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HolobiomicsLab

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1. ▌
   Metabolomics Data Format Validation · holobiomicslab

   Use when you have a tab-delimited metabolomics data file (raw measurement output from xcms, Sciex OS, or similar acquisition pipelines) and need to load it into mzQuality before building a SummarizedExperiment.
   0 installs
2. ▌
   Metabolomics Data Output Formatting · holobiomicslab

   Use when after completing feature annotation with the annotateRC function on LC–MS All-ion fragmentation (AIF) datasets, when you need to persist ranked metabolite candidates, matched ion spectra, and global summary tables to disk for archival, manual review, or integration into downstream.
   0 installs
3. ▌
   Mgf Metadata Completion From Smiles · holobiomicslab

   Use when when processing MGF-format MS2 spectral libraries (e.g., GNPS) that contain SMILES but lack the Molecular Formula field, and you need to prepare the library for MS-DIAL import or polarity-based separation workflows.
   0 installs
4. ▌
   Mispicked Ion Detection And Merging · holobiomicslab

   Use when immediately after importing raw LC-MS peak tables (e.g., Progenesis format) and before applying group or replicability filters.
   0 installs
5. ▌
   Model Validation Regression Metrics · holobiomicslab

   Use when after training a deep-learning model on paired MS/MS spectra with annotated structural similarity labels, use this skill to assess whether predicted similarity scores correlate with ground-truth reference similarities on data the model has never seen.
   0 installs
6. ▌
   Molecular Family Graph Construction · holobiomicslab

   Use when you have downloaded and extracted a GNPS archive (from METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING for GNPS1, or classical_networking_workflow/feature_based_molecular_networking_workflow for GNPS2) and need to construct a queryable molecular family graph.
   0 installs
7. ▌
   Molecular Property Data Structuring · holobiomicslab

   Use when you have a CSV file with rows of molecule definitions (chemical formulas, retention times, intensities, or other peak properties) and need to feed them into SMITER's simulation workflow.
   0 installs
8. ▌
   Ms2 Spectral Similarity Computation · holobiomicslab

   Use when you have two or more LC-MS/MS datasets (in mzML, mzXML, or MGF format) and need to quantify their overall spectral content similarity—typical scenarios include data quality control, species identification, molecular phylogenetics, or proteome comparison across samples, cell lines, or.
   0 installs
9. ▌
   Msms Spectrum Metadata Preservation · holobiomicslab

   Use when removing invalid or malformed entries (e.g., SMILES validation, format errors) from large spectral datasets (GNPS, MoNA, MTBLS1572, MassBank).
   0 installs
10. ▌
    Multi Criterion Scoring Integration · holobiomicslab

    Use when you have an LC-HRMS feature table (m/z, retention time, isotope ratios, fragmentation patterns) and a suspect compound database with reference properties (m/z, expected RT windows, theoretical isotope ratios, characteristic neutral losses), and you need to rank which features most likely.
    0 installs
11. ▌
    Multidimensional Feature Annotation · holobiomicslab

    Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic signatures to distinguish monoisotopic peaks from isotopologues, reduce feature redundancy, and support multi-dimensional.
    0 installs
12. ▌
    Multidimensional Ms Data Conversion · holobiomicslab

    Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments, and you need to: (1) store multidimensional spectra in a vendor-neutral, platform-agnostic format;
    0 installs
13. ▌
    Nearest Neighbor Index Construction · holobiomicslab

    Use when when you have millions of high-resolution MS/MS spectra converted to low-dimensional vectors (via feature hashing) and need to compute a sparse pairwise distance matrix for downstream density-based clustering.
    0 installs
14. ▌
    Network Based Functional Prediction · holobiomicslab

    Use when you have an untargeted metabolomics feature table with m/z values, retention times, intensity measurements, and p-values from statistical testing, but lack or wish to bypass metabolite identification.
    0 installs
15. ▌
    Nextflow Pipeline Configuration Hpc · holobiomicslab

    Use when your analysis target is an HPC environment (e.g., Slurm-managed cluster, university research computing center) where Singularity is available but Docker is restricted or unavailable; your workflow is already packaged in Docker but needs portability to HPC;
    0 installs
16. ▌
    Paired Omics Data Structure Mapping · holobiomicslab

    Use when when you have a paired omics project document (JSON format) that combines MS/MS mass spectrometry data with genome identifiers, biosynthetic gene cluster information, sample preparation, extraction method, and instrumentation metadata, and you need to verify it conforms to the platform's.
    0 installs
17. ▌
    Peak Area And Intensity Measurement · holobiomicslab

    Use when when you have vendor-format GC-CI-MS or LC-MS data from stable isotope labeling experiments, a target list of compounds with known monoisotopic m/z, retention time, and elemental formula, and you need per-isotopologue area and intensity values for quantification or downstream statistical.
    0 installs
18. ▌
    Per Sample Pass Fail Classification · holobiomicslab

    Use when after LC-MS data acquisition is complete (or during real-time monitoring) and you have loaded processed LC-MS data in mzML or vendor format and defined QC criteria (retention time windows, m/z tolerances, intensity thresholds) for your internal standards and target analytes.
    0 installs
19. ▌
    Permutation Test P Value Estimation · holobiomicslab

    Use when after computing Multi-Block Variable Importance in Projection (MB-VIP) scores on a fitted MB-PLS discriminant model, when you need to distinguish signal features from noise by establishing empirical significance thresholds rather than relying on parametric assumptions.
    0 installs
20. ▌
    Publication Image Asset Preparation · holobiomicslab

    Use when you have resolved a USI string pointing to a spectrum in a supported repository (GNPS, MassBank, MassIVE, MetaboLights, Metabolomics Workbench, ProteoXchange, or MS2LDA) and need to embed a publication-ready visualization or machine-readable reference that preserves the spectrum's.
    0 installs
21. ▌
    Retention Time Alignment Clustering · holobiomicslab

    Use when you have two or more nontargeted LCMS feature tables from the same analytical method and need to establish matched feature correspondences across datasets, then consolidate redundant features.
    0 installs
22. ▌
    Retention Time Alignment Correction · holobiomicslab

    Use when when processing a batch of centroided mzML or mzXML LC-MS raw data files where chromatographic retention times drift between sample acquisitions (common in large-scale metabolomics studies).
    0 installs
23. ▌
    Retention Time Alignment Validation · holobiomicslab

    Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
    0 installs
24. ▌
    Retention Time And Mz Weight Tuning · holobiomicslab

    Use when after anchor selection and RT mapping spline construction, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to tune the scoring metric that combines retention time, m/z, and cosine similarity components.
    0 installs
25. ▌
    Retention Time Clustering Alignment · holobiomicslab

    Use when you have extracted feature tables (via MS1 peak picking, MS2 recognition, or targeted list extraction) from two or more individual LC-MS samples and need to identify which features represent the same metabolite across samples before generating a unified, sample-aligned feature table for.
    0 installs
26. ▌
    Retention Time Co Elution Detection · holobiomicslab

    Use when after matching mass-to-charge ratios to a compound database (e.g., KEGG) and assigning adduct/fragment types, when you have an annotated feature table with retention times, m/z values, and intensity profiles across samples.
    0 installs
27. ▌
    Retention Time Intensity Tabulation · holobiomicslab

    Use when when you have a resolved mzML or mzXML spectrum file and need to visualize or analyze the temporal intensity profile of a specific analyte (defined by its m/z value).
    0 installs
28. ▌
    Retention Time Mz Intensity Mapping · holobiomicslab

    Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications with retention times, m/z values, and intensity measurements across multiple samples, and you need to rapidly detect instrumental drift, retention time shifts, or.
    0 installs
29. ▌
    Root Mean Squared Error Calculation · holobiomicslab

    Use when when you have paired predictions and ground-truth structural similarity labels (e.g., predicted Tanimoto scores from a neural network and reference Tanimoto scores from RDKit Daylight fingerprints) and need to report a single scalar metric of model prediction error across all pairs.
    0 installs
30. ▌
    S4 Class Definition And Inheritance · holobiomicslab

    Use when you are designing a new backend or data container that must integrate seamlessly with an existing Spectra-based workflow. You have identified a virtual parent class (e.
    0 installs
31. ▌
    Sample Metadata Annotation For Lcms · holobiomicslab

    Use when when you have loaded centroided .mzML files into a Spectra object and plan to use TARDIS (tardisPeaks) with an MsExperiment object rather than file paths, and you need TARDIS to distinguish QC runs from sample runs for separate quality metric calculation, polarity filtering, and.
    0 installs
32. ▌
    Set Activity Prioritization Ranking · holobiomicslab

    Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
    0 installs
33. ▌
    Similarity Threshold Interpretation · holobiomicslab

    Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide which matches are sufficiently confident to include in per-motif annotation output.
    0 installs
34. ▌
    Singly Charged Ion Mass Calculation · holobiomicslab

    Use when you have detected monoisotopic features (m/z, drift_time, retention_time, intensity) from LC-IMS-MS/MS data and need to identify and cluster their C13 isotopologues for charge state z=+1.
    0 installs
35. ▌
    Singularity Container Backend Setup · holobiomicslab

    Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers Singularity for security and portability. You have .mzML or .
    0 installs
36. ▌
    Skyline Import Format Specification · holobiomicslab

    Use when you have computationally generated precursor m/z values, fragment m/z values, collision energies, and retention time predictions for a set of lipid targets (e.
    0 installs
37. ▌
    Sparse Distance Matrix Construction · holobiomicslab

    Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on low-dimensional spectrum vectors (via feature hashing), and you need to compute only the relevant pairwise distances between.
    0 installs
38. ▌
    Spectral Entropy Quality Assessment · holobiomicslab

    Use when after feature detection and alignment in untargeted MS data processing, when you need to filter or rank candidate metabolite annotations by spectral quality before committing to xenobiotic metabolite assignments. Use when combining fragmentation similarity scores (e.
    0 installs
39. ▌
    Spectral Feature Vector Aggregation · holobiomicslab

    Use when you have generated per-sample MS2 fingerprints (as spec2vec document representations counting MS2 peaks and neutral losses to precursor in each sample) and need to align them into a single matrix for downstream cross-sample comparison, filtering, or visualization (e.
    0 installs
40. ▌
    Spectral Library Record Structuring · holobiomicslab

    Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, molecular weight, annotation fields) that you need to bind together into a queryable spectral library record for local compound.
    0 installs
41. ▌
    Spectral Match Result Consolidation · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single coherent view.
    0 installs
42. ▌
    Spectral Peak Binning Preprocessing · holobiomicslab

    Use when when you have raw high-resolution tandem mass spectra (mzML, mzXML, or MGF format) that you intend to cluster or compare at scale, and you need to convert continuous m/z and intensity measurements into discrete bins suitable for feature hashing or similarity searching.
    0 installs
43. ▌
    Spectral Peak Intensity Aggregation · holobiomicslab

    Use when you have multiple replicate MS/MS spectra for the same metabolic feature (e.g., 66 top-TIC spectra for feature 1982) and need to identify robust peaks by merging nearby m/z values and pooling their signal strength.
    0 installs
44. ▌
    Spectral Quality Control Assessment · holobiomicslab

    Use when after MS1 extraction (coarse/fine error correction, EIC window extraction) and retention time windowing on a set of mzML files tagged with ionization mode and compound adducts.
    0 installs
45. ▌
    Spectral Scan Generation And Export · holobiomicslab

    Use when you have real LC-MS/MS data (mzML) from a complex sample (e.g., beer, metabolomics extract) and need to prototype or validate a new data-dependent acquisition (DDA) strategy—such as Top-N fragmentation—before deploying it on physical instrumentation.
    0 installs
46. ▌
    Spectral Vectorization For Indexing · holobiomicslab

    Use when when you have a collection of MS/MS reference spectra and unknown query spectra that must be rapidly matched against a large spectral library, and you need to enable approximate nearest neighbor indexing to reduce computational cost from exhaustive pairwise comparison to K-nearest neighbor.
    0 installs
47. ▌
    Spectrum Pair Retrieval And Ranking · holobiomicslab

    Use when you have a test set of annotated MS/MS spectra with known structural similarity (via molecular fingerprints or InChIKey), and you want to assess how well a spectral similarity measure (learned or classical) retrieves structurally related compound pairs across a full range of thresholds.
    0 installs
48. ▌
    Substructure Annotation Integration · holobiomicslab

    Use when you have (1) a GNPS molecular network (classical or feature-based) with cluster/feature identifiers, (2) MS2LDA output containing Mass2Motif assignments with probability and overlap scores for those same clusters/features, and (3) a goal to annotate network nodes with substructural and.
    0 installs
49. ▌
    Table Join Alignment On Identifiers · holobiomicslab

    Use when you have a feature quantification table output from MZmine3 feature detection (rows = features, columns = sample abundance values) and a separate sample metadata file (rows = samples, columns = sample attributes) that need to be unified before downstream statistical analysis, data cleanup.
    0 installs
50. ▌
    Tandem Mass Spectra Standardization · holobiomicslab

    Use when you have acquired raw tandem MS data from ProteomeXchange or vendor instruments in proprietary formats (e.g., Thermo .raw files) and need to perform comparative clustering benchmarks or quality assessments across multiple clustering tools.
    0 installs
51. ▌
    Targeted Transition List Generation · holobiomicslab

    Use when you have a set of lipid targets defined by species name, acyl chain composition, and expected adducts, and you need to configure a targeted mass spectrometry workflow (PRM or MRM) in Skyline.
    0 installs
52. ▌
    Technical Replicate Signal Modeling · holobiomicslab

    Use when your LCMS metabolomics dataset exhibits run-order-dependent intensity drift (signal decay or gain over the course of a sample batch), you have pooled technical replicates (identical biospecimen injected multiple times across the run sequence) and/or known internal standard compounds, and.
    0 installs
53. ▌
    Theoretical Fragment Ion Generation · holobiomicslab

    Use when when you have a peptide sequence and need to predict its fragment ion spectrum for stable isotope labeling validation, particularly when comparing against observed mass spectrometry data with natural or enriched isotopic abundance (e.g., 1% or 50% 13C incorporation).
    0 installs
54. ▌
    Throughput Optimization Ms Querying · holobiomicslab

    Use when you have experimental MS/MS spectra that must be matched against a large hierarchical fragmentation library (e.g., 168.
    0 installs
55. ▌
    Time Series Intensity Normalization · holobiomicslab

    Use when when LCMS metabolomics abundance tables show systematic intensity drift across the injection sequence (e.g., instrument signal decay or gain over hours), and you have pooled technical replicate injections and/or internal standard compounds distributed throughout the run.
    0 installs
56. ▌
    Tracer Impurity Correction Modeling · holobiomicslab

    Use when when processing LC-MS data from isotope labeling experiments where the tracer (13C, 2H, 15N, 18O, or 34S) has known isotopic impurity and you observe discrepancies between measured isotopologue abundances (FAM) and expected labeling patterns.
    0 installs
57. ▌
    Transition Group Feature Extraction · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA mass spectrometry data) and need to identify precise peak boundaries, apex retention/drift time, and intensity values for quantitative feature detection.
    0 installs
58. ▌
    Untargeted Lc Ms Data Preprocessing · holobiomicslab

    Use when when you have raw untargeted LC-MS metabolomics data and need to detect low-quality or mis-integrated peaks in an XCMS-processed xcmsSet object before performing metabolite annotation, statistical analysis, or biomarker discovery.
    0 installs
59. ▌
    Virtual Chemical Mixture Generation · holobiomicslab

    Use when you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass spectrometry analysis.
    0 installs
60. ▌
    Workflow Architecture Documentation · holobiomicslab

    Use when you need to understand how a complex MS/MS spectral search system routes query spectra through multiple parallel processing pipelines with different objectives (e.g., reliable exact matching vs. fast approximate matching).
    0 installs
61. ▌
    Workflow Reproducibility Validation · holobiomicslab

    Use when after implementing or deploying a containerized Nextflow workflow that processes LC-HRMS metabolomics .
    0 installs
62. ▌
    Xcms Grouping Result Interpretation · holobiomicslab

    Use when xCMS grouping has been performed on LC-MS data from studies with hundreds of samples or data acquisition periods longer than a week, where retention time drift structures are complex and the single-warping-function assumption is likely violated.
    0 installs
63. ▌
    Browser Security Policy Configuration · holobiomicslab

    Use when you need to run a web application locally (by opening index.html directly in the browser) and the application uses WebWorker or WebAssembly modules that fail to load with cross-origin policy or file-access errors.
    0 installs
64. ▌
    Cumulative Distribution Visualization · holobiomicslab

    Use when when you have per-feature quality metrics (such as CV values from NMR or MS reproducibility analysis) and need to: (1) confirm that a specified proportion of features meet regulatory thresholds (e.g., 99% < 0.30, 92% < 0.15 for CV);
    0 installs
65. ▌
    Deep Learning Spectral Language Model · holobiomicslab

    Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format with mandatory PRECURSOR_MZ and IONMODE tags) and need to identify structurally related metabolites from a reference database.
    0 installs
66. ▌
    Memory Mapped File Selection Strategy · holobiomicslab

    Use when initializing a Dataset object in NMRFx and must decide which storage backend to use for in-memory or memory-mapped file access.
    0 installs
67. ▌
    Peak Network To Metabolite Assignment · holobiomicslab

    Use when after peak clustering has produced peak network groups (ideally from the same compound) and you need to assign chemical identities.
    0 installs
68. ▌
    Repository Cloning And Initialization · holobiomicslab

    Use when you have a GitHub repository URL, a documented Python version requirement, and a list of pinned package versions, and you need to verify that the application will initialize without import or runtime errors before proceeding to data analysis or method replication.
    0 installs
69. ▌
    Spectral Similarity Scoring Parent Tp · holobiomicslab

    Use when after generating TP candidates (via in-silico prediction or library lookup) and extracting MS/MS peak lists for both parent features and TP feature candidates, use spectral similarity scoring to quantify fragmentation pattern overlap.
    0 installs
70. ▌
    Summarized Experiment Object Handling · holobiomicslab

    Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS) with epidemiological confounders.
    0 installs
71. ▌
    Top K Accuracy Ranking And Evaluation · holobiomicslab

    Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the correct answer appears in the top-k predictions.
    0 installs
72. ▌
    Transformer Cnn Hybrid Model Training · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data with compound labels and need to identify multiple compounds in a flavor mixture where both local spectral patterns (handled by CNN) and long-range spectral dependencies (handled by Transformer) are diagnostic.
    0 installs
73. ▌
    Anndata Backed Object Manipulation · holobiomicslab

    Use when when working with large single-cell ATAC-seq or multi-omics datasets where in-memory storage is infeasible (>1M cells), and you need to iteratively add or modify count matrices (tile-based, peak-based, or gene-based) while preserving fragment-level data for reproducibility and re-analysis.
    0 installs
74. ▌
    Differential Tf Occupancy Analysis · holobiomicslab

    Use when you have aligned ATAC-seq BAM files and peak annotations from two or more experimental conditions (e.
    0 installs
75. ▌
    Genomic Feature Annotation Overlap · holobiomicslab

    Use when after you have identified a set of differentially methylated bases or regions (e.
    0 installs
76. ▌
    Hi C Fastq To Contact Map Pipeline · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a sequencing experiment and need to generate kilobase-resolution Hi-C contact maps conforming to ENCODE reference standards.
    0 installs
77. ▌
    Hic Contact Map Feature Annotation · holobiomicslab

    Use when you have completed Hi-C map generation (producing .hic files from aligned reads) and need to detect and annotate topological features such as chromatin loops, topologically associating domains (TADs), or interaction peaks.
    0 installs
78. ▌
    Illumina 450k Epic Dataset Loading · holobiomicslab

    Use when you have raw .idat files or a beta-valued matrix from an Illumina HumanMethylation450 or EPIC array experiment and need to import the full probe set into R for downstream quality control, normalization, and differential methylation analysis.
    0 installs
79. ▌
    Methylation Batch Effect Detection · holobiomicslab

    Use when you have loaded a normalized beta-valued methylation matrix (e.
    0 installs
80. ▌
    Methylation Probe Count Validation · holobiomicslab

    Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.
    0 installs
81. ▌
    Module Import And API Verification · holobiomicslab

    Use when before invoking any Python module in a multi-step Hi-C processing pipeline, or when a dependency has been freshly installed or reinstalled.
    0 installs
82. ▌
    Paired Insertion Counting Strategy · holobiomicslab

    Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
    0 installs
83. ▌
    Peak Calling Output Interpretation · holobiomicslab

    Use when you have run a peak-calling algorithm on sparse CUT&RUN bedGraph data and received a BED-format output file;
    0 installs
84. ▌
    System Dependency Version Checking · holobiomicslab

    Use when you are preparing to run a complex multi-tool bioinformatics pipeline (such as HiC-Pro) on a new system or cluster, and need to confirm that all required binaries exist in the execution environment and meet minimum version thresholds (e.g., samtools >=1.9, Python >3.
    0 installs
85. ▌
    Assembly Version String Retrieval · holobiomicslab

    Use when when you need to validate that a .NET assembly (such as ThermoFisher.CommonCore.RawFileReader) is correctly installed and accessible before attempting data reading operations.
    0 installs
86. ▌
    Atom Feature Extraction Chemistry · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical database (e.
    0 installs
87. ▌
    Bayesian Meta Learning Projection · holobiomicslab

    Use when you need to transfer retention time predictions from one chromatographic method to another, but have access to only a small number (≥10) of molecules with known retention times in both methods.
    0 installs
88. ▌
    C Sharp Wrapper Method Validation · holobiomicslab

    Use when when integrating an R package that wraps a compiled .NET assembly (such as rawrr), you need to verify that the internal dispatch mechanism between the R layer and the C# layer is operational before attempting to read actual raw data files.
    0 installs
89. ▌
    Calibration Curve Fitting Ms Data · holobiomicslab

    Use when you have raw mass spectrometry intensity data from targeted analytes and a set of calibration standard measurements with known concentrations.
    0 installs
90. ▌
    Chemodiversity Metric Calculation · holobiomicslab

    Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment groups (e.g., inoculated vs. control samples).
    0 installs
91. ▌
    Conditional Dependency Resolution · holobiomicslab

    Use when a Python library exposes functionality that depends on external packages (like sqlalchemy, pandas, or lxml) that are not required for core operations.
    0 installs
92. ▌
    Container Image Size Verification · holobiomicslab

    Use when after completing a multi-stage Docker build targeting a compiled runtime environment (e.g., airdpro:cli produced from a Wine + .NET Framework 4.8 + Ubuntu 22.
    0 installs
93. ▌
    Count Verification And Validation · holobiomicslab

    Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity, medium-diversity, high-diversity) match published or curated reference values.
    0 installs
94. ▌
    Cross Domain Masst Output Parsing · holobiomicslab

    Use when you have executed batch searches against one or more domain-specific MASST tools and received multiple output files (_microbe.html, _plant.html, _tissue.html, _microbiome.html, _food.html, _matches.tsv, _library.tsv, _datasets.tsv, _count_*.
    0 installs
95. ▌
    Custom Metabolite Set Integration · holobiomicslab

    Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
    0 installs
96. ▌
    Dataframe Lazy Loading Comparison · holobiomicslab

    Use when when designing or optimizing an MsBackend implementation (or similar columnar data structure) you must decide whether to pre-allocate all known columns in the backing DataFrame at initialization or defer column creation until first access.
    0 installs
97. ▌
    Docker Multistage Build Execution · holobiomicslab

    Use when you need to containerize a C#-based Windows application (like AirdPro CLI) for Linux deployment, require Wine and .NET Framework 4.
    0 installs
98. ▌
    Dotnet Assembly Path Verification · holobiomicslab

    Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass spectrometry data extraction operations.
    0 installs
99. ▌
    Environment Variable Provisioning · holobiomicslab

    Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb, joblauncher, job, pubchem) receives the correct configuration—such as port mappings, service URLs, and data paths—without.
    0 installs
100. ▌
     File Format Compliance Validation · holobiomicslab

     Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification before integration into a production workflow, data repository, or downstream analysis pipeline.
     0 installs