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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Community Metabolic Reconstruction Synthesis · holobiomicslab

   Use when you have draft metabolic reconstructions (in SBML or equivalent format) for multiple organisms sampled from a single ecological community (e.
   0 installs
2. ▌
   Conditional Dispatch Workflow Implementation · holobiomicslab

   Use when when you have loaded a raw mass spectrum (e.g., ESI_NEG_SRFA.d in Bruker or .raw format) and need to apply one of several noise-threshold strategies based on user preference or spectrum metadata.
   0 installs
3. ▌
   Converter Pipeline Integration And Execution · 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.
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4. ▌
   Intensity Dependent Missing Value Simulation · holobiomicslab

   Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real detector behavior where lower-intensity pixels are more likely to be missed or undetected.
   0 installs
5. ▌
   Internal Standardization With Isotope Labels · holobiomicslab

   Use when your IM-MS lipidomics samples have been spiked with fully labeled isotopic internal standards (e.
   0 installs
6. ▌
   JSON Serialization And Data Structure Design · holobiomicslab

   Use when you have inferred or discovered structured results (e.g., LDA-derived motif sets with mass compositions, neutral-loss patterns, and ranked database matches) that must be shared between tools, stored durably, or consumed by visualization or annotation pipelines.
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7. ▌
   Mass Spectrometry Molecular Formula Handling · holobiomicslab

   Use when you have raw or processed FT-ICR MS spectra with detected peaks (m/z values) and need to: (1) assign elemental compositions to each peak, (2) filter assignments by mass error tolerance and isotopic presence, or (3) prepare a peak table with molecular formula annotations for chemodiversity.
   0 installs
8. ▌
   Molecular Fingerprint Bit Frequency Analysis · holobiomicslab

   Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties before using them for classification, similarity search, or method validation.
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9. ▌
   Neural Network Layer Metadata Interpretation · holobiomicslab

   Use when after deploying a TensorFlow-backed classification service, you need to verify that the model's input layer names ('input_2048' and 'input_4096') and output layer name ('output') are correctly configured before constructing inference requests.
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10. ▌
    Olden Method Feature Attribution Calculation · holobiomicslab

    Use when after training multiple MLPNN models (via cross-validation) on paired microbiome and metabolome data when you need to extract interpretable feature importance scores from network weights to identify which microbes drive metabolite predictions and group them into co-functional modules.
    0 installs
11. ▌
    Python Environment Setup And Reproducibility · holobiomicslab

    Use when when you need to execute a multi-backend visualization library (e.g., pyOpenMS-Viz with matplotlib, Bokeh, and Plotly) and must measure or validate execution times, memory usage, and output consistency across runs or team members.
    0 installs
12. ▌
    Pytorch Model Instantiation And Forward Pass · holobiomicslab

    Use when after defining a transformer encoder architecture with multi-head self-attention and positional encoding, and before training or inference on mass spectrometry data.
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13. ▌
    Random Access Seekable File Interface Design · holobiomicslab

    Use when you have a large mzML file or text corpus (e.g., Moby Dick, proteomics run) stored in compressed or database format and need to retrieve specific spectra or chapters by ID without sequential iteration or full decompression.
    0 installs
14. ▌
    Regression Metric Computation And Comparison · holobiomicslab

    Use when you have trained two or more regression models (e.g., original vs. alternative GNN architectures) on the same training set and need to evaluate which generalizes better on held-out test data.
    0 installs
15. ▌
    Sqlite Query Execution And Cursor Management · holobiomicslab

    Use when you have mass spectrometry data stored in a SQLite database indexed by spectrum ID and need to retrieve specific spectra by ID (random access via __getitem__) or iterate through all spectra sequentially (via read method).
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16. ▌
    Statistical Summary Computation Median Range · holobiomicslab

    Use when when you have a table of execution times or performance metrics indexed by two or more categorical dimensions (e.g., plot_type × backend, or sample × condition), and you need to compare central tendency and spread across groups to rank or benchmark alternatives.
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17. ▌
    Strain Correlation Hypergeometric Adjustment · holobiomicslab

    Use when you have genomic clusters (GCFs) and metabolomic features (MFs) from paired microbial datasets, each with strain membership information, and you need to score potential links between them.
    0 installs
18. ▌
    Transformation Classification Biotic Abiotic · holobiomicslab

    Use when after mass-difference network generation has matched pairwise peak mass differences to a reference biochemical transformation key with mass error ≤1 ppm, and you need to distinguish metabolic transformations driven by microbial activity from those arising from non-biological chemical.
    0 installs
19. ▌
    XML Element Parsing And Object Serialization · holobiomicslab

    Use when you have spectrum or chromatogram data stored as XML strings (e.g., in a SQLite database indexed by spectrum ID) and need to access individual spectra by ID or iterate through them sequentially while working with a library like pymzML that expects Spectrum or Chromatogram objects.
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20. ▌
    Automated Executable Distribution Generation · holobiomicslab

    Use when you need to produce final distributable executable artifacts for a Qt5-based C++ application across multiple platforms (macOS, Windows, Linux), and you want to avoid manual build–package–release steps.
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21. ▌
    Baseline Model Implementation For Comparison · holobiomicslab

    Use when you are introducing a novel spectrum prediction model and need to demonstrate that performance improvements come from architectural innovation rather than experimental advantage.
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22. ▌
    Batch Structure Inspection Macroscopic Scale · holobiomicslab

    Use when after loading log-transformed, pre-processed metabolomics feature abundance tables (samples × features, with batch identifiers in the first column) and prior to selecting a batch-effect correction model.
    0 installs
23. ▌
    Biomolecule Filtering By Abundance Threshold · holobiomicslab

    Use when after data transformation (e.g., log2 normalization) but before statistical analysis, when you have an expression matrix with missing values or high variance across samples and you need to remove unreliable biomolecules.
    0 installs
24. ▌
    Chemical Structure Web Service Communication · holobiomicslab

    Use when you have a collection of chemical compounds (identified by name, SMILES, InChI, or other standard identifier) that you need to classify by structural features, and you want to submit them in batch to a remote web service rather than performing local computation.
    0 installs
25. ▌
    Spectral Intensity Normalization Across Modalities · holobiomicslab

    Use when you have raw spectral data from multiple complementary spectroscopic techniques (NMR, HSQC, COSY, IR) that must be combined into joint training records for a multimodal deep learning model, and the raw intensity values or chemical shift ranges differ significantly between modalities due to.
    0 installs
26. ▌
    Chromatin Accessibility Footprint Visualization · holobiomicslab

    Use when use this skill after performing Tn5 bias correction and footprint scoring on ATAC-seq BAM files when you need to inspect the spatial distribution of Tn5 insertions around transcription factor binding sites, validate footprinting quality, or communicate differential TF occupancy patterns.
    0 installs
27. ▌
    System Path Configuration And Environment Setup · holobiomicslab

    Use when you are setting up HiC-Pro or a similar multi-tool pipeline for the first time, or you need to validate that all required dependencies are installed and discoverable.
    0 installs
28. ▌
    Chemical Structure Sanitization And Validation · holobiomicslab

    Use when you have translated or raw SMILES strings from a chemical structure curation pipeline and need to remove invalid chemical structures, resolve sanitization errors (e.
    0 installs
29. ▌
    Class Stratified Calibration Model Application · holobiomicslab

    Use when you have a feature table with assigned biomolecular class labels (e.g., from preceding class assignment step) and raw ion mobility arrival time measurements from TWIM-MS data, and you need to compute class-appropriate CCS values for downstream multi-omic analysis.
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30. ▌
    Container Volume Mounting And File Persistence · holobiomicslab

    Use when executing containerized conversion tools (e.g., AirdPro CLI) that must read vendor-format mass spectrometry raw files from the host filesystem and write converted output (e.g., .aird files) back to a persistent host directory. This is essential when first-run Wine initialization and .
    0 installs
31. ▌
    Ion Mobility Mass Spectrometry Data Processing · holobiomicslab

    Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C labeled internal standards (e.g., fully labeled yeast extract) and need to quantify and correct systematic CCS bias before downstream lipid identification or quantification.
    0 installs
32. ▌
    Metabolomics Quality Control Report Generation · holobiomicslab

    Use when after completing outlier detection, batch correction, and quality metric calculation on a SummarizedExperiment object using mzQuality's doAnalysis function, and after manually or automatically filtering compounds and samples using the 'use' column in rowData and colData.
    0 installs
33. ▌
    Molecular Weight Prediction With Modifications · holobiomicslab

    Use when when you have metabolite structures (as SMILES strings) and need to predict their observable m/z ions under non-standard ionization conditions imposed by a derivatizing matrix reagent (such as FMP-10).
    0 installs
34. ▌
    Representation Vector Dimensionality Reduction · holobiomicslab

    Use when after obtaining 512-dimensional representation vectors from the Encoder module, when you need to compress these vectors for visualization, clustering, or downstream classification tasks on mass spectrometry imaging data while maintaining interpretability of ion relationships.
    0 installs
35. ▌
    Abundance Normalization And Summary Statistics · holobiomicslab

    Use when after peaks have been assigned to heteroatom classes (e.g., CHO, CHON, CHOS, CHOP) and you need to compare molecular composition across samples, classes, or time series.
    0 installs
36. ▌
    Biweight Midcorrelation Similarity Computation · holobiomicslab

    Use when you have normalized and imputed metabolite abundance measurements (as a MultiAssayExperiment object or similar matrix) and need to construct a correlation network for co-expression module discovery. Use it specifically when outlier-robust similarity is required—i.
    0 installs
37. ▌
    Checkpoint Serialization And Model Persistence · holobiomicslab

    Use when after completing a full training loop on preprocessed molecular graph data and validating model performance on a held-out validation set.
    0 installs
38. ▌
    Circular Dependency Avoidance In Method Design · holobiomicslab

    Use when you are implementing multiple accessor methods on a backend class that logically depend on each other (e.g., one returns full data and another returns column metadata), and both methods are required by downstream code.
    0 installs
39. ▌
    Coding Potential Prediction And Classification · holobiomicslab

    Use when you have differentially expressed isoform or exon FASTA sequences from transcript assembly or isoform-level analysis (e.g., IsoformSwitchAnalyzer output) and need to distinguish functional protein-coding transcripts from non-coding RNA.
    0 installs
40. ▌
    Command Line Software Installation From Github · holobiomicslab

    Use when you need to install a Python package that is distributed via GitHub but not yet (or only occasionally) published to PyPI, such as pyBaf2Sql for Bruker .baf/.d mass spectrometry imaging data conversion.
    0 installs
41. ▌
    Comparative Statistical Testing Across Methods · holobiomicslab

    Use when when you have applied multiple pathway analysis methods to the same metabolomics peak intensity dataset and need to determine which method produces more stable pathway activity scores under realistic perturbation conditions (noise and missing peaks).
    0 installs
42. ▌
    Cosine Distance Clustering Of Genomic Clusters · holobiomicslab

    Use when you have pre-computed BGC feature vectors (e.g., from HMM domain hits extracted via antiSMASH or BiG-SLiCE) and need to group similar BGCs into families for comparative genomics, functional prediction, or novelty assessment.
    0 installs
43. ▌
    Docker Container Orchestration For Ml Services · holobiomicslab

    Use when you have trained or pre-trained ML models (Keras, TensorFlow) that need to be exposed as HTTP endpoints for programmatic classification or inference, require reproducible deployment across environments, or need to coordinate multiple services (e.
    0 installs
44. ▌
    Eigenmetabolite Direction Of Effect Validation · holobiomicslab

    Use when after computing module significance (MS) statistics for metabolic modules against a sample grouping factor (e.g., tumor vs. normal), and detecting a statistically significant module association (p < 0.05).
    0 installs
45. ▌
    Environmental Microbial Degradation Prediction · holobiomicslab

    Use when you have a small-molecule structure (in SMILES, MOL, or SDF format) and need to predict how soil or aquatic microbiota will degrade or biotransform it, particularly for environmental risk assessment, metabolite identification in biodegradation studies, or tracing microbial transformation.
    0 installs
46. ▌
    Experiment Design Specification For Clustering · holobiomicslab

    Use when you have a CSV feature table from XCMS or other MS feature detection tools and are about to run RAMClustR clustering, but need to encode which samples are QC replicates, which batch they belong to, and their run order.
    0 installs
47. ▌
    Feature Property Refinement From Training Data · holobiomicslab

    Use when you have a set of training LC-HRMS chromatograms (retention time × m/z matrix format) and a manually curated reference list of isolated single chromatographic peaks, and you need to update the reference peak properties (retention time, m/z, peak shape) to match the actual peak signatures.
    0 installs
48. ▌
    Feature Redundancy Reduction With Ion Identity · holobiomicslab

    Use when when processing MZmine2/MZmine3 peak tables from LC–MS metabolomics data where you observe inflated feature counts due to multiple ionization states, isotopic satellites, and neutral losses of the same parent compound, particularly before computing extract-level metrics (e.
    0 installs
49. ▌
    Isotopologue Quantification Data Normalization · holobiomicslab

    Use when after autoQ has extracted and integrated peak areas for all isotopologues of your targeted compounds.
    0 installs
50. ▌
    Log Fold Change Computation And Interpretation · holobiomicslab

    Use when when you have completed differential expression analysis (via edgeR, DESeq2, or RankProduct) on preprocessed count matrices or abundance tables and need to quantify and interpret the magnitude of expression changes between conditions.
    0 installs
51. ▌
    Marker Feature Visualization Retention Time Mz · holobiomicslab

    Use when after NPFimg's automated detection algorithm has identified marker features from a two-dimensional MS map (m/z vs retention time), especially when you need to validate feature positions, inspect co-localization patterns, or communicate results to stakeholders.
    0 installs
52. ▌
    Mass Difference Transformation Pair Derivation · holobiomicslab

    Use when you have a formula-assigned DOM dataset from FT-ICR MS (or other mass spectrometry with compound annotations) and need to characterize how molecular transformations occur across the sample—e.
    0 installs
53. ▌
    Mass Spectrometry Feature Detection Validation · holobiomicslab

    Use when when you have processed LC-HRMS mzML files through a non-targeted preprocessing tool (e.g., XCMS, MZmine 2, MS-DIAL) and need to assess whether peak detection rates, isotopologue ratio fidelity, and alignment accuracy meet acceptable thresholds before downstream analysis.
    0 installs
54. ▌
    Mass Spectrometry Peak Detection And Alignment · holobiomicslab

    Use when after normalization, smoothing, and baseline reduction have been performed on raw MSImagingArrays data.
    0 installs
55. ▌
    Mass Spectrometry Plot Taxonomy Implementation · holobiomicslab

    Use when you are building a visualization library that must support multiple plot kinds (chromatogram, spectrum, mobilogram, peakmap) across multiple rendering backends (matplotlib, bokeh, plotly) and want to avoid code duplication.
    0 installs
56. ▌
    Metabolite Adduct Correlation Spatial Analysis · holobiomicslab

    Use when you have annotated mass-difference peaks with known adduct identities (via mass-matching to reference adduct tables) and possess MSI intensity matrices where each peak's abundance is measured across multiple tissue pixels or voxels.
    0 installs
57. ▌
    Metabolite Significance Filtering Volcano Plot · holobiomicslab

    Use when you have meta-analyzed metabolomic results from multiple studies with p-values and fold-change estimates (e.g., from amanida quantitative meta-analysis), and you need to identify compounds that meet both statistical rigor (p ≤ 0.05) and biological magnitude (|fold-change| ≥ 3.
    0 installs
58. ▌
    Microbial Metabolomics Phage Impact Assessment · holobiomicslab

    Use when you have normalized peak intensities (with assigned molecular formulas) from FT-ICR MS analysis of treated and control bacterial samples (or environmental microbial communities), grouped by two or more treatment factors (e.g., phage type: HP1, HS2, control;
    0 installs
59. ▌
    Model Training And Hyperparameter Optimization · holobiomicslab

    Use when you have raw co-elution profiles (27 fractions × 2+ proteins per pair) and a gold-standard PPI reference set, want to avoid manual feature engineering, and need to handle severe class imbalance (negative PPIs >> positive PPIs).
    0 installs
60. ▌
    Molecular Graph Construction Pytorch Geometric · holobiomicslab

    Use when when you have parsed molecular structures (SMILES or SDF) and need to represent them as attributed graphs for neural network models that accept graph-based inputs. Specifically applicable when your architecture requires dual representations (e.
    0 installs
61. ▌
    Msi Metadata Harmonization Across Image Stacks · holobiomicslab

    Use when you have processed and quantified MSI data from one or more imzML files in LipidQMap and need to export them as a unified, standards-compliant HDF5 container that preserves feature-by-pixel intensity matrices, per-feature lipid annotations (m/z, lipid class, adduct, neutral ID), per-pixel.
    0 installs
62. ▌
    Multi Backend Plot Generation And Benchmarking · holobiomicslab

    Use when when you have a suite of Sphinx gallery example scripts targeting multiple plotting library backends and need to verify that all examples execute successfully within expected time constraints and produce output across matplotlib (static), bokeh (interactive), and plotly (interactive).
    0 installs
63. ▌
    Multiple Hypothesis Correction In Metabolomics · holobiomicslab

    Use when after computing raw p-values from differential metabolomics analysis or Fisher's exact test enrichment, and before reporting significant pathways or metabolites. Essential when testing multiple metabolites against multiple pathway hypotheses (e.
    0 installs
64. ▌
    Mzml Spectrum Chromatogram Object Construction · holobiomicslab

    Use when you have an indexed gzip–compressed mzML file (mzML.gz with internal index structure) and need to retrieve and work with individual spectra or chromatograms by integer index without decompressing the entire file.
    0 installs
65. ▌
    P Value And Confidence Interval Interpretation · holobiomicslab

    Use when after running gentab_lm_long with mode='lm' to obtain a results table for multiple metabolomic features.
    0 installs
66. ▌
    Quality Control Metric Threshold Configuration · holobiomicslab

    Use when you have a SummarizedExperiment object from a metabolomics study with compound peak areas, internal standard assignments, and sample type annotations (QC, Study, Calibration, Blank), and you need to decide which samples and compounds are reportable.
    0 installs
67. ▌
    Redundant Node Removal And Edge Classification · holobiomicslab

    Use when after network partitioning, when you have identified connected subnetworks of features matched by isotope or adduct patterns and need to sanitize and categorize the relationships before tree construction. Use it when redundant features (e.
    0 installs
68. ▌
    Reproducibility Signal Detection Nonparametric · holobiomicslab

    Use when when you have high-dimensional replicate experimental data (e.g., metabolomics, proteomics, genomics assays) where technical or biological variability threatens reproducibility, and you need to distinguish genuine reproducible signals from noise without assuming normality.
    0 installs
69. ▌
    Sequential And Random Access Dual Mode Support · holobiomicslab

    Use when when parsing mzML or other blockwise-structured scientific data files where analysis requires both sequential scanning (e.g., iterating all spectra) and random direct access by identifier (e.
    0 installs
70. ▌
    Spectrum Metadata Normalization Across Formats · holobiomicslab

    Use when you have mass-spectrometry data files in mixed formats (e.
    0 installs
71. ▌
    Statistical Result Interpretation And Plotting · holobiomicslab

    Use when after statistical analysis has produced a results table with lipid identities, quantitative expression values, p-values, fold-changes, and experimental condition labels.
    0 installs
72. ▌
    Statistical Significance Threshold Application · holobiomicslab

    Use when you have generated omu_summary or anova_function output (a dataframe with padj values for all tested metabolites) and need to subset compounds for class-specific frequency counting, fold-change analysis, or visualization.
    0 installs
73. ▌
    Statistical Threshold Application Metabolomics · holobiomicslab

    Use when when you have completed a weighted meta-analysis of metabolomic studies using amanida and need to isolate robust, reproducible metabolite signals from the combined results.
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74. ▌
    Temporal Signal Drift Detection And Adjustment · holobiomicslab

    Use when raw MS quantification data (feature-by-sample intensity matrix) shows systematic variation in detector response across the run sequence—i.e., when the same analyte produces different intensities at different timepoints in the measurement despite constant sample concentration.
    0 installs
75. ▌
    Variable Importance Ranking And Interpretation · holobiomicslab

    Use when after fitting a random forest classifier to metabolomics count data with a binary or multiclass grouping variable (e.
    0 installs
76. ▌
    Gene Identifier Deduplication And Filtering · holobiomicslab

    Use when when loading gene expression data (e.g., from GEO via getGEO or microarray ExpressionSet objects) that contains duplicate rows mapped to the same Gene ID, missing gene identifiers, or identifiers encoded with placeholder strings ('///') that indicate failed or ambiguous annotation.
    0 installs
77. ▌
    Multi Conditional Data Coregulation Scoring · holobiomicslab

    Use when you have a normalized gene expression matrix (bulk RNA-seq or microarray) from a time-course or multi-condition experiment and need to quantify whether known gene sets (pathways, functional modules) show statistically significant coordinated expression changes.
    0 installs
78. ▌
    Single Cell Graph Construction Neighborhood · holobiomicslab

    Use when you have preprocessed single-cell RNA-seq data (normalized and dimensionality-reduced via PCA) and need to establish cell-to-cell connectivity for trajectory inference, clustering validation, or graph-based visualization.
    0 installs
79. ▌
    Spatial Coordinate Indexing Dense To Sparse · holobiomicslab

    Use when you have computed k-nearest neighbors for spatial coordinates (e.g., via pynndescent or another NN backend) and need to store the resulting adjacency and distance information in a memory-efficient format compatible with downstream graph algorithms.
    0 installs
80. ▌
    Statistical Comparison P Value Conservation · holobiomicslab

    Use when you have run the same pathway enrichment analysis (e.
    0 installs
81. ▌
    Test Failure Diagnosis And Logging Analysis · holobiomicslab

    Use when you have modified the Scanpy codebase (e.g., added a feature or bugfix) and need to confirm that all unit and integration tests pass before submitting a pull request, or when a CI workflow fails and you need to reproduce the failure locally to diagnose the root cause.
    0 installs
82. ▌
    Annotation Quality Filtering By Cosine Similarity · holobiomicslab

    Use when you have in silico annotations (e.g. from GNPS, timaR, or SIRIUS) paired with experimental MS/MS spectra and need to select only the highest-confidence structural matches.
    0 installs
83. ▌
    Mirror Plot Visualization For Spectrum Comparison · holobiomicslab

    Use when after computing compareSpectra similarity scores between an experimental consensus MS2 spectrum and candidate reference spectra (e.
    0 installs
84. ▌
    Least Squares Optimization Spectral Deconvolution · holobiomicslab

    Use when after GCMSFormer has predicted the pure mass spectral matrix S from overlapped GC-MS peaks.
    0 installs
85. ▌
    Missing Fraction Quality Filtering For Embeddings · holobiomicslab

    Use when after converting MS/MS spectra to fixed-length vector representations using a pre-trained Word2Vec model (as in Spec2Vec), filter spectra before computing similarity scores to flag those where a large fraction of the observed intensity comes from peaks or neutral losses not present in the.
    0 installs
86. ▌
    Parallel Computation For Large Library Processing · holobiomicslab

    Use when your input consists of multiple large MSP files (hundreds of megabytes) with associated structure folders containing hundreds of thousands of MOL or SDF files that require sequential processing steps (structure extraction, SMILES matching, RI assignment).
    0 installs
87. ▌
    Peak Intensity Normalization Weighted Aggregation · holobiomicslab

    Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments without allowing a single dominant peak to overwhelm the learned word associations.
    0 installs
88. ▌
    Adduct Signature Identification Mass Spectrometry · holobiomicslab

    Use when you have statistically significant LC-MS features (e.g., filtered by p-value < 0.01) from multi-assay metabolomics datasets and need to group features that represent the same metabolite ionized under different ESI conditions (e.g., [M+H]+, [M+Na]+, [M+NH4]+).
    0 installs
89. ▌
    Bayesian Meta Learning Chromatographic Projection · holobiomicslab

    Use when you have experimental retention times (RTs) for a small set of calibration molecules (≥10) measured on both a source chromatographic method and a target method, and you need to predict RTs for candidate metabolites on the target method to rank annotation candidates.
    0 installs
90. ▌
    Comparative Performance Evaluation Across Methods · holobiomicslab

    Use when when you have developed a new spectral similarity scoring method and need to quantify its retrieval performance relative to established methods (e.g., modified cosine, Spec2Vec). Use this skill if you have: (1) a test set of spectra with ground-truth structural similarity labels (e.
    0 installs
91. ▌
    Computational Resource Profiling And Benchmarking · holobiomicslab

    Use when when evaluating a new or updated version of a data processing tool (especially asari or similar LC-MS workflows) before production deployment, or when verifying claims about scalability, memory efficiency, or throughput on specific hardware classes (e.g., ≤16 GB RAM single-core systems).
    0 installs
92. ▌
    Cross Language Function Invocation And Validation · holobiomicslab

    Use when your R-based Spectra analysis workflow requires a specific mass spectrometry algorithm (e.g., CosineGreedy similarity scoring, spectral normalization, or advanced filtering) that is available only in a Python MS package (matchms, spectrum_utils) and not yet in native R.
    0 installs
93. ▌
    Drop Down Interface Population From Filtered Data · holobiomicslab

    Use when you have search results from DIA mass spectrometry data containing feature Q-value scores and need to restrict the analyte choices available to users in a GUI to only those meeting a 1% feature Q-value threshold.
    0 installs
94. ▌
    Feature Table Moniker Registration And Versioning · holobiomicslab

    Use when after Asari completes feature detection and produces multiple feature table variants (full and quality-filtered preferred tables) from centroid mzML files within a PCPFM experiment.
    0 installs
95. ▌
    File Format Conversion Peak Picking To Lipidmatch · 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.
    0 installs
96. ▌
    Fragmentation Strategy Comparison Across Datasets · holobiomicslab

    Use when you have extracted a chemical mixture from a real mzML acquisition (e.g., Beer1pos), simulated the same chemicals through ViMMS using a chosen controller (e.
    0 installs
97. ▌
    Hierarchical Clustering Dendrogram Interpretation · 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.
    0 installs
98. ▌
    Ion Mobility Mass Spectrometry Data Preprocessing · holobiomicslab

    Use when when you have raw IM-MS data from drift tube (DT) or SLIM instruments in Agilent MassHunter (.
    0 installs
99. ▌
    Mass Spectrometry Annotation Engine Customization · holobiomicslab

    Use when when you have baseline MS/MS peak annotations from a known compound but need to refine them using newly available structural information (e.
    0 installs
100. ▌
     Mass Spectrometry Fragmentation Pattern Discovery · holobiomicslab

     Use when you have preprocessed MS/MS spectral data (in positive or negative ion mode) and seek to discover recurring fragmentation and neutral-loss patterns that characterize molecular substructures across a dataset.
     0 installs