic Database Construction 3 · holobiomicslab

    Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified peptides (RiPPs) by integrating genomic and mass spectrometry data.
    9 installs
31. ▌
    Metabolomic Feature Tree Construction 3 · holobiomicslab

    Use when when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform chemical phylogeny-based diversity analyses or meta-analyses comparing metabolomic profiles across multiple samples or.
    8 installs
32. ▌
    Metadata Harmonization Across Sources 3 · holobiomicslab

    Use when you have completed independent batch searches across one or more domain-specific MASST tools (microbeMASST, plantMASST, tissueMASST, microbiomeMASST, foodMASST) and received multiple separate output files (_microbe.html, _plant.json, _matches.tsv, _library.tsv, _datasets.tsv, _count_domain.
    9 installs
33. ▌
    Module Dispatch Architecture Analysis 4 · holobiomicslab

    Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its declared data type (LC vs. GC vs. IMS vs. MS imaging).
    6 installs
34. ▌
    Notification Configuration Management 2 · holobiomicslab

    Use when setting up a Rapid QC-MS monitoring job and you need to define WHERE and HOW QC-fail alerts should be sent.
    8 installs
35. ▌
    Double Bond Positional Isomer Generation 2 · holobiomicslab

    Use when when constructing a comprehensive lipid spectral reference library that must disambiguate lipids differing only in carbon-carbon double-bond position (e.
    6 installs
36. ▌
    Ei Mass Spectra Structure Representation 2 · holobiomicslab

    Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing. Specifically, when you must extract precursor m/z values, peak intensity pairs, and spectrum metadata (e.
    10 installs
37. ▌
    Feature Table Annotation Standardization 2 · holobiomicslab

    Use when after Blueshift or Gravity processing has produced a feature abundance table with annotations, but before final reporting or integration with sample/injection metadata.
    10 installs
38. ▌
    Internal Standard Selection Optimization 2 · holobiomicslab

    Use when after batch correction of metabolomics QC samples using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to determine which one stabilizes the compound/internal standard ratio for each compound.
    8 installs
39. ▌
    Metabolic Model Constraint Specification 3 · holobiomicslab

    Use when you have a generic constraint-based metabolic model (SBML format) and cross-sectional omics data (RNA-seq, intracellular metabolomics, YSI or bioanalyzer extracellular flux measurements) for multiple biological samples and need to create sample-specific models that discriminate whether.
    7 installs
40. ▌
    Metabolomics Data Loading And Formatting 2 · holobiomicslab

    Use when you have raw metabolomics count data (e.g., from mass spectrometry or NMR experiments) in tabular format and associated sample metadata (e.g., treatment groups, experimental factors) that need to be imported into R for analysis with packages like Omu.
    8 installs
41. ▌
    Microbiome Metabolome Data Preprocessing 3 · holobiomicslab

    Use when when starting with raw paired microbiome (16S rRNA, metagenomic taxonomic or functional features) and metabolome (LC-MS/MS, NMR) count tables from the same biospecimens, and planning to train prediction models or co-abundance networks.
    10 installs
42. ▌
    Missing Value Imputation In Metabolomics 3 · holobiomicslab

    Use when after feature extraction and quality control filtering (blank masking, sample dropping, normalization) have been applied, but before statistical analysis or machine learning.
    10 installs
43. ▌
    Molecular Graph Construction From Smiles 2 · holobiomicslab

    Use when you have raw SMILES strings from a chemical database (e.g., CCSBase, METLIN, or custom sources) and need to feed them into a graph neural network model.
    10 installs
44. ▌
    Molecular Graph Encoder Decoder Training 2 · holobiomicslab

    Use when when you have a training dataset of NMR spectra-derived molecular fragments encoded as token sequences, and you need to predict both the molecular formula and complete bond connectivity of unknown molecules.
    9 installs
45. ▌
    Multivariate Statistical Quality Control 2 · holobiomicslab

    Use when after data normalization (Step 7) when you have a preprocessed feature matrix and need to identify samples that deviate significantly from the multivariate center of the data distribution due to instrumental drift, batch effects, sample degradation, or genuine biological outliers that.
    10 installs
46. ▌
    Neural Network Regularization Techniques 3 · holobiomicslab

    Use when when training a deep neural network on paired MS/MS spectra to predict structural similarity scores, especially when the training dataset is moderate-sized (109,734 spectra across 15,062 molecules) and overfitting risk is high.
    7 installs
47. ▌
    Per Browser Developer Setting Navigation 2 · holobiomicslab

    Use when you are attempting to run a web application (such as COLMARvista) locally by opening index.html directly in a browser, the application uses WebWorker and/or WebAssembly components, and these fail to load due to default file-access policies.
    7 installs
48. ▌
    Siamese Network Inference Spectrum Pairs 3 · holobiomicslab

    Use when you have a collection of preprocessed tandem mass spectra (binned into 10,000 equally-sized m/z bins, intensities square-root transformed, top 1,000 peaks retained), a trained MS2DeepScore Siamese model, and you need to predict structural similarity scores (Tanimoto or Dice) for all or a.
    8 installs
49. ▌
    Similarity Matrix Generation And Storage 2 · holobiomicslab

    Use when when you have cleaned and filtered mass spectrometry spectral data (in mzML, mzXML, msp, MGF, or JSON format) and need to identify or rank spectra by similarity for library matching, metabolite annotation, or network analysis.
    7 installs
50. ▌
    Spectral Library Compilation And Merging 3 · holobiomicslab

    Use when you have multiple mass spectral library files in different formats (MSP, MGF, MOL folders) from sources like NIST, MoNA, RIKEN, or GNPS, and need to produce a single consolidated MSP file with complete SMILES, InChIKey, and experimental retention index (RI) annotations for metabolomics or.
    10 installs
51. ▌
    Configuration File Interpretation 2 · holobiomicslab

    Use when when you have PSM files from proteomics search engines (MaxQuant, MSGFPlus, Sage, etc.) that use non-standard modification notation (e.g., 'ox', '+57.02146', or mass-shift labels) and need to resccore peptide identifications with MS²Rescore.
    10 installs
52. ▌
    Dataframe Lazy Loading Comparison 3 · holobiomicslab

    Use when when designing or optimizing an MsBackend implementation (or similar columnar data structure) you must decide whether to pre-allocate all known columns in the backing DataFrame at initialization or defer column creation until first access.
    12 installs
53. ▌
    Dotnet Assembly Path Verification 3 · holobiomicslab

    Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass spectrometry data extraction operations.
    10 installs
54. ▌
    File Format Compliance Validation 3 · holobiomicslab

    Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification before integration into a production workflow, data repository, or downstream analysis pipeline.
    7 installs
55. ▌
    File Format Validation Proteomics 2 · holobiomicslab

    Use when when raw MS files are uploaded to MSConnect via the Raw File Uploader and must be verified for compatibility with downstream processing tools (e.g., Proteomics_Data_Processor) before routing to the processing queue.
    10 installs
56. ▌
    File Io Error Handling Robustness 2 · holobiomicslab

    Use when when designing or integrating a file parser for mass spectrometry formats (.raw Thermo RAW format, .mzml XML-based format) in a metabolomics processing pipeline, or when reading legacy or heterogeneous instrument output where file integrity cannot be guaranteed.
    8 installs
57. ▌
    Inchikey Identifier Normalization 2 · holobiomicslab

    Use when gNPS has stopped supplying ClassyFire ontology information for spectral library matches (as of the ConCISE documentation snapshot) and you need to manually retrieve chemical classifications.
    8 installs
58. ▌
    Lipid Concentration Normalization 2 · holobiomicslab

    Use when your lipidomics experiment includes spiked internal lipid standards with known absolute concentrations, and you have a data matrix of signal intensities (samples × lipids) from LipidSearch or LIQUID output.
    6 installs
59. ▌
    Memory Profiling And Benchmarking 3 · holobiomicslab

    Use when when designing or optimizing backends that handle large MS datasets (mzML, mzXML, CDF files via MsBackendMzR), to verify that claimed memory advantages of on-disk or chunked approaches actually materialize in practice.
    7 installs
60. ▌
    Multi Inheritance Class Hierarchy 3 · holobiomicslab

    Use when when you need to support multiple plotting library backends (static or interactive) for the same data visualization domain (e.
    9 installs
61. ▌
    Noise Estimation Snr Thresholding 2 · holobiomicslab

    Use when after normalizing, smoothing, and baseline-reducing mass spectra via normalize(), smooth(), and reduceBaseline(), when you need to distinguish true peaks from noise-induced artifacts.
    7 installs
62. ▌
    Mass Tolerance Calibration Ppm Units 2 · holobiomicslab

    Use when when linking statistically significant LC-MS features into structural clusters based on adduct signatures and cross-assay references (e.g., [M+H]+/[M-H]−), and you need to specify the maximum allowed deviation (in ppm) between observed m/z values and calculated neutral masses.
    7 installs
63. ▌
    Metabolomics Data Quality Assessment 2 · holobiomicslab

    Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to statistical analysis or functional interpretation.
    8 installs
64. ▌
    Modality Contribution Quantification 2 · holobiomicslab

    Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you need to understand their relative importance for the downstream prediction task (e.g., molecular structure elucidation).
    8 installs
65. ▌
    Ms1 Full Scan Acquisition Simulation 2 · holobiomicslab

    Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
    12 installs
66. ▌
    Peak Detection Threshold Application 2 · holobiomicslab

    Use when converting raw MS/MS spectra from library files (e.g., .msp format) into structured library entries, or when annotating experimental LC–MS features against fragment databases.
    9 installs
67. ▌
    Peptide Spectrum Matching Evaluation 2 · holobiomicslab

    Use when when you have a tandem mass spectrum (MSMS) with known peptide sequence and wish to assess whether enabling neutral loss annotation (e.g., NH3: −17.026549, H2O: −18.010565) increases the proportion of observed m/z peaks that can be matched to predicted fragment ions.
    11 installs
68. ▌
    Mass Spectrometry Metadata Validation 2 · holobiomicslab

    Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or MSNovelist web services.
    5 installs
69. ▌
    Mass Spectrometry Package Integration 2 · holobiomicslab

    Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.
    10 installs
70. ▌
    Non Pathway Metabolite Classification 3 · holobiomicslab

    Use when you have metabolomics intensity data with peak annotations, and you want to rank and prioritize metabolite groupings (Molecular Families, Mass2Motifs, or other non-pathway metabolite sets) by their activity levels across experimental contrasts.
    12 installs
71. ▌
    R Python Interoperability Via Wrapper 2 · holobiomicslab

    Use when you have a Spectra object in R and need to apply a specialized Python MS algorithm (e.
    8 installs
72. ▌
    Scoring Function Sensitivity Analysis 2 · holobiomicslab

    Use when you have two or more complementary scoring functions (e.g., strain correlation and IOKR scores) that you wish to combine, and you need to determine which combination strategy and parameters maximize enrichment of known true links in a validation set.
    10 installs
73. ▌
    Spectral Library Molecular Networking 3 · holobiomicslab

    Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their similarity relationships, and identify spectral families without prior library matching.
    10 installs
74. ▌
    Spectral Network Propagation Analysis 2 · holobiomicslab

    Use when after running MetaMiner's Dereplicator stage to identify some RiPPs via direct database matching against a constructed structure database, apply this skill to enlarge the set of identifications by propagating those matches through spectral clusters and visualizing the connected components.
    11 installs
75. ▌
    Spectral Quality Assurance Proteomics 2 · holobiomicslab

    Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment ions rise substantially above noise—i.
    10 installs
76. ▌
    Top K Accuracy Ranking And Evaluation 2 · holobiomicslab

    Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the correct answer appears in the top-k predictions.
    9 installs
77. ▌
    Adduct Assignment Accuracy Assessment 3 · holobiomicslab

    Use when you have a trained formula ranking model (such as MIST-CF) and want to measure the specific performance gain from incorporating multiple positive-mode adduct types (e.g., [M+H]+, [M+Na]+, [M+K]+, [M+NH4]+) instead of restricting predictions to [M+H]+ only.
    8 installs
78. ▌
    Aird Format Conversion And Validation 3 · holobiomicslab

    Use when you have vendor mass spectrometry raw files (e.g., .raw, .d, .
    7 installs
79. ▌
    Batch Script Execution And Automation 2 · holobiomicslab

    Use when you have generated a peak table or feature list output file from an external peak-picking tool (MZmine, XCMS, MS-DIAL, or Compound Discoverer) in its native export format and need to ingest it into LipidMatch for lipid identification without manual column remapping or format conversion.
    8 installs
80. ▌
    Chemical Fragmentation Event Tracking 2 · holobiomicslab

    Use when when running a ViMMS Environment simulation with save_eval flag enabled and you need to correlate fragmentation events in the output mzML file back to their originating chemical compounds for downstream evaluation, optimization, or validation of acquisition strategies.
    8 installs
81. ▌
    Compositional Data Transformation Clr 2 · holobiomicslab

    Use when apply CLR transformation when you have microbiome or metabolomic count data that sums to a constant across samples (relative abundance or compositional data) and intend to train supervised or unsupervised machine learning models (especially neural networks) that assume unbounded, linear.
    11 installs
82. ▌
    Cosine Similarity Spectral Clustering 4 · holobiomicslab

    Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural relationships and enable compound annotation.
    9 installs
83. ▌
    Deep Learning Model Layer Composition 2 · holobiomicslab

    Use when you have unpaired mass spectrometry spectra and need to predict Tanimoto-based molecular structural similarity scores between spectrum pairs.
    6 installs
84. ▌
    Dot Product Based Spectral Comparison 2 · holobiomicslab

    Use when when searching an unknown MS/MS spectrum against a spectral library and you need to rapidly identify the most relevant candidate library spectra before applying cascade scoring with false discovery rate control.
    6 installs
85. ▌
    Quality Assurance Contamination Removal 2 · holobiomicslab

    Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data that includes both biological samples and blank/control samples, and you need to identify and exclude features whose intensity is driven by contamination in blanks rather than true.
    8 installs
86. ▌
    Separation Technique Workflow Alignment 4 · holobiomicslab

    Use when when evaluating whether an MS data processing platform (such as mzmine) supports the full range of separation/ionization techniques your laboratory uses, or when assessing whether gaps exist in the software architecture that would require external pre- or post-processing for specific.
    10 installs
87. ▌
    Spectral Data Processing And Annotation 3 · holobiomicslab

    Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular features, build a molecular network from fragmentation spectra, and annotate those features using both spectral.
    10 installs
88. ▌
    Ion Mobility Feature Classification 3 · holobiomicslab

    Use when you have high-dimensional TWIM-MS data (arrival time and m/z dimensions) from a multi-omic sample and need to associate experimental features with biomolecular classes *before* running peak detection or feature identification pipelines.
    6 installs
89. ▌
    Cross Script Consistency Verification 3 · holobiomicslab

    Use when when a deep learning pipeline processes mass spectrometry spectra through multiple independent scripts (e.g., train_rescore.py, run_fiddle.py, test_caffeine.py) and a specific feature must be removed or masked to prevent the model from learning directly from a protected input (e.
    8 installs
90. ▌
    Spectral Library Matching And Ranking 3 · holobiomicslab

    Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a reference library.
    8 installs
91. ▌
    Summary Statistics Table Construction 3 · holobiomicslab

    Use when when you need to quantify and compare the effect of multiple filtering thresholds (e.g., Match.Factor ≥65, ≥80, ≥90) on the size of a retained compound set.
    10 installs
92. ▌
    Theoretical To Observed Peak Matching 2 · holobiomicslab

    Use when you have a mass spectrum scan containing observed precursor ions (m/z, intensity pairs) in a narrow isolation window, a known peptide sequence with specified charge state and stable isotope labeling parameters (atom type, incorporation probability), and you need to determine which observed.
    9 installs
93. ▌
    Domain Context To Application Routing 3 · holobiomicslab

    Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the search must be executed against the appropriate domain-curated spectral library.
    8 installs
94. ▌
    Mass Spectrometry Imaging Data Import 2 · holobiomicslab

    Use when you have raw MS imaging data in imzML (continuous or processed) or Analyze 7.5 format and need to load it into R for spectral processing, normalization, peak-picking, or statistical analysis.
    10 installs
95. ▌
    Bioconductor Object Structure Inspection 2 · holobiomicslab

    Use when after constructing a SummarizedExperiment object from raw metabolomics data via buildExperiment, or after batch correction and ratio computation steps, inspect rowData, colData, and assays slots to verify that compound identities, sample annotations, and computed assay values (primary.
    8 installs
96. ▌
    Spectral To Structure Mapping Prediction 2 · holobiomicslab

    Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula and connectivity) rapidly without access to 2D NMR experiments (HSQC, HMBC, COSY) or mass spectrometry.
    6 installs
97. ▌
    Ablation Study Design And Interpretation 3 · holobiomicslab

    Use when when you have a neural network or machine learning model with multiple tunable hyperparameters (layer size, regularization strength, dropout) or design choices (e.
    8 installs
98. ▌
    Compound Area Aggregation Across Samples 2 · holobiomicslab

    Use when you have a GC-MS dataset with multiple sample files (e.g., Std_soln_00, Std_soln_07, Std_soln_00a) where the same chemical is detected in different runs with varying Match.Factor scores, and you need to consolidate area values by compound identity rather than by individual peak detection.
    9 installs
99. ▌
    Compound Structural Similarity Retrieval 3 · holobiomicslab

    Use when you have a collection of preprocessed MS/MS spectra with structural annotations (InChIKey, SMILES, or InChI) and need to identify pairs of compounds that are structurally related above a specified similarity threshold.
    10 installs
100. ▌
     Correlation Matrix Heatmap Visualization 3 · holobiomicslab

     Use when after computing a correlation matrix (e.g., Pearson correlation across samples) on statistically significant LC-MS features, particularly when you need to inspect hierarchical dendrogram structure, validate cluster assignments from different flattening methods (constant-threshold vs..
     8 installs