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HolobiomicsLab

@holobiomicslab source repo

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• 7.4k skills
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• 2 days ago last updated

1. ▌
   Isotope Display Logic Modification · holobiomicslab

   Use when when isotope visibility in the Maven GUI isotopes widget does not respect user selections made in application preferences, or when you need to restrict the widget display to a user-configured subset of available isotopes without modifying the underlying data model.
   0 installs
2. ▌
   JSON Data Structure Transformation · holobiomicslab

   Use when when you have intermediate JSON data in the Experiment Description Specification schema and need to convert it to a different JSON structure or a repository-specific format (e.g., mwTab for Metabolomics Workbench submission).
   0 installs
3. ▌
   Keras Tensorflow Model Compilation · holobiomicslab

   Use when you have defined a Keras model architecture (convolutional and dense layers) accepting raw mass spectrometry imaging data tensors and need to prepare it for training on tumor/non-tumor probabilistic classification without prior peak picking.
   0 installs
4. ▌
   Linear Model Formula Specification · holobiomicslab

   Use when when you have metabolomic feature intensities (dependent variables) and want to quantify how independent variables (e.
   0 installs
5. ▌
   Lipid Class Annotation And Parsing · holobiomicslab

   Use when immediately after loading raw lipid identifiers from LipidSearch or LIQUID output, or when importing lipidomic data from the Metabolomics Workbench.
   0 installs
6. ▌
   Lipid Nomenclature Standardization · holobiomicslab

   Use when you have lipid names or abbreviations sourced from multiple databases (HMDB, LIPID MAPS, LipidHome, RefMet, SwissLipids) or software tools (LipidSearch, MS-DIAL, LipidBlast, etc.), and you need to unify them into a single canonical identifier system to enable cross-database comparison.
   0 installs
7. ▌
   Logging And Audit Trail Generation · holobiomicslab

   Use when when implementing a metadata annotation pipeline for mass spectra that fetches values from multiple external services (e.
   0 installs
8. ▌
   Lossless Compression Decompression · holobiomicslab

   Use when when you have raw mzML or mzXML mass spectrometry files with uncompressed numeric arrays (not pre-compressed with zlib or msnumpress) and need to reduce file size for archival or transfer while guaranteeing that decompressed data is byte-identical to the original.
   0 installs
9. ▌
   Mass Spectrometry Data Preparation · holobiomicslab

   Use when you have raw mass spectrometry data in CSV or mzML format and need to visualize it using pyOpenMS-viz, or you are working with MS data that contains retention time (rt), m/z, intensity, and optionally ion mobility dimensions that must be structured as a Pandas DataFrame before plotting.
   0 installs
10. ▌
    Mass Spectrometry Metadata Parsing · holobiomicslab

    Use when you have a Thermo Fisher Orbitrap .raw file and need to programmatically inspect or validate its acquisition parameters (instrument type, total scan count, acquisition duration, file name) before extracting spectral data, or when you need to serialize metadata to JSON for data provenance.
    0 installs
11. ▌
    Mass Spectrometry Peak Enumeration · holobiomicslab

    Use when you have preprocessed MSI data (peaks already binned and normalized) and need to detect adduct formation patterns across the dataset.
    0 installs
12. ▌
    Maximum Score Selection Over Pairs · holobiomicslab

    Use when when you have individual pairwise scores (e.g., between BGCs and spectra) and need to rank composite links where one or both sides are collections (e.
    0 installs
13. ▌
    Metabolite Abundance Normalization · holobiomicslab

    Use when after loading a raw metabolite abundance table (rows=metabolites, columns=samples) from Metabolomics Workbench format and before mapping metabolites to pathway identifiers or computing enrichment statistics.
    0 installs
14. ▌
    Metabolite Benchmark Peak Matching · holobiomicslab

    Use when you have LC-HRMS mzML files processed by a non-targeted peak-detection tool (XCMS, MZmine 2/3, MS-DIAL, OpenMS, etc.) and want to quantify how many of a known set of target molecules (47+ compounds with isotopologues) were correctly detected, aligned, and preserved with intact isotopologue.
    0 installs
15. ▌
    Metabolite Data Log Transformation · holobiomicslab

    Use when you have raw or baseline-corrected metabolite abundance measurements from mass spectrometry and need to prepare them for batch effect correction (e.g., CordBat) or multivariate analysis (e.g., PCA).
    0 installs
16. ▌
    Metabolite Feature Standardization · holobiomicslab

    Use when after loading raw metabolomics measurement data (samples × metabolites matrix) into R but before computing covariance matrices or Jacobian analysis.
    0 installs
17. ▌
    Metabolite Fold Change Calculation · holobiomicslab

    Use when you have paired count data and metadata from a two-group metabolomics experiment (e.g., Strep vs Mock treatment) and need to identify which metabolites show significant abundance shifts.
    0 installs
18. ▌
    Metabolite Genomic Network Mapping · holobiomicslab

    Use when you have independent metabolomic GWAS results (metabolite p-values, effect sizes) and separate meta-genome GWAS results (variant p-values, effect sizes) from similar diseases or phenotypes, and you want to identify statistically enriched metabolite–gene co-occurrences without paired.
    0 installs
19. ▌
    Metabolite Kegg Pathway Enrichment · holobiomicslab

    Use when you have an annotated list of metabolite compounds (with associated m/z features or compound IDs) and want to determine which KEGG metabolic pathways are significantly enriched or depleted in your experimental samples.
    0 installs
20. ▌
    Metabolite Set Enrichment Analysis · holobiomicslab

    Use when you have differential metabolomics results (p-values and log2 fold changes) for a set of metabolites and want to identify which known metabolic pathways or metabolite sets show concerted enrichment in your condition of interest.
    0 installs
21. ▌
    Metabolomics Feature Cv Assessment · holobiomicslab

    Use when you have a feature intensity matrix from untargeted metabolomics (samples in rows, compounds in columns) and a sample legend identifying QC samples.
    0 installs
22. ▌
    Metabolomics Matrix Manipulation R · holobiomicslab

    Use when you have a log2-scaled metabolomics feature matrix in CSV format with samples in rows, metabolic features in columns, and batch identifiers in the first column, and you need to remove technical heterogeneity or drift across analytical batches before estimating biological mechanisms.
    0 installs
23. ▌
    Metadata Extraction And Population · holobiomicslab

    Use when when importing raw mass spectrometry data from files in supported formats (mzML, mzXML, msp, MGF, JSON, metabolomics-USI) and you need to extract and standardize metadata fields so that spectra are ready for metadata cleaning, validation, and comparative analysis.
    0 installs
24. ▌
    Metadata Structure Standardization · holobiomicslab

    Use when when you have experimental metadata (e.g., sample annotations, plate layouts, compound lists) with inconsistent or missing column names, non-standard field formats, or incomplete information required for downstream database queries (PubChem, DrugBank, LOTUS) or sequence generation for mass.
    0 installs
25. ▌
    Container Resource Allocation Tuning · holobiomicslab

    Use when deploying a containerized .NET Framework application (e.g., AirdPro) that performs computationally intensive batch operations such as vendor file conversion to Aird format.
    0 installs
26. ▌
    Containerized API Service Validation · holobiomicslab

    Use when after building and starting a Dockerized server via docker-compose orchestration, particularly when deploying machine learning inference services that depend on pre-trained models behind an API gateway.
    0 installs
27. ▌
    Correlation Network Characterization · holobiomicslab

    Use when after constructing a correlation-based network (adjacency matrix, edge list, or correlation-thresholded output) and you need to quantify its structural properties—such as which nodes are most central, how tightly clustered communities are, or how the network responds to perturbation.
    0 installs
28. ▌
    Cross Database Entity Reconciliation · holobiomicslab

    Use when you have chemical entity records scattered across two or more public repositories (e.g., HMDB, ChEMBL, PubChem, KEGG) and need a single authoritative, deduplicated knowledge base indexed by a queryable identifier (e.g., m/z value or chemical formula).
    0 installs
29. ▌
    Custom Mzml Index Pattern Definition · holobiomicslab

    Use when your mzML file contains custom or non-standard spectrum index identifiers that do not follow the default mzML indexing convention, and you need random-access retrieval of spectra by these identifiers.
    0 installs
30. ▌
    Data Quality Flagging And Annotation · holobiomicslab

    Use when after peak integration and feature alignment in metabolomic processing, when you have a feature table (rows=features, columns=samples) and need to identify which features are corrupted by processing artifacts (faulty peak integration, feature misalignment).
    0 installs
31. ▌
    Decoy Psm Identification And Tagging · holobiomicslab

    Use when ingesting PSM files from proteomics search engines (MS Amanda, MSGFPlus, MaxQuant, etc.) that contain a mixture of target and decoy PSMs, and you need to ensure accurate FDR calculation during or after rescoring.
    0 installs
32. ▌
    Derivatization Chemistry Enumeration · holobiomicslab

    Use when when performing metabolite identification in mass spectrometry imaging and the metabolites have been chemically derivatized with a known derivatizing matrix (such as FMP-10) that produces ions other than the standard [M+H]+ in positive mode or [M-H]− in negative mode.
    0 installs
33. ▌
    Dna Adduct Compound Database Loading · holobiomicslab

    Use when you have downloaded fragment records from the experimental or predicted DNA adductomics databases and need to verify that each fragment can be matched to its corresponding compound entry in the SDF-format reference compound database, or when auditing completeness of a DNA adduct resource.
    0 installs
34. ▌
    Documentation Driven Reproducibility · holobiomicslab

    Use when you have inherited a multi-language analysis codebase (R and/or MATLAB scripts) with accompanying documentation (Read-Me.txt, link-to-codes-and-data-objects files) and need to verify that the entire simulation workflow runs correctly on a reference dataset (typically a sub-sample scenario).
    0 installs
35. ▌
    Documentation Generation With Sphinx · holobiomicslab

    Use when you have a Python package with docstrings and want to produce publicly browsable API documentation. Typical triggers: (1) package is being released or deployed; (2) you need to host documentation on ReadTheDocs or similar;
    0 installs
36. ▌
    Fastq Quality Assessment With Fastqc · holobiomicslab

    Use when immediately after FASTQ file acquisition (whether from SRA download or local ingestion) and before any trimming or alignment steps.
    0 installs
37. ▌
    Feature Consolidation Across Samples · holobiomicslab

    Use when you have extracted multiple per-sample feature tables (in CSV format, each with feature ID, m/z, intensity, and retention time columns) and need to identify which features are the same compound detected across different breath samples.
    0 installs
38. ▌
    Feature Dereplication Mass Tolerance · holobiomicslab

    Use when you have a raw XCMS CentWave feature extraction table with m/z values, retention times, and intensities, and you observe that multiple features cluster around the same nominal mass and retention window.
    0 installs
39. ▌
    File Format Specification Compliance · holobiomicslab

    Use when when preparing metabolomics data (feature tables, sample metadata) for ingestion into a SECIMTools standalone tool, or when validating that a tool has produced outputs in the correct format and location. Apply this skill when format ambiguity exists (e.
    0 installs
40. ▌
    Fold Change Calculation Metabolomics · holobiomicslab

    Use when you have a feature-by-sample metabolomic intensity matrix (finalData) with corresponding sample group labels (finalLabel), and you need to identify metabolic markers ranked by their fold-change between two or more groups.
    0 installs
41. ▌
    Frame Metadata Extraction And Export · holobiomicslab

    Use when after completing multidimensional smoothing and saturation repair on Agilent MassHunter (.
    0 installs
42. ▌
    Frequency Threshold Adduct Selection · holobiomicslab

    Use when after feature clustering has grouped co-eluting features and assigned candidate KEGG metabolites with multiple potential adduct forms, use this skill when you need to reduce false positive annotations by filtering out low-frequency adducts.
    0 installs
43. ▌
    Hardware Specification Documentation · holobiomicslab

    Use when releasing or evaluating scientific software with claimed performance benefits, particularly when the software processes large datasets (e.g., multi-gigabyte files) or when execution speed is marketed as a key feature.
    0 installs
44. ▌
    Hdf5 File Format Reading And Writing · holobiomicslab

    Use when you have isotope-corrected or raw ion-image intensity matrices from LipidQMap or similar MSI software and need to: (1) export them as persistent HDF5 containers for archival or sharing, (2) programmatically read an existing Cardinal::HDF5 export to extract intensity matrices and feature.
    0 installs
45. ▌
    Heatmap Clustering And Visualization · holobiomicslab

    Use when you have a gene expression matrix (samples × genes, with numeric values) and corresponding sample group/phenotype labels, and you need to identify co-expression patterns, sample clustering, or condition-specific expression trends.
    0 installs
46. ▌
    In Silico Spectrum Metadata Curation · holobiomicslab

    Use when when processing collections of in-silico mass spectra from OMSLs (Open Mass Spectra Libraries) where the adduct field is absent, null, or not explicitly specified in the source file;
    0 installs
47. ▌
    Integrative Omics Pathway Enrichment · holobiomicslab

    Use when you have a preprocessed peak table with statistically significant or differentially abundant metabolites (e.g., from ANCOVA or PLS/PLS-DA), and you want to move beyond individual peak-level interpretation to understand which biological pathways or metabolic networks are perturbed.
    0 installs
48. ▌
    Isotope Corrected Image Quantitation · holobiomicslab

    Use when after isotopic correction has been performed on MSI ion images and you need to convert normalized intensities into absolute quantitative values.
    0 installs
49. ▌
    Isotopic Peak Intensity Distribution · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their isotopic distribution pattern for MS instrument simulation, peak deconvolution, or validation of observed isotopic envelopes.
    0 installs
50. ▌
    Isotopologue Ratio Quality Filtering · holobiomicslab

    Use when when extracting isotopologue patterns from centroided mzML files in non-targeted metabolomics workflows, apply this filter after detecting candidate isotopologue peaks but before finalizing the benchmark dataset.
    0 installs
51. ▌
    Java Library Dependency Provisioning · holobiomicslab

    Use when deploying a Java-based scientific application (such as CEU Mass Mediator) to an application server and the deployment documentation specifies required JAR libraries.
    0 installs
52. ▌
    JSON Schema Validation For Dashboard · holobiomicslab

    Use when after running the msfeast_pipeline notebook to generate dashboard_data.json from quantification tables, metadata, and spectral data. Use this skill to verify that the exported JSON contains all required fields and structure before attempting to load the file into msFeaST_Dashboard_bundle.
    0 installs
53. ▌
    Lipid Adduct Pairing By Neutral Mass · holobiomicslab

    Use when when processing mass spectrometry imaging data with multiple adduct forms of the same lipid species, and you need to correct one adduct form (e.g. [M+H]+) for isotopic interference from a co-occurring adduct (e.g. [M+Na]+).
    0 installs
54. ▌
    Lipid Feature Annotation And Sorting · holobiomicslab

    Use when after quantifying ion images in LipidQMap and before exporting to HDF5 format, when you need to organize per-feature metadata (lipid ID, class, adduct, m/z, internal standard flag) into aligned datasets that can be linked to intensity data via dimension scales and sorted for reproducible.
    0 installs
55. ▌
    Lipid Species Classification Mapping · holobiomicslab

    Use when you have a table of lipid species names or identifiers output from LipidSearch or LIQUID (with associated quantification data) and need to annotate each lipid with its standardized LIPID MAPS classification (e.
    0 installs
56. ▌
    Mass Spectrometry Data Serialization · holobiomicslab

    Use when after RAMClustR clustering and molecular weight inference via do.findmain, when you need to export deconvoluted cluster spectra for import into external annotation tools (MSFinder or Sirius).
    0 installs
57. ▌
    Mass Spectrometry Feature Collapsing · holobiomicslab

    Use when after XCMS CentWave feature extraction when your feature table contains redundant entries — multiple features with highly similar m/z and retention time values that represent the same metabolite.
    0 installs
58. ▌
    Mass Spectrometry Feature Extraction · holobiomicslab

    Use when you have raw mzML mass spectrometry data and need to detect which predicted candidate metabolites are present in the sample.
    0 installs
59. ▌
    Mass Tolerance Parameter Calibration · holobiomicslab

    Use when when converting raw line-scan mass spectrometry imaging data (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .mzML formats) and must decide which m/z values from a reference mass list correspond to peaks in the raw spectra.
    0 installs
60. ▌
    Memory Efficient Pairwise Statistics · holobiomicslab

    Use when you have an MSI intensity matrix (msimat object) and an annotated mass-difference table (massdiff object with known or hypothesized parent–adduct ion pairs) where the number of peak pairs exceeds available RAM.
    0 installs
61. ▌
    Meta Analysis Effect Size Estimation · holobiomicslab

    Use when when you have tabulated results (p-value, fold-change, study size N) from two or more independent metabolomics studies addressing the same research question and need a single meta-analytic estimate of effect size and statistical significance without access to raw data or variance estimates.
    0 installs
62. ▌
    Metabolite Abundance Standardization · holobiomicslab

    Use when you have a metabolomics featuredata matrix with known batch effects, matrix effects, or unwanted technical variation, and you have identified a set of negative control metabolites (e.g., spiked internal standards or blank-derived features) that are expected to show no biological signal.
    0 installs
63. ▌
    Metabolite Cluster Export Formatting · holobiomicslab

    Use when after running do.findmain on a RAMClustR-clustered object to infer molecular weights and assign features to compound clusters, when you need to conduct structural elucidation in MSFinder or Sirius and require spectra in their native import formats rather than the intermediate MSP or.
    0 installs
64. ▌
    Metabolite Interaction Visualization · holobiomicslab

    Use when after computing a Jacobian matrix from covariance data in MInfer, when you need to render metabolite-to-metabolite interaction networks as publication-quality figures.
    0 installs
65. ▌
    Metabolite Overdispersion Correction · holobiomicslab

    Use when working with untransformed metabolomics count data (e.g., c57_nos2KO_mouse_countDF) that will be input to variance-sensitive methods such as random forest classification or univariate statistical tests.
    0 installs
66. ▌
    Metabolite Retention Time Comparison · holobiomicslab

    Use when after executing retention-order prediction on a test set of metabolites, you have both predicted retention orderings and experimentally measured ground-truth retention orderings for the same set of compounds, and you need to quantify prediction accuracy to validate the model's performance.
    0 installs
67. ▌
    Metabolomics Batch Effect Adjustment · holobiomicslab

    Use when you have a log-transformed metabolomics featuredata matrix with missing values handled (via knn or replacement) and you observe systematic variation across batches, quality control samples, or sample order that is NOT of biological interest.
    0 installs
68. ▌
    Metabolomics Batch Effect Correction · holobiomicslab

    Use when you have log-transformed, imputed metabolomics data from multiple experimental batches (rawImpute assay) that shows visible batch effects in PCA plots or signal drift across runs, and your study design includes intra-batch replicates (technical replicates within a run) and inter-batch.
    0 installs
69. ▌
    Metabolomics Data Import And Parsing · holobiomicslab

    Use when when you have metabolomics comparison results from one or more studies in tabular format (spreadsheet or text file) with columns for compound name/identifier, statistical p-value, relative fold-change (including negative values indicating down-regulation), study sample size (N), and.
    0 installs
70. ▌
    Metacyc Database Query And Retrieval · holobiomicslab

    Use when you need to (1) quantify how many MetaCyc reactions can be represented by different numbers of generalized rules, (2) select a subset of rules for reaction network expansion based on coverage targets (e.
    0 installs
71. ▌
    Missing Data Simulation And Recovery · holobiomicslab

    Use when you have metabolomics peak intensity data with pathway annotations and want to benchmark whether a pathway scoring method (PALS, ORA, GSEA) degrades gracefully under conditions of missing peaks and measurement noise.
    0 installs
72. ▌
    Molecular Coordinate Generation 2d3d · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical structure database and need both 2D (flat) and 3D (conformer) representations for molecular visualization, molecular docking, or structure archival.
    0 installs
73. ▌
    Molecular Fingerprint Generation Rdk · holobiomicslab

    Use when you have a set of chemical compounds represented as InChI or SMILES strings and need to extract molecular features for input into a neural network or traditional ML model.
    0 installs
74. ▌
    Molecular Model Benchmark Comparison · holobiomicslab

    Use when when you have (1) a candidate foundation model or pre-trained weights for natural products (e.g., NaFM), (2) one or more baseline models pre-trained on synthetic molecules (e.g., ChemBERTa, MolBERT), (3) a held-out test set from a downstream task (e.
    0 installs
75. ▌
    Molecular Structure Dataset Curation · holobiomicslab

    Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values, and you need to format and validate them as input to a machine learning CCS prediction model.
    0 installs
76. ▌
    Morphological Alignment Optimization · holobiomicslab

    Use when you have two or more spatial omics datasets (e.
    0 installs
77. ▌
    Ms1 Data Preprocessing Normalization · holobiomicslab

    Use when when you have loaded raw MS1 data from multiple instrument formats (Agilent, Thermo, Bruker, mzML) across a multi-sample cohort and need to prepare the ion intensity feature matrix for PCA analysis or cross-sample quality assessment.
    0 installs
78. ▌
    Multi Algorithm Comparative Analysis · holobiomicslab

    Use when when you have prepared metabolomics data (e.g., covid_data) with a binary outcome variable and need to select the most appropriate predictive algorithm for your classification task.
    0 installs
79. ▌
    Multimodal Input Tensor Construction · holobiomicslab

    Use when when you have completed multimodal dataset production via data_prep.py and need to prepare sample or production input batches that combine molecular graph features and SMILES embeddings for forward pass validation or model training on TransG-Net.
    0 installs
80. ▌
    Natural Product Database Preparation · holobiomicslab

    Use when you need to update your local LOTUS natural-product database file before running metadata enrichment or structure-query workflows, or when a pre-existing provided LOTUS file is unavailable or suspected to be stale. Trigger on project initialization or on a scheduled basis (e.
    0 installs
81. ▌
    Nearest Neighbor Candidate Retrieval · holobiomicslab

    Use when when you have a large spectral library (thousands to millions of spectra represented as high-dimensional vectors) and need to search unknown query spectra against it, particularly under open modification search scenarios where all possible mass shifts must be considered.
    0 installs
82. ▌
    Network Graph Filtering By Hierarchy · holobiomicslab

    Use when your network contains multiple edge types between the same pair of nodes and you need a deterministic, single-edge representation per node pair.
    0 installs
83. ▌
    Network Visualization Ranked Scoring · holobiomicslab

    Use when when you have computed betweenness centrality (or other igraph topology metrics) for metabolites in a pathway-metabolite bipartite network and wish to highlight which metabolites occupy central positions—i.e., have high regulatory potential through bridging multiple pathways.
    0 installs
84. ▌
    Numeric List Construction Validation · holobiomicslab

    Use when implementing a backendInitialize() method for a custom MsBackend class and you have raw m/z and intensity vectors (from files, data frames, or lists) that must be converted into the internal NumericList representation required by the Spectra package.
    0 installs
85. ▌
    Omics Data Integration Visualization · holobiomicslab

    Use when you have completed statistical analysis of omics data (proteomics, metabolomics, transcriptomics, or multi-omic) and possess both abundance/expression measurements and computed statistical metrics (p-values, effect sizes, fold-changes).
    0 installs
86. ▌
    Organism Taxonomy Identifier Mapping · holobiomicslab

    Use when integrating organism records from 31 or more initial open databases with inconsistent taxonomy nomenclature, or when you need to count unique organisms in a validated structure-organism pair collection and verify the count against a known aggregate (e.
    0 installs
87. ▌
    Pairwise Mass Comparison Computation · holobiomicslab

    Use when after peak m/z values and molecular formulas have been extracted and pre-processed from FT-ICR MS data, and you need to reconstruct biochemical transformation networks ab initio.
    0 installs
88. ▌
    Pairwise Mass Difference Computation · holobiomicslab

    Use when after loading preprocessed MSI intensity data (via msimat from CSV export) or a simple numeric vector of mass peak values, when you need to discover which masses in your dataset co-vary as parent–adduct pairs.
    0 installs
89. ▌
    Pareto Scaling Multivariate Analysis · holobiomicslab

    Use when apply Pareto scaling when preparing normalized metabolomics data for unsupervised multivariate analysis (PCA or hierarchical clustering heatmaps) where features span multiple orders of magnitude in intensity and you want to reduce the influence of high-abundance metabolites without.
    0 installs
90. ▌
    Pathway Annotation Database Matching · holobiomicslab

    Use when after marker identification or metabolite annotation has produced a curated list of compound IDs (e.g., KEGG IDs or CAS numbers) and you need to determine which metabolic pathways are statistically overrepresented in your dataset.
    0 installs
91. ▌
    Pca Score Interpretation In Networks · holobiomicslab

    Use when you have both (1) a sparse network graph from GLASSO showing conditional dependencies among variables, and (2) PCA scores representing variance or loadings in a lower-dimensional space.
    0 installs
92. ▌
    Peak Detection Targeted Metabolomics · holobiomicslab

    Use when you have mass spectrometry data in .raw, .d, or mzXML format and a predefined list of target compounds (m/z and retention time ranges) you wish to quantify.
    0 installs
93. ▌
    Peak Mass Intensity Feature Encoding · holobiomicslab

    Use when you have raw mass spectra (e.g., from NIST 2017 or MassBank) and need to prepare them for Word2vec embedding or other token-based neural models. Use it as a preprocessing step before training spectral embedding models, especially when scale and accuracy of spectrum matching are priorities.
    0 installs
94. ▌
    Permanova Effect Size Interpretation · holobiomicslab

    Use when after running PERMANOVA on distance matrices derived from FT-ICR MS metabolite peak intensities or other high-dimensional compositional data, when p-values indicate statistical significance but ordination plots (NMDS, PCA) fail to discriminate among treatment groups.
    0 installs
95. ▌
    Principal Component Analysis Scaling · holobiomicslab

    Use when you have a log2-transformed metabolite abundance matrix and need to visualize sample clustering patterns, batch structure, or the effect of batch correction. Scaling is essential because metabolites often have widely different absolute concentrations;
    0 installs
96. ▌
    Protein Interaction Score Prediction · holobiomicslab

    Use when you have co-fractionation/mass-spectrometry (CF-MS) elution profiles (raw intensity vectors across fractions) paired with a gold standard of known positive and negative protein–protein interactions, and your goal is to predict interaction scores for all protein pairs without hand-crafted.
    0 installs
97. ▌
    Query Latency Throughput Measurement · holobiomicslab

    Use when when you have implemented or obtained a spectral library search algorithm (such as Flash Entropy Search) and need to empirically verify its performance against reported benchmark metrics, or when comparing query performance across different library sizes, mass spectral file formats (.mgf, .
    0 installs
98. ▌
    Raw Mass Spectrometry Data Ingestion · holobiomicslab

    Use when you have raw mass spectrometry data in mzML, abf (Reifycs), or cdf (NetCDF) format and need to load it into MS-DIAL or a similar open-source metabolomics platform.
    0 installs
99. ▌
    Reactomics Annotation And Clustering · holobiomicslab

    Use when you have a formula-assigned dataset from FT-ICR MS or other mass spectrometry with molecular formulas assigned to each mass feature, and you want to identify and quantify the molecular transformations (e.
    0 installs
100. ▌
     Reference Database Tolerance Mapping · holobiomicslab

     Use when you have calculated pairwise mass differences from MS peaks (via massdiff()) and binned them into a histogram, and now need to identify which observed mass differences correspond to known molecular adducts (e.g., [M+Na]+, [M+H]+, matrix-related species) rather than random noise.
     0 installs