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HolobiomicsLab

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1. ▌
   Spectral Corpus Representation · holobiomicslab

   Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
   0 installs
2. ▌
   Spectral Feature Consolidation · holobiomicslab

   Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint data into a single matrix for comparative analysis.
   2 installs
3. ▌
   Spectral Feature Normalization · holobiomicslab

   Use when when you have raw LC-MS metabolomics data in .mzML or .npy format from multiple disease groups with varying ionization efficiencies or detector sensitivities, and you need to train a deep learning model for disease classification.
   0 installs
4. ▌
   Spectral Library Data Modeling · holobiomicslab

   Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata filters, similarity scoring across large spectral collections, or integration into downstream tools like MS2Query that.
   0 installs
5. ▌
   Spectral Library Matching Ripp · holobiomicslab

   Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by matching experimental spectra against a database of predicted post-translationally modified RiPP structures derived from.
   0 installs
6. ▌
   Substructural Motif Annotation · holobiomicslab

   Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to associate each network node with its constituent substructural motifs and visualize which motifs are shared between.
   0 installs
7. ▌
   Target List Coordinate Mapping · holobiomicslab

   Use when you have a CSV-formatted target list with m/z, retention time, or ion mobility identifiers and need to locate and extract peak abundances from raw MS data files (Agilent .d, Thermo .raw, Bruker .d, mzML) acquired across LC-MS, LC-IMS-MS, DDA, DIA, or direct infusion modes.
   0 installs
8. ▌
   Targeted Metabolite Extraction · holobiomicslab

   Use when you have centroided LC-MS data (.mzML format) and a curated list of targeted metabolites or lipids (with m/z, retention time, and polarity) that you want to quantify and quality-assess across multiple analytical runs, and you need both per-run AUC values and averaged QC metrics for each.
   0 installs
9. ▌
   Theoretical Mz Grid Generation · holobiomicslab

   Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of the same neutral compound.
   0 installs
10. ▌
    Thermo Raw File Format Parsing · holobiomicslab

    Use when you have acquired multidimensional mass spectrometry data (MS1, MS/MS, or data-independent acquisition) from a Thermo instrument saved in the proprietary '.
    0 installs
11. ▌
    Annotation Confidence Assessment · holobiomicslab

    Use when after MS-FINDER in silico annotation has been executed on exported LC-MS features and multiple database matches (with HRR scores) have been returned.
    0 installs
12. ▌
    Clustered Peak Output Formatting · holobiomicslab

    Use when after peak clustering has been completed in pyINETA (i.
    0 installs
13. ▌
    Docker Environment Configuration · holobiomicslab

    Use when you need to deploy CloMet for the first time on a new system, or when you want to ensure reproducible execution of metabolomics data harmonization tasks without manual dependency management.
    2 installs
14. ▌
    File API Endpoint Implementation · holobiomicslab

    Use when when you need to construct a POST endpoint that ingests raw spectral data files from multiple vendor formats (jcamp, RAW, mzML) and must standardize them for downstream processing.
    0 installs
15. ▌
    Metabolite Dataset Preprocessing · holobiomicslab

    Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs. serum], cohort identifiers) and need to investigate how delays affect measured metabolic parameters.
    0 installs
16. ▌
    Metabolite Identifier Annotation · holobiomicslab

    Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by comparing them to computationally predicted metabolism pathways.
    0 installs
17. ▌
    Metabolomics Data Representation · holobiomicslab

    Use when you have a raw MGF file containing fragmented LC-MS-MS metabolomics spectra and want to apply Latent Dirichlet Allocation (LDA) to discover hidden topics (molecular families, biochemical patterns) across your sample set.
    0 installs
18. ▌
    Metabolomics File Format Parsing · holobiomicslab

    Use when you have mwTab-formatted files from the Metabolomics Workbench containing MS or NMR experimental metadata and tabular data sections (e.g., METABOLITES, DATA blocks), and need to load them into memory for downstream conversion, validation, or analysis rather than manual text parsing.
    0 installs
19. ▌
    Model Metadata Schema Inspection · holobiomicslab

    Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names and schema, especially before implementing or updating code that constructs JSON payloads for the /api/smart3/search.
    0 installs
20. ▌
    Molecular Connectivity Inference · holobiomicslab

    Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its molecular formula and connectivity graph.
    0 installs
21. ▌
    Nmr Spectrum Object Construction · holobiomicslab

    Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
    0 installs
22. ▌
    Replicate Consistency Assessment · holobiomicslab

    Use when after NMR or MS data acquisition and preprocessing (phasing, baseline correction) when you have a SummarizedExperiment object containing assay intensity matrix with QC sample columns designated.
    0 installs
23. ▌
    Signal To Noise Ratio Assessment · holobiomicslab

    Use when when preparing a 1D 1H NMR spectral peak list for input to the NMRformer metabolite identification model, and you have access to peak intensity measurements and noise level estimates.
    2 installs
24. ▌
    Spatial Overlap Analysis Imaging · holobiomicslab

    Use when when annotating matrix-related peaks in MSI datasets where candidate peaks have identical or near-identical m/z values (isobaric ions), or when multiple peaks exhibit overlapping spatial distributions across the tissue image that could confound downstream annotation filtering.
    2 installs
25. ▌
    Spearman Correlation Computation · holobiomicslab

    Use when : (1) you have metabolomic data (NMR or MS-derived) and a continuous phenotype variable; (2) you need to quantify associations while controlling for known confounders (age, gender, disease status);
    0 installs
26. ▌
    Spectra To Structure Elucidation · holobiomicslab

    Use when you have one or more spectroscopic datasets (IR, Raman, UV-Vis, mass spectra, NMR) from an unknown compound and need to generate candidate molecular structures ranked by likelihood. Use this when retrieval-based approaches are infeasible (e.
    2 installs
27. ▌
    Spectral Roi Boundary Definition · holobiomicslab

    Use when when you have identified a spectral window of interest in a 1H NMR spectrum from a complex biological sample (serum, urine, CSF, tissue, saliva, or sweat) and need to systematically retrieve all metabolites from HMDB whose reference proton NMR chemical shifts fall within that window.
    0 installs
28. ▌
    Spectroscopic Data Preprocessing · holobiomicslab

    Use when when you have raw spectroscopic measurements in heterogeneous formats (IR, Raman, UV-Vis, mass spectra, or NMR) and need to feed them into a spectrum-conditioned diffusion model for de novo molecular structure elucidation.
    0 installs
29. ▌
    Summarized Experiment Subsetting · holobiomicslab

    Use when when you have a SummarizedExperiment containing metabolomic abundances and a corresponding vector of quality metrics (e.g., coefficient of variation computed across QC samples), and you need to filter to retain only features meeting a reproducibility threshold (e.g., CV ≤ 0.
    1 install
30. ▌
    Tool Initialization Verification · holobiomicslab

    Use when after completing Docker installation and container build steps for CloMet, before attempting substantive data analysis or pipeline execution.
    0 installs
31. ▌
    Wasserstein Distance Computation · holobiomicslab

    Use when when you have both an observed NMR mixture spectrum and a candidate reconstructed spectrum (each represented as intensity distributions across chemical shift bins), and you need a scalar similarity metric to evaluate how closely the reconstruction matches the observed data.
    0 installs
32. ▌
    Atac Seq Signal Normalization · holobiomicslab

    Use when you have aligned ATAC-seq BAM files and need to detect transcription factor binding sites via footprint analysis. The skill is essential because raw Tn5 insertion signal contains systematic bias toward certain DNA sequences;
    0 installs
33. ▌
    Encode Hic Pipeline Execution · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited accession) and need to reproduce or validate Hi-C map generation following the ENCODE uniform processing standard, or you need to verify that your pipeline output conforms to reference format and.
    0 installs
34. ▌
    Genomic Coordinate Conversion · holobiomicslab

    Use when you need to map computed per-bin metrics (insulation scores, boundary calls, contact frequencies) back to genomic coordinates for export to BED/GFF format, cross-reference with external annotations, or validate that computed features fall within expected genomic ranges.
    0 installs
35. ▌
    Hi C Fastq Read Preprocessing · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a Hi-C wet-lab protocol and need to convert them into processed Hi-C contact maps (.hic files) for loop detection, TAD identification, or 3D structure inference. Use when starting from deposited public Hi-C datasets (e.
    0 installs
36. ▌
    Kmer Motif Synergy Assessment · holobiomicslab

    Use when after computing deviations for both motif and kmer annotations on the same chromVAR dataset, when you need to determine whether kmers and motifs are redundant predictors of chromatin accessibility variability or provide complementary information for downstream clustering, annotation, or.
    1 install
37. ▌
    Monocle3 Trajectory Embedding · holobiomicslab

    Use when you have an ArchR project object with dimensionality reduction results (LSI or combined dimensions from scATAC-seq ± scRNA-seq) and want to infer pseudotime trajectories and cell-state transitions.
    0 installs
38. ▌
    Python Environment Management · holobiomicslab

    Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure consistent module versions across multiple runs or compute nodes.
    2 installs
39. ▌
    Scatac Seq Peak Matrix Export · holobiomicslab

    Use when after completing peak calling and cell annotation in an ArchR project, when you intend to perform trajectory analysis using STREAM rather than ArchR's native monocle3 or Slingshot integrations, or when you need to share peak-by-cell matrices with collaborators using STREAM pipelines.
    0 installs
40. ▌
    Sparse Matrix Subset Indexing · holobiomicslab

    Use when when you have a chromVARDeviations object with multiple annotation sets (e.
    0 installs
41. ▌
    Tn5 Insertion Bias Correction · holobiomicslab

    Use when you have aligned ATAC-seq BAM files from Tn5-based chromatin accessibility assays and need to perform footprinting analysis.
    1 install
42. ▌
    API Specification Extraction · holobiomicslab

    Use when you have access to the source code of a webservice component (Python, configuration files, route definitions) and need to produce machine-readable API documentation (OpenAPI 3.
    0 installs
43. ▌
    Backend Routing And Dispatch · holobiomicslab

    Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their preferred rendering engine (matplotlib, bokeh, or plotly) at call time without modifying the core plotting logic.
    0 installs
44. ▌
    Command Line Tool Invocation · holobiomicslab

    Use when you have an existing mass spectrometry data file in a vendor or standard format (mzML, NetCDF, etc.) and need to convert it to mzPeak format for downstream analysis, visualization, or archival.
    0 installs
45. ▌
    Configuration Object Pattern · holobiomicslab

    Use when when designing a library that needs to support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and you want to avoid reimplementing parameter validation, storage, and dispatch logic for each backend.
    0 installs
46. ▌
    Conversion Directive Parsing · holobiomicslab

    Use when you have validated intermediate JSON data (conforming to the Experiment Description Specification) and need to configure how it should be converted to a supported output format (e.g., mwTab for Metabolomics Workbench submission).
    0 installs
47. ▌
    Dataset Integrity Assessment · holobiomicslab

    Use when when you have downloaded a released version of a structured dataset (e.g., LOTUS from Zenodo) and need to confirm it matches the documented headline statistics before downstream analysis, or when auditing data integrity after ingestion into a processing pipeline.
    0 installs
48. ▌
    Enrichment Ratio Calculation · holobiomicslab

    Use when after generating combined or alternative scores for a set of BGC-metabolite (GCF-MF) link candidates, you need to evaluate whether a scoring function preferentially ranks true validated links higher than spurious ones.
    0 installs
49. ▌
    Export Tag Syntax Validation · holobiomicslab

    Use when you have a tabular file (CSV or Excel) that has been manually or semi-automatically tagged with export tags, and you need to verify tag correctness before running the extract command to convert the tagged table into intermediate JSON.
    0 installs
50. ▌
    Github Repository Operations · holobiomicslab

    Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project documentation, or when you must reproduce pass/fail results for package-testing workflows distinct from unit tests to establish.
    0 installs
51. ▌
    HTTP API Integration Testing · holobiomicslab

    Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with correct schema, field names, and data types before consuming them in production workflows or downstream applications.
    1 install
52. ▌
    HTTP Endpoint Identification · holobiomicslab

    Use when when you have source code access to a webservice component (such as the MAGMa joblauncher) and need to enumerate all exposed HTTP endpoints, their methods (GET, POST, etc.), URL patterns, parameter names, request/response payload structures, and authentication requirements in order to.
    0 installs
53. ▌
    Mandatory Field Verification · holobiomicslab

    Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry data repository or sharing them with collaborators. Use it when specification compliance is a hard requirement (e.
    2 installs
54. ▌
    Metabolomics Ora Methodology · holobiomicslab

    Use when you have a metabolomics dataset and want to perform pathway enrichment analysis using ORA, but need to first understand its behavior, limitations, and correct application through reproducible simulation.
    2 installs
55. ▌
    Model Deployment Preparation · holobiomicslab

    Use when you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer naming or format does not yet match the target runtime's expectations (e.
    0 installs
56. ▌
    Msp File Parsing And Writing · holobiomicslab

    Use when you have one or more .msp spectral library files (NIST format) that need to be ingested for metadata curation, enrichment via web services, or export after transformation. Use this skill as the entry and exit point for any .msp-based annotation or analysis pipeline.
    2 installs
57. ▌
    Mzml Data Access Abstraction · holobiomicslab

    Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
    0 installs
58. ▌
    Pathway Database Integration · holobiomicslab

    Use when you have intensity measurements (peak features, protein intensities, or gene expression values) with compound or gene annotations (KEGG IDs, ChEBI IDs, UniProt IDs, or ENSEMBL IDs), and you need to aggregate them into biologically meaningful pathway groups for differential analysis.
    2 installs
59. ▌
    Peak Abundance Normalization · holobiomicslab

    Use when after peak detection and before any comparative analysis (e.g., diversity indices, ordination, or statistical testing) when working with direct injection FT-ICR MS data where raw peak intensities vary across samples due to instrumental factors. The task_id=task_005 example applies it to S.
    2 installs
60. ▌
    Peak Table Schema Validation · holobiomicslab

    Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format. Use this skill when you need to verify that the converted file will be successfully read by LipidMatch before proceeding to lipid identification;
    0 installs
61. ▌
    Pull Request Change Tracking · holobiomicslab

    Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query's two-branch workflow split) modified the codebase architecture, control flow, or data routing.
    0 installs
62. ▌
    Qcpool Sample Identification · holobiomicslab

    Use when you have Sciex Multiquant (≥v3.0.3) TXT export files containing metabolomics or lipidomics analytical sequences that include pooled QC samples, and you need to verify that QCpool samples were injected at the designed regular intervals and extract their positional metadata for quality.
    2 installs
63. ▌
    Repository Source Code Setup · holobiomicslab

    Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.
    0 installs
64. ▌
    Repository Structure Parsing · holobiomicslab

    Use when when you encounter a multi-module scientific software project (e.
    0 installs
65. ▌
    Simulation Output Validation · holobiomicslab

    Use when after executing a reproducible simulation pipeline (particularly for Over-representation Analysis in metabolomics), compare the newly generated outputs against reference results to confirm that the simulation was correctly implemented and that the computational environment did not.
    0 installs
66. ▌
    Spectral Metadata Enrichment · holobiomicslab

    Use when you have a .msp spectral library file with sparse or incomplete metadata (e.
    2 installs
67. ▌
    Structured Result Validation · holobiomicslab

    Use when after retrieving a JSON or tabular response from a web service endpoint (such as CANOPUS), validate the result before parsing or integrating it into your analysis pipeline.
    1 install
68. ▌
    Validation Report Generation · holobiomicslab

    Use when when you have loaded a project JSON document from the Pairing Omics Data Platform and need to identify and document constraint violations (such as whitespace in URL fields) defined in the JSON schema.
    2 installs
69. ▌
    YAML JSON Structural Parsing · holobiomicslab

    Use when you have a versioned workflow definition file (YAML or JSON) from a specific release commit and need to verify it conforms to the project's schema specification, validate the presence of all required metadata fields (name, version, inputs, outputs, steps), and detect syntax errors or.
    0 installs
70. ▌
    API Documentation Automation · holobiomicslab

    Use when when you have a Python package with docstrings in the source code and need to generate comprehensive, browsable HTML API documentation.
    0 installs
71. ▌
    Arrow Columnar Data Decoding · holobiomicslab

    Use when when reading mzPeak files or other Parquet-backed mass spectrometry archives where spectral m/z and intensity arrays are stored in columnar layouts (point or chunked format) and you need to reconstruct them into Python NumPy arrays, pandas DataFrames, or equivalent in-memory structures for.
    0 installs
72. ▌
    Artifact Removal In Ims Data · holobiomicslab

    Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated detector signals that distort elution and mobility profiles.
    0 installs
73. ▌
    Bgc Sequence Domain Scanning · holobiomicslab

    Use when you have BGC sequences (in FASTA or GenBank format) from antiSMASH or other sources and need to extract biosynthetic domain composition as the primary signal for GCF (Gene Cluster Family) clustering or similarity queries.
    2 installs
74. ▌
    Big Slice Workflow Execution · holobiomicslab

    Use when you have a collection of antiSMASH-processed GenBank files (or custom BGC GenBank files prepared via the provided converter script) organized in a structured input folder, and you want to cluster them into Gene Cluster Families (GCFs) to chart biosynthetic diversity or identify.
    1 install
75. ▌
    Biobase Object Serialization · holobiomicslab

    Use when when you have raw peak table data from mass spectrometry or other metabolomic instruments in either a standardized tabular format or one of 12 common software tool outputs (e.
    0 installs
76. ▌
    Bruker Transient Data Import · holobiomicslab

    Use when you have Bruker Solarix raw transient data (.d folders containing ser or fid files) from an FT-ICR instrument and need to load it into a Python environment for noise thresholding, peak picking, mass calibration, or molecular formula assignment.
    0 installs
77. ▌
    Calibration Curve Validation · holobiomicslab

    Use when when you have loaded standard compound MS intensity measurements with known concentrations and need to select between linear or quadratic regression models before applying the calibration to unknown samples.
    0 installs
78. ▌
    Conditional Expression Logic · holobiomicslab

    Use when you need to create a derived image array where the output value at each pixel depends conditionally on the values of one or more element channels at that pixel. Common triggers include: (1) you want to mask or zero out pixels where an element concentration falls below a detection limit;
    0 installs
79. ▌
    Consensus Mass Determination · holobiomicslab

    Use when after constructing individual mass tracks from mzTree data bins and before alignment across samples.
    0 installs
80. ▌
    Cox Regression Model Fitting · holobiomicslab

    Use when you have expression or metabolomic feature matrices, paired with event indicators (e.g., disease recurrence, mortality) and follow-up times for a cohort of samples, and you need to derive risk scores or prognosis indices for survival prediction or patient stratification.
    0 installs
81. ▌
    Cross Omics Feature Matching · holobiomicslab

    Use when when you have two feature matrices from different omics modalities (e.
    0 installs
82. ▌
    Cross Origin Policy Override · holobiomicslab

    Use when you are loading index.html locally in a browser and WebWorker or WebAssembly components fail to initialize with cross-origin or file-access policy errors. This occurs when the default browser file-access policy blocks local resource sharing required by these technologies.
    0 installs
83. ▌
    Deep Learning Model Assembly · holobiomicslab

    Use when you have transformer encoder components and a prediction head specification, and need to wire them into a single trainable model that maps molecular structure inputs (SMILES, molecular graphs, or feature vectors) to scalar or vector molecular property predictions.
    2 installs
84. ▌
    Deep Learning Model Training · holobiomicslab

    Use when you have raw or preprocessed mass spectrometry feature matrices (e.g., from low mass resolution or sparse acquisition) and want to enhance signal quality and spatial resolution across tissue or single-cell samples.
    0 installs
85. ▌
    Docker Compose Orchestration · holobiomicslab

    Use when when you need to deploy the NP Classifier locally with TensorFlow Serving backend and nginx frontend on the same host, and you want to avoid manual container lifecycle management and inter-container networking configuration.
    0 installs
86. ▌
    Dotnet Framework Development · holobiomicslab

    Use when you need to compile and test a .NET-based metabolomics or bioinformatics desktop application (e.g., MS-DIAL version 5 series) from source code, or you are implementing new parsing or data-processing modules that must integrate with WPF UI frameworks and ReactiveExtensions patterns.
    0 installs
87. ▌
    Enrichment Score Computation · holobiomicslab

    Use when after you have normalized metabolite abundances across samples and mapped metabolites to pathway or ontology identifiers. Use it when your goal is to identify statistically significant metabolite pathways or classes rather than analyze individual metabolite abundance changes.
    0 installs
88. ▌
    Enrichment Table Compilation · holobiomicslab

    Use when you have completed Fisher's exact test enrichment analysis on a set of metabolites or lipids against a pathway/ontology reference (e.
    2 installs
89. ▌
    Feature Encoding Atoms Bonds · holobiomicslab

    Use when you have parsed SMILES or SDF molecular structures from a chemical dataset (e.g., SMRT dataset) and need to convert them into graph representations for input to a graph neural network or RT-Transformer model.
    0 installs
90. ▌
    Feature Matrix Normalization · holobiomicslab

    Use when after aggregating Pfam domain hits from HMM scanning into a domain-feature matrix (rows = BGCs, columns = Pfam domains, cells = bit-scores or binary presence), and before computing pairwise distances or clustering BGCs into gene cluster families (GCFs).
    0 installs
91. ▌
    Feature Matrix Preprocessing · holobiomicslab

    Use when you have raw metabolomics data in CSV format (samples as rows, features as columns, batch identifier in the first column) that contains missing values (zeros or NAs) and requires standardization before batch effect correction.
    0 installs
92. ▌
    Feature Pair Mass Refinement · holobiomicslab

    Use when after temporal correlation has identified feature pairs with matching intensity profiles across direct-injection MS experiments.
    0 installs
93. ▌
    Fragment Ion Peak Annotation · holobiomicslab

    Use when you have experimental MS/MS spectra matched against a reference library (via cosine similarity or dot-product scoring) and need to map individual fragment peaks in the experimental spectrum to their corresponding m/z and intensity values in the matched library entry.
    0 installs
94. ▌
    Genbank Accession Validation · holobiomicslab

    Use when you have a collection of sequence files (e.g., in a `genbanks` directory) and need to determine which are publicly available via NCBI and which are maintained locally only. This is critical for repositories like MIBiG that curate sequence data with mixed provenance.
    2 installs
95. ▌
    Glasso Regularization Tuning · holobiomicslab

    Use when when estimating a sparse network graph from a feature matrix using GLASSO and you need to determine the regularization strength.
    2 installs
96. ▌
    Group Annotation Integration · holobiomicslab

    Use when you have an expression matrix (e.g., heatmap_test.csv with genes as rows and samples as columns) and a corresponding group annotation file (e.g., group_info.csv with sample IDs and their group assignments).
    2 installs
97. ▌
    Gzip Index Structure Parsing · holobiomicslab

    Use when when you have an indexed gzip-compressed mzML file (mzML.gz with an internal index) and need to retrieve specific spectra or chromatogram data blocks by integer index without decompressing the entire archive.
    0 installs
98. ▌
    Integration Test Development · holobiomicslab

    Use when when you have implemented or modified a data ingestion module (e.g., mzML parser) and need to verify that file deserialization produces correct internal representations.
    2 installs
99. ▌
    JSON Spectral Format Parsing · holobiomicslab

    Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness, check for required metadata fields (SMILES, InChI, InChIKey, precursor m/z, adduct), and separate spectra by acquisition.
    0 installs
100. ▌
     Linear Axis Spatial Analysis · holobiomicslab

     Use when you have deposited mass spectrometry imaging datasets in NetCDF (CDF) format with accompanying MATLAB workspace files (.
     0 installs