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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Regression Model Training Comparison · holobiomicslab

   Use when you have a labeled dataset of molecular structures with experimental continuous outcomes (e.
   0 installs
2. ▌
   Retention Time Mz Alignment Matching · holobiomicslab

   Use when you have extracted feature tables (m/z, intensity, retention time) from multiple breath samples (mzML or mzXML files) via feature extraction, and need to identify which features represent the same volatile organic compound (VOC) across samples to enable cross-sample intensity comparisons.
   0 installs
3. ▌
   Retention Time Mz Coordinate Mapping · holobiomicslab

   Use when when you have mass-spectrometry data in tabular form (Pandas DataFrame) with columns for m/z, retention time or ion mobility, and intensity, and you need to visualize the 2D distribution of peaks to assess peak separation, detect co-elution, or examine chromatographic and mass resolution.
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4. ▌
   Retention Time Mz Feature Extraction · holobiomicslab

   Use when you have LC-HRMS profile-mode data (e.g., netCDF or mzML format) and need to convert detected or reference chromatographic peaks into fixed-size 2D arrays (rt × mz regions) to train or apply a convolutional neural network for peak classification and bounding-box prediction.
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5. ▌
   Rust Library Compilation And Testing · holobiomicslab

   Use when when you have access to Rust source code in a repository with a Cargo manifest (Cargo.toml) and need to verify that a library's read and write APIs produce byte-equivalent or structurally equivalent output.
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6. ▌
   Self Contained Pipeline Construction · holobiomicslab

   Use when when you have metabolomics datasets (loaded as SummarizedExperiment objects) and need to apply a sequence of data-processing and analytical steps (e.
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7. ▌
   Smiles String Parsing And Validation · holobiomicslab

   Use when when you have SMILES strings as input to a molecular machine learning pipeline (e.g., retention time prediction, spectral prediction) and need to convert them into structured molecular representations before calculating descriptors or constructing molecular graphs.
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8. ▌
   Sparse Inverse Covariance Estimation · holobiomicslab

   Use when when you have a feature matrix (samples × features) and need to infer sparse conditional dependencies among features—particularly when the number of features is comparable to or exceeds sample size, and you want to identify which features are directly related after accounting for all.
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9. ▌
   Spatial Spot Coordinate Registration · holobiomicslab

   Use when when you have paired spatial transcriptome and metabolome datasets with spot-based coordinates that need to be aligned for multi-modal integration.
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10. ▌
    Spectral Database Search And Scoring · holobiomicslab

    Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected) from DI-MS, ASAP-MS, or LDI-MS instruments and need to identify unknown samples by comparing their spectral fingerprints against a validated reference database of known species or compounds.
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11. ▌
    Spectral Ion Matching Across Vendors · holobiomicslab

    Use when you have raw line-scan MSI data from any supported vendor (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .
    0 installs
12. ▌
    Spectral Peak Parent Product Pairing · holobiomicslab

    Use when you have mass spectrometry imaging data with a histogram of pairwise mass differences that have already been matched to known adducts (via adductMatch), and you need to retrieve the actual mass peak pairs corresponding to a specific adduct of interest—particularly when you want to test.
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13. ▌
    Spectral Smoothing Method Comparison · holobiomicslab

    Use when when you have raw mass spectra in an MSImagingArrays object and need to decide between Savitzky-Golay and Gaussian smoothing methods based on their effects on peak shape fidelity and baseline noise. Apply this skill when peak preservation is a priority (e.
    0 installs
14. ▌
    Spike Artifact Detection And Removal · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that exhibits isolated high-intensity noise artifacts or instrumental artifacts that appear as discrete, non-continuous signals in the retention time, ion mobility, or m/z dimensions.
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15. ▌
    Stochastic Weight Averaging Ensemble · holobiomicslab

    Use when training a heavily regularized deep neural network on molecular property prediction tasks (e.g., retention time prediction) where you observe signs of overfitting despite L1/L2 penalties, or when you need to reduce variance in predictions on held-out test sets.
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16. ▌
    Strain Correlation Score Computation · holobiomicslab

    Use when when you have paired genomics and metabolomics data from multiple strains (e.g., from Paired Omics Data Platform), have clustered BGCs into GCFs and detected molecular features, and need to score all potential GCF–MF links to prioritise true biosynthetic relationships.
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17. ▌
    Structure Standardization Validation · holobiomicslab

    Use when you have raw or heterogeneous molecular structure inputs (SMILES strings or SDF files) that will be used for fingerprint calculation, descriptor extraction, or retention time prediction modeling.
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18. ▌
    Tensorflow Model Metadata Inspection · holobiomicslab

    Use when deploying a TensorFlow model through TensorFlow Serving and you need to verify that the exposed model's input layer names ('input_2048' and 'input_4096') and output layer name ('output') match the specifications required by downstream code.
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19. ▌
    Training Convergence Loss Monitoring · holobiomicslab

    Use when executing a multi-stage deep learning pipeline (pretraining → fine-tuning → alignment) where each stage loads a checkpoint from the previous stage and you need to confirm that loss is decreasing monotonically within each stage, that checkpoints are being saved, and that no training.
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20. ▌
    Variance Stabilization Normalization · holobiomicslab

    Use when after k-nearest neighbor imputation (cutoff ≥0.6 data retention) and outlier sample removal have been completed on your MultiAssayExperiment object.
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21. ▌
    Web Application Server Logic Mapping · holobiomicslab

    Use when you are wrapping an existing R package or analytical library in a web interface and need to connect UI form inputs (file uploads, parameter selections, configuration checkboxes) to the backend computation functions and render their outputs reactively.
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22. ▌
    XML Spectrum Element Deserialization · holobiomicslab

    Use when when you have retrieved a decompressed XML data block from an indexed gzip file (via GSGR bracket notation) and need to convert that raw XML string into a usable Python spectrum or chromatogram object for downstream analysis, filtering, or comparison.
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23. ▌
    Graph Builder Subclassing Squidpy · holobiomicslab

    Use when you have spatial molecular data (e.g., coordinates from microscopy or sequencing assays stored in an AnnData object), you need to compute a k-nearest-neighbor graph for spatial statistics (e.
    0 installs
24. ▌
    Moderated T Statistic Computation · holobiomicslab

    Use when you have a fitted linear model (lmFit object) from microarray, RNA-seq, qPCR, or proteomics data and need to test for differential expression across genes while maintaining statistical stability despite having few biological replicates or arrays.
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25. ▌
    Rna Seq Abundance Matrix Handling · holobiomicslab

    Use when you have transcript-level quantification output files (quant.sf, quant.gz) from salmon, kallisto, sailfish, or oarfish and need to produce gene-level count matrices, abundance matrices, and length-based offsets for differential expression analysis in DESeq2, edgeR, or limma-voom.
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26. ▌
    Rna Seq Quantification Validation · holobiomicslab

    Use when you have quantification output from two versions or implementations of the same tool (e.g., C++ vs. Rust rewrites, pre- and post-bugfix releases) and need to verify that they produce equivalent results before deploying the new version.
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27. ▌
    Sam Bam Mapping Record Inspection · holobiomicslab

    Use when after quantifying the same read set with two versions of a mapping/quantification tool (e.g., C++ salmon 1.11.
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28. ▌
    Sam Record Parsing And Validation · holobiomicslab

    Use when salmon quant is run with the --writeMappings/-z flag and you need to verify that all mapped reads appear in the SAM output file.
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29. ▌
    Single Cell Rna Seq Normalization · holobiomicslab

    Use when immediately after loading raw single-cell gene expression count matrices (AnnData objects) and before identifying highly variable genes or performing dimensionality reduction.
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30. ▌
    Sparse Matrix Csr Format Assembly · holobiomicslab

    Use when when you have computed k-nearest neighbor indices and distances (e.
    0 installs
31. ▌
    Spatial Statistics Interpretation · holobiomicslab

    Use when when you have a spatial molecular dataset (e.g., Visium, MERFISH) with categorical cell-type or feature annotations and want to test whether specific categories are preferentially located near or away from each other in tissue space, beyond what random spatial distribution would predict.
    0 installs
32. ▌
    Statistical Ranking Wilcoxon Test · holobiomicslab

    Use when when you have leiden or louvain cluster assignments in single-cell data (stored in adata.obs) and need to identify cluster-specific marker genes.
    0 installs
33. ▌
    Temporal Gene Expression Dynamics · holobiomicslab

    Use when you have time-ordered gene expression data (e.
    0 installs
34. ▌
    Transcript Level Abundance Import · holobiomicslab

    Use when you have transcript-level quantification files (quant.sf.gz or quant.gz) from salmon, sailfish, kallisto, or oarfish and need to aggregate them into gene-level or transcript-level count, abundance, and length matrices for input to DESeq2, edgeR, or limma-voom.
    0 installs
35. ▌
    Chemical Annotation Matrix Construction · holobiomicslab

    Use when you have selected a subset of public tandem MS files from ReDU/MassIVE that have been processed through GNPS spectral library matching, and you need to organize their chemical annotations into a matrix (rows = files, columns = annotated features) before performing PCA or other multivariate.
    0 installs
36. ▌
    Electron Ionization Spectral Comparison · holobiomicslab

    Use when you have a query electron ionization (EI) mass spectrum in msp format and wish to identify it by matching against a reference spectral library. Apply this skill when you need ranked similarity scores between the query and each library entry to prioritize candidate identifications.
    0 installs
37. ▌
    Ms Spectra Extraction And Preprocessing · holobiomicslab

    Use when you have raw LC-MS/MS data in mzML or mzXML format and need to: (1) identify the top-abundance MS1 signals in an LC run, (2) compute a single scalar metric (separation efficiency) that summarizes how well compounds are resolved across the chromatogram, and (3) feed that metric into a.
    0 installs
38. ▌
    Parameter Driven Preprocessing Pipeline · holobiomicslab

    Use when you have converted mass spectrometry data in mzXML or mzML format and need to extract metabolic features via region-of-interest (ROI) search followed by preprocessing and augmentation.
    0 installs
39. ▌
    Reconstruction Algorithm Implementation · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry data (feature matrices or transient files) acquired at lower mass resolution or with signal degradation, and you possess high-resolution reference MSI data or simulated ground truth to train a reconstruction model.
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40. ▌
    Analyte Discrimination Machine Learning · holobiomicslab

    Use when you have raw chromatography–mass spectrometry data (GC-MS or LC-MS) in 2D m/z–retention time format and need to identify and discriminate multiple analytes while avoiding false peak detections inherent in conventional peak picking.
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41. ▌
    Baseline Correction Algorithm Selection · holobiomicslab

    Use when when you have imported a raw GCxGC-MS chromatogram as a 2D-TIC (2D Total Intensity Chromatogram) object from a NetCDF file and observe steady or increasing baseline intensity caused by instrumental contamination, column bleeding, or thermal drift.
    0 installs
42. ▌
    Chromatographic Modality Classification · holobiomicslab

    Use when when ingesting raw or vendor-format mass spectrometry data files of unknown or mixed acquisition modality, and you need to automatically determine whether the input originated from liquid chromatography (LC), gas chromatography (GC), ion mobility spectrometry (IMS), or MS imaging (e.
    0 installs
43. ▌
    Chromatographic Peak Overlap Resolution · holobiomicslab

    Use when analyzing GC-MS data containing overlapping chromatographic peaks—a common scenario in untargeted metabolomics and environmental screening where sample complexity or chromatographic resolution limitations cause co-elution of structurally similar or temporally proximate compounds.
    0 installs
44. ▌
    Chromatographic Retention Time Matching · holobiomicslab

    Use when you have GC-MS data with multiple replicate injections or samples, need to identify a predefined set of query chemicals by name, and want to consolidate all instances of those chemicals (which may appear with varying match factors or peak areas across different samples or injection.
    0 installs
45. ▌
    Ei Spectral Library Parsing And Merging · holobiomicslab

    Use when you need to build a comprehensive EI spectral reference library for GC-MS compound identification in MS-DIAL, starting from raw downloads of NIST, RIKEN, MoNA, or SWGDRUG libraries that have inconsistent metadata organization (SMILES in different fields or absent, RI values missing or.
    0 installs
46. ▌
    Injection Order Direction Specification · holobiomicslab

    Use when when configuring a multi-well plate design (96-well, 384-well, or other format) in InjectionDesign for LC/GC-MS analysis and you need to specify whether analytical samples and QC controls should be injected row-by-row or column-by-column.
    0 installs
47. ▌
    Mass Error And Retention Time Alignment · holobiomicslab

    Use when when processing low- or high-resolution mass spectrometry data (mzML profile or centroided format) for isotopologue quantification and you need to match detected peaks to a targeted formulaTable of compounds.
    0 installs
48. ▌
    Mass Spectrometry Spectrum Tokenization · holobiomicslab

    Use when you have pre-processed MS/MS spectra and need to prepare them for word-embedding-based similarity methods (e.g., Spec2Vec).
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49. ▌
    Mass Spectrum Extraction And Formatting · holobiomicslab

    Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical component prior to molecular networking, spectral matching, or metabolite identification workflows.
    0 installs
50. ▌
    Multi Dimensional Sample Stratification · holobiomicslab

    Use when you have a parsed sample list with metadata (sample IDs, classification dimensions, QC designations) and need to generate a physical injection-plate layout that (1) will be run across multiple batches, (2) has a known confounding dimension (e.
    0 installs
51. ▌
    Neutral Loss Calculation From Precursor · holobiomicslab

    Use when when converting MS/MS spectra into spectral documents for Spec2Vec embedding, and you want to capture chemical relationships implicit in the fragmentation pattern (e.g., loss of water, ammonia, or CO2) that may correlate with structural similarity. Use this when the neutral loss range (5.
    0 installs
52. ▌
    Peak Integration Parameter Optimization · holobiomicslab

    Use when after peak detection and clustering have been completed on aligned and baseline-corrected GC-IMS data, and before imputation or statistical analysis.
    0 installs
53. ▌
    Retention Index Calibration Application · holobiomicslab

    Use when when processing GC-MS data where retention time alone is insufficient for compound identification due to instrument drift or method variation, and you need to match detected peaks against a spectral library (e.
    0 installs
54. ▌
    Retention Time Alignment Across Batches · holobiomicslab

    Use when you have extracted peaks from multiple LC/HRMS batches (n > 500 samples across different analytical runs or days) and observe systematic retention time drift or offset between batches, preventing reliable cross-batch peak matching on m/z and RT alone.
    0 installs
55. ▌
    Separation Technique Workflow Alignment · 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.
    0 installs
56. ▌
    Signal Acquisition Error Quantification · holobiomicslab

    Use when you have processed the same GC–MS dataset (m/z vs retention time) through two independent signal acquisition pipelines and need to compute and compare their detection accuracy. Use this skill when one method (e.
    0 installs
57. ▌
    Spectral Similarity Scoring Computation · holobiomicslab

    Use when you have a query spectrum (or set of query spectra) and need to rank candidate library spectra by their likelihood of sharing the same chemical structure.
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58. ▌
    Aif Spectrum Fragment Database Matching · holobiomicslab

    Use when you have a feature table from untargeted LC–MS all-ion fragmentation (AIF) chromatograms processed by xcms and RamClustR, and you want to assign metabolite annotations to individual features by comparing their experimental MS/MS spectra against curated fragment libraries (e.
    0 installs
59. ▌
    Bipartite Graph Maximum Weight Matching · holobiomicslab

    Use when you have two MS/MS fragmentation spectra with fragment ion lists and computed pairwise mass differences (m/z deltas) between them, and you need to find the alignment of ion pairs that: (1) does not reuse any ion from either spectrum, (2) maximizes total matching quality (e.
    0 installs
60. ▌
    Candidate Metadata Record Serialization · holobiomicslab

    Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage, sharing, and interpretation.
    0 installs
61. ▌
    Changelog Maintenance And Documentation · holobiomicslab

    Use when you have added or modified user-facing parameters to a model class (such as L1/L2 regularization in SiameseModel), written unit tests to verify the new functionality, and need to communicate these changes to users and maintain a historical record.
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62. ▌
    Chemical Structure Annotation Retrieval · holobiomicslab

    Use when you have MS/MS spectra from public repositories (e.g., GNPS) that lack chemical structure annotations (InChI/SMILES), or have incomplete/inconsistent annotations.
    0 installs
63. ▌
    Chromatogram Peak Matching Registration · holobiomicslab

    Use when you have multiple LC-MS samples in mzML or mzXML format with variable retention times, at least one designated as a quality control (QC) reference file, and you need to correct for RT drift before peak/feature detection.
    0 installs
64. ▌
    Chromatographic Peak Quality Assessment · holobiomicslab

    Use when when you have a feature table (CSV with m/z and retention time columns) and corresponding LC-MS raw data files (.mzXML or .mzML) from an untargeted metabolomics experiment, and need to filter out spurious peaks before downstream statistical or biological interpretation.
    0 installs
65. ▌
    Chunk Wise Data Processing Optimization · holobiomicslab

    Use when you have a large mass spectrometry dataset stored across multiple mzML, mzXML, or CDF files and need to perform operations (e.g., normalization, filtering, feature extraction) on the full dataset but memory constraints prevent loading all peak data simultaneously.
    0 installs
66. ▌
    CLI Invocation With File Path Arguments · holobiomicslab

    Use when you have vendor raw mass spectrometry data files (e.g., .raw, .d, .wiff2 formats) that must be converted to mzML or Aird format, and you need to automate the conversion in a batch workflow, Docker container, or non-interactive environment.
    0 installs
67. ▌
    Collision Cross Section Calibration Ccs · holobiomicslab

    Use when when you have acquired ion mobility–mass spectrometry data (drift time and m/z dimensions) and need to convert observed drift times into calibrated CCS values.
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68. ▌
    Computational Environment Configuration · holobiomicslab

    Use when at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers.
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69. ▌
    Conformer Ensemble Generation Via Crest · holobiomicslab

    Use when you have a molecular geometry (XYZ format) and need to explore its conformational space prior to quantum mechanical property calculation or when QCxMS2 workflow requires an ensemble of low-energy structures to enable systematic fragmentation pathways for EI mass spectrum simulation.
    0 installs
70. ▌
    Consensus Classification Reconciliation · holobiomicslab

    Use when you have spectral features annotated by both in silico structural prediction tools (e.g., SIRIUS/CANOPUS) and spectral library matching (GNPS), and you need a single authoritative chemical classification per feature rather than a list of competing candidates.
    0 installs
71. ▌
    Correlation Cluster Network Integration · holobiomicslab

    Use when after identifying structural clusters (isotopologue groups, adduct groups, and cross-assay links) and assigning features to correlation clusters via hierarchical clustering.
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72. ▌
    Cross Dataset Generalization Assessment · holobiomicslab

    Use when you have a pre-trained MS/MS spectral embedding model evaluated on one or more source datasets (GNPS, MoNA, MTBLS1572) and need to verify that it performs well on independent, high-quality curated spectral libraries to claim robustness.
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73. ▌
    Cross Language Interface Implementation · holobiomicslab

    Use when you have a mature R analysis pipeline (e.g., using Spectra objects for MS data) but need access to specialized algorithms or calculations available only in Python libraries (e.g., CosineGreedy similarity from matchms).
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74. ▌
    CSV Serialization For Mass Spectrometry · holobiomicslab

    Use when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to export it for use in either Excalibur-based DDA experiments on an Orbitrap mass spectrometer, or in Skyline for targeted.
    0 installs
75. ▌
    Dense Neural Network Layer Construction · holobiomicslab

    Use when when you have a binned MS/MS spectrum vector (e.g., 9948-dimensional input from 10,000 equally-spaced m/z bins in the 10–1000 Da range) and need to compress it into a learned latent representation (e.
    0 installs
76. ▌
    Distance Matrix Generation From Indexes · holobiomicslab

    Use when you have pre-computed feature-hashed spectrum vectors and nearest neighbor indexes constructed from those vectors, and you need a pairwise distance matrix as input to density-based clustering (e.g., DBSCAN).
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77. ▌
    Duplicate Feature Detection And Removal · holobiomicslab

    Use when you have peak-picked LC-MS data with multiple features that may represent the same metabolite detected at slightly different m/z or retention time values due to instrument precision limits, isotope variants, or adduct forms.
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78. ▌
    Entropy Search Algorithm Implementation · holobiomicslab

    Use when you need to search one or more query MS/MS spectra against large spectral libraries (hundreds of thousands to millions of spectra) and require real-time or near-real-time compound identification.
    0 installs
79. ▌
    False Positive Mitigation In Annotation · holobiomicslab

    Use when you have implemented an automated feature annotation or adduct detection module and need to verify that assigned labels (e.g., [M+NH4]+, [M+K]+, [M+H2O+H]+, [M-H2O+H]+) are accurate and do not produce erroneous assignments on a reference feature set.
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80. ▌
    Fatty Acyl Chain Variant Identification · holobiomicslab

    Use when when a metabolite feature has been assigned a top-rank lipid annotation (e.g., LPC(14:0)) but you need to assess whether related lipid species containing the same fatty acyl chain(s) (e.g., PC fragments with 14:0 acyl chains) also match the observed spectrum with lower scores.
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81. ▌
    Feature Missingness Threshold Filtering · holobiomicslab

    Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage before feature alignment.
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82. ▌
    Feature Similarity Network Construction · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering, containing m/z, retention time, and peak intensity metrics) and need to identify groups of co-eluting or structurally similar features before extracting parental signals or annotating metabolites.
    0 installs
83. ▌
    Feature Table Alignment And Integration · holobiomicslab

    Use when you have aligned feature tables (CSV format) paired with MS2 spectral data (MGF or mzML files) and need to compare chemodiverse samples with poor feature overlap or strong retention-time shifts across different LC methods or mass spectrometer technologies (e.g., Orbitrap vs. Q-ToF).
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84. ▌
    Feature Table Blank Intensity Detection · holobiomicslab

    Use when after loading an MZmine3-exported feature quantification table from non-targeted LC-MS/MS data when your experiment includes blank (negative control) samples and you need to remove features attributable to contamination or instrument background before downstream statistical analysis.
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85. ▌
    Feature Wise Spectrum Count Aggregation · holobiomicslab

    Use when when you have extracted concatenated MS/MS spectra for multiple features from replicate mzML files and need to verify that a TIC-based filtering step (e.g., top x% TIC extraction) reduces per-feature spectrum counts to expected target levels.
    0 installs
86. ▌
    Filter Outcome Aggregation And Counting · holobiomicslab

    Use when after applying one or more mpactr filters (mispicked, group, cv, insource) to a feature table, you need to quantify the distribution of ions by their pass/fail status across filters to understand filtering impact, identify potential over-filtering, or communicate QC results via treemap or.
    0 installs
87. ▌
    Formula Annotation Capping By Frequency · holobiomicslab

    Use when when preparing multi-formula MS/MS training data for a rescore model, if the raw positive examples show extreme imbalance (some formulas represented by hundreds of spectra while others have only a few).
    0 installs
88. ▌
    Formula Assignment In Mass Spectrometry · holobiomicslab

    Use when you have m/z values from mass spectrometry imaging (or similar MSI experiments) and need to assign molecular formulae to them. This is especially valuable when working with spatially-resolved metabolomics data where annotation precision lags behind traditional LC-MS approaches.
    0 installs
89. ▌
    Fragmentation Pattern Spectral Matching · holobiomicslab

    Use when when you have detected m/z values from LC-IM-MS/MS that match a candidate CCS prediction database but require structural confirmation. Apply this skill to disambiguate isomers (e.
    0 installs
90. ▌
    Gnps Data Format Conversion And Mapping · holobiomicslab

    Use when you have GNPS molecular networking output (from GNPS1 at https://gnps.ucsd.edu or GNPS2 at https://gnps2.org) that must be integrated with antiSMASH BGC data and MIBiG metadata for natural product mining.
    0 installs
91. ▌
    Graphical Time Warping Parameter Tuning · holobiomicslab

    Use when your XCMS-processed LC-MS dataset exhibits retention-time drift or misalignment artifacts—particularly when analyzing hundreds of samples, data acquisition spans longer than one week, or you observe feature groups with inconsistent m/z or RT that XCMS grouped under a single global warping.
    0 installs
92. ▌
    Instrument Agnostic Feature Engineering · holobiomicslab

    Use when you have DIA raw mass spectrometry files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) and need to build a single machine learning model to predict data quality across all platforms, or when you need to compare quality characteristics of files produced by different.
    0 installs
93. ▌
    Interactive Plot Construction Mass Spec · holobiomicslab

    Use when after LC-MS data has been converted to mzML format and processed through peak detection (e.g., MS-DIAL output) to yield a feature table with internal standard identifications, retention times, m/z values, and intensity measurements across multiple samples.
    0 installs
94. ▌
    Ion Current Calculation And Aggregation · holobiomicslab

    Use when when raw LC-MS feature tables exhibit inter-sample intensity variation due to instrument sensitivity drift, sample ionization efficiency differences, or loading differences, and you need to normalize intensities to a common reference scale before downstream statistical analysis.
    0 installs
95. ▌
    Isotopologue Adduct Link Identification · holobiomicslab

    Use when you have selected statistically significant features from multi-assay untargeted LC-MS metabolomics data and need to group them by structural relationships defined by their mass-to-charge ratios (m/z) and retention times (RT).
    0 installs
96. ▌
    JSON Serialization Of Metabolomics Data · holobiomicslab

    Use when after pre-annotation grouping (e.g., via khipu) has assigned features to empirical compounds, or when exporting feature tables and metadata from asari for downstream analysis in MetaboAnalyst or custom R/Python workflows.
    0 installs
97. ▌
    K Fold Cross Validation Model Selection · holobiomicslab

    Use when when fitting a multi-block PLS discriminant model on multi-assay LC-MS metabolomics data and you need to determine the number of latent variables to retain without overfitting.
    0 installs
98. ▌
    Knowledge Data Driven Layer Integration · holobiomicslab

    Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.
    0 installs
99. ▌
    Lipid Derivatization Chemistry Modeling · holobiomicslab

    Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before experimental acquisition, or to build a reference spectral library for isomer-level sterol identification in tissue samples.
    0 installs
100. ▌
     Lipid Fragmentation Pattern Application · holobiomicslab

     Use when you have an enumerated list of lipid species (identified by class, fatty acid composition, and chain length) and need to generate theoretical precursor m/z values, fragment ion masses, and relative intensities for targeted or untargeted lipidomics experiments.
     0 installs