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HolobiomicsLab

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1. ▌
   Ms Quantitative Analysis Standards · holobiomicslab

   Use when you have raw MS intensity data paired with known-concentration calibration standard measurements, and you need to convert intensities to absolute or relative concentrations.
   0 installs
2. ▌
   Ms Vendor Documentation Extraction · holobiomicslab

   Use when you need to determine the complete set of validated instrument/vendor and acquisition mode combinations for a mass spectrometry analysis tool, when assessing whether your specific instrument platform (vendor, model, acquisition method) is supported before committing to a workflow, or when.
   0 installs
3. ▌
   Multi Library Comparative Analysis · holobiomicslab

   Use when you need to evaluate whether a newly released or candidate library (e.g., spectrum_utils v0.4.
   2 installs
4. ▌
   Multivariate Regression Comparison · holobiomicslab

   Use when you have paired microbiome and metabolomic (or similar compositional) data with a new regression model and want to rigorously demonstrate its predictive advantage over alternatives (Elastic Net, Random Forest, CCA).
   2 installs
5. ▌
   Network Module Interaction Scoring · holobiomicslab

   Use when after biclustering a normalized microbe-metabolite feature attribution score matrix into distinct functional modules, use this skill to summarize pairwise module interactions by aggregating scores between all microbe-metabolite pairs from different modules.
   0 installs
6. ▌
   Neural Network Layer Instantiation · holobiomicslab

   Use when when you have a neural network layer definition (parameters, weight initialization, embedding dimension) from a trained or pretrained model checkpoint and need to generate embeddings or activations for a new batch of chemical formulas or spectrum fragments.
   0 installs
7. ▌
   Parameter Sharing Mechanism Design · holobiomicslab

   Use when designing a contrastive learning pipeline for ion images or other data modalities where you need to process multiple augmented versions of the same input through an encoder and enforce similarity between the resulting representations.
   0 installs
8. ▌
   Parser Error Reporting Diagnostics · holobiomicslab

   Use when when implementing or extending a DSL parser (lexer + recursive descent or LALR parser) that accepts user-authored query strings.
   0 installs
9. ▌
   Plant Metabolic Network Validation · holobiomicslab

   Use when after community-dependent gap-filling has proposed reactions to fill metabolic gaps in individual consensus reconstructions.
   0 installs
10. ▌
    Platform Specific Code Refactoring · holobiomicslab

    Use when a Shiny application or R package currently runs only on Windows and you need to enable deployment on Linux or macOS.
    0 installs
11. ▌
    Quality Control Interval Detection · holobiomicslab

    Use when when you have Sciex Multiquant TXT export files containing injection sequences from metabolomics or lipidomics studies where pooled QC samples were deliberately injected at regular intervals to monitor analytical quality.
    0 installs
12. ▌
    Quantitative Ms Data Preprocessing · holobiomicslab

    Use when you have raw MS intensity tables showing systematic drift during a measurement sequence (e.g., declining or variable ion counts across a run), particularly in targeted quantification workflows where external calibration standards are available.
    0 installs
13. ▌
    Random Access Index Implementation · holobiomicslab

    Use when you have a large compressed scientific data file (e.g., indexed gzip mzML) where you need to retrieve specific spectra, chapters, or records by integer ID without loading the entire file into memory.
    0 installs
14. ▌
    Regression Error Metric Evaluation · holobiomicslab

    Use when when you have trained multiple regression models (e.g., using different feature sets: descriptors-only, fingerprints-only, or combined) on the same training data and need to objectively rank their generalization performance on unseen test data.
    2 installs
15. ▌
    Representation Collapse Prevention · holobiomicslab

    Use when training a contrastive learning model on ion image data (mass spectrometry imaging) where augmented pairs of the same ion image must maximize similarity while different images minimize similarity.
    0 installs
16. ▌
    Smiles Inchi Round Trip Validation · holobiomicslab

    Use when you have implemented a new RDKit-based ComputeConverter for SMILES↔InChI conversions and need to verify that the conversion methods preserve molecular structure integrity across round-trip transformations (SMILES → InChI → SMILES or vice versa) before registering it in the MSMetaEnhancer.
    0 installs
17. ▌
    Structured Data Quality Assessment · holobiomicslab

    Use when when you have deposited a collection of JSON project documents in a platform or repository and need to verify that all conform to a published JSON Schema specification before publication, distribution, or integration with downstream systems.
    2 installs
18. ▌
    Technical Specification Tabulation · holobiomicslab

    Use when when you need to verify whether a specific mass spectrometry instrument platform (vendor and model), acquisition mode (e.g., targeted, ddMS2-topN, AIF, direct infusion, imaging), or file format is compatible with a lipidomics or proteomics software tool;
    0 installs
19. ▌
    Validated Link Enrichment Analysis · holobiomicslab

    Use when when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated links for the same strain(s), and need to assess whether combining or filtering by percentile thresholds improves.
    0 installs
20. ▌
    Abstract Base Class Implementation · holobiomicslab

    Use when when building a visualization library that must support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and multiple data types (e.g., chromatograms, spectra, peak maps) without duplicating core logic or configuration handling across backend–plot-type combinations.
    0 installs
21. ▌
    Adduct Mass Adjustment Calculation · holobiomicslab

    Use when you have a set of in silico-predicted compounds (with SMILES structures) and an experimental metabolomics peak list (m/z values), and you need to filter predictions to only those that could plausibly be detected.
    0 installs
22. ▌
    Autoencoder Encoder Decoder Design · holobiomicslab

    Use when when working with imaging mass spectrometry (IMS) datasets where you need to extract latent low-dimensional peak features from high-dimensional peak intensity data while preserving spatial adjacency information.
    2 installs
23. ▌
    Batch Corrected Data Visualization · holobiomicslab

    Use when after doAnalysis() has been completed and batch correction applied (ratio_corrected assay populated), use this skill when you need to inspect the effect of batch correction on QC sample clustering, verify that study samples group appropriately by type or aliquot, or identify remaining.
    0 installs
24. ▌
    Batch Effect Correction Combat Sva · holobiomicslab

    Use when you have a normalized count matrix (from Salmon or similar quantification tool) with sample metadata that documents batch variables (e.g., sequencing run, processing date, lab site), and you observe or suspect that batch effects—not biological signal—are driving variance across samples.
    2 installs
25. ▌
    Betweenness Centrality Computation · holobiomicslab

    Use when when you have a pathway-metabolite bipartite network and a filtered set of input metabolites (e.g., from differential analysis or experimental selection), and you need to rank metabolites by their topological importance within the network structure—i.
    0 installs
26. ▌
    Bgc Tokenization With Pfam Domains · holobiomicslab

    Use when you have GenBank-format BGC sequences annotated with Pfam domain assignments and you need to prepare them for sub-cluster detection, redundancy filtering via similarity networks, or linking to natural product substructures.
    0 installs
27. ▌
    Binary Data Integrity Verification · holobiomicslab

    Use when after implementing a lossless compression–decompression cycle on mzML or mzXML mass spectrometry files, or when validating that a lossy compression pipeline meets acceptable error thresholds.
    0 installs
28. ▌
    Biotransformation Rule Application · holobiomicslab

    Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to predict its fate in soil or aquatic environments through microbial degradation pathways.
    2 installs
29. ▌
    Bounding Box Regression Prediction · holobiomicslab

    Use when when you have a trained CNN binary classifier for peak detection on rt×mz LC-HRMS images and need to additionally output precise bounding-box coordinates (left, right, top, bottom) and peak-center pixel positions for each detected peak to enable accurate feature quantitation or visual.
    0 installs
30. ▌
    Classyfire Batch Database Querying · holobiomicslab

    Use when you have a GNPS DBResult file with InChIKey identifiers but lack corresponding ClassyFire superclass, class, and subclass taxonomy annotations—particularly when GNPS spectral library matches no longer include this ontology information by default.
    0 installs
31. ▌
    Collision Cross Section Prediction · holobiomicslab

    Use when you have molecular structures (SMILES or SDF format) and need to predict their collision cross sections for ion mobility mass spectrometry workflows, particularly when generating large-scale searchable CCS databases for compound identification and characterization.
    0 installs
32. ▌
    Compound Reliability Rsd Filtering · holobiomicslab

    Use when after batch correction and internal standard ratio calculation when you have pooled study quality control (SQC) or pooled quality control (QC) samples and need to determine which compounds are sufficiently reliable for downstream reporting.
    2 installs
33. ▌
    Concentration Based Signal Scaling · holobiomicslab

    Use when you have loaded m/z peak data with metadata that includes a concentration column representing sample loading mass or volume, and systematic intensity variation across samples is suspected to reflect preparation differences rather than true biological variation.
    2 installs
34. ▌
    Correlation Threshold Optimization · holobiomicslab

    Use when after computing pairwise correlations across all features in a dataset (especially those exceeding 10,000 features), before constructing the final network object.
    0 installs
35. ▌
    Cross Table Metadata Harmonization · holobiomicslab

    Use when when you have obtained raw metabolite abundance data in a format that separates the measurement matrix from sample-level metadata (e.g., run day, plate ID, cohort variables) and feature-level annotations (e.
    0 installs
36. ▌
    Cross Validation Model Aggregation · holobiomicslab

    Use when after training multiple neural network models via k-fold cross-validation (e.g., 10 iterations × 10-fold = 100 models), when you need to extract and aggregate learned feature interactions rather than relying on a single trained model.
    0 installs
37. ▌
    CSV File Parsing And Peak Indexing · holobiomicslab

    Use when you have a metabolomics dataset (CSV format) containing detected peaks with m/z values and optionally retention time windows, and you need to filter a Pickaxe-generated compound expansion to keep only compounds whose masses match these observed peaks within a specified mass tolerance.
    0 installs
38. ▌
    Data Object Loading And Inspection · holobiomicslab

    Use when you have identified example R or MATLAB scripts in a repository's Codes-Explained folder and need to execute them on a documented sub-sample scenario. The link-to-codes-and-data-objects file specifies which data object(s) to load, and the Read-Me.
    2 installs
39. ▌
    Data Quality Validation Lipidomics · holobiomicslab

    Use when after loading and parsing raw MRM export files (TSV, CSV, or vendor-specific formats) into a pandas DataFrame and decomposing lipid nomenclature, before performing lipid matching, statistical analysis, or visualization.
    0 installs
40. ▌
    Database Record Conditional Update · holobiomicslab

    Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field (e.g., ionmode: 'pos'/'neg') that can deterministically populate the missing field.
    0 installs
41. ▌
    Datatype Validation Helper Methods · holobiomicslab

    Use when when implementing a custom MsBackend subclass and need to verify that spectra variables (e.g., precursor m/z, retention time, MS level) conform to expected data types before exposing them to Spectra objects.
    0 installs
42. ▌
    Deep Neural Network Regularization · holobiomicslab

    Use when when training a DNN on molecular properties (e.g., retention time) using high-dimensional feature sets (>2000 fingerprints + descriptors) where test performance is critical and overfitting risk is high due to model capacity or limited validation data;
    0 installs
43. ▌
    Dot Product Similarity Computation · holobiomicslab

    Use when when performing open modification spectral library searching and you need to sensitively match query spectra that may carry unknown post-translational or chemical modifications to an unmodified spectral library.
    2 installs
44. ▌
    Dotnet Project Build Configuration · holobiomicslab

    Use when you are attempting to compile a WPF-based .NET desktop application from source code that targets multiple .NET Framework versions, have cloned a repository with an .sln solution file, and need to resolve framework-specific NuGet dependencies (e.
    0 installs
45. ▌
    External Calibration Model Fitting · holobiomicslab

    Use when you have acquired targeted mass spectrometry data with measured ion intensities for known standard compounds at multiple concentration levels, and you need to convert sample intensities into absolute or relative concentrations.
    0 installs
46. ▌
    Feature Branch Workflow Management · holobiomicslab

    Use when when implementing a new feature or bug fix in a shared repository (such as Maven GUI metabolomics analysis software) where multiple contributors work in parallel and code quality is enforced via CI/CD pipelines (Travis, Appveyor).
    0 installs
47. ▌
    Feature Correlation Sparsification · holobiomicslab

    Use when you have a feature matrix (rows=samples, columns=features) and want to infer the conditional independence structure among features.
    2 installs
48. ▌
    Feature Set Performance Evaluation · holobiomicslab

    Use when when deciding which molecular representation to use for retention time prediction or similar regression tasks on small molecules, and you have access to multiple feature generation options (e.g., alvaDesc can generate both molecular descriptors and multiple fingerprint types).
    0 installs
49. ▌
    Feature Transformation And Scaling · holobiomicslab

    Use when after imputation and QC sample correction when: (1) your peak intensity data show heteroscedastic variance (e.g., variance increases with mean intensity); (2) you aim to improve normality of feature distributions for parametric statistical tests;
    0 installs
50. ▌
    Fingerprint Generation From Smiles · holobiomicslab

    Use when you have molecule IDs from PubChem or HMDB that have been converted to RDKit molecule objects, and you need to create a standardized fingerprint modality to combine with graph-based and physicochemical descriptor features for multimodal deep learning on molecular property prediction.
    0 installs
51. ▌
    Formula Deduplication And Counting · holobiomicslab

    Use when when you have loaded a chemical database (e.g., HMDB pickle file) and need to understand how many distinct molecular formulas remain after filtering for a specific m/z range (e.g., 100–1000) and MS acquisition level (typically MS level 1).
    0 installs
52. ▌
    Gene Domain Co Occurrence Analysis · holobiomicslab

    Use when you have a collection of BGCs tokenised as Pfam domain / subPfam combinations, have filtered them for redundancy using domain-based similarity networks, and need to discover latent gene sub-clusters that group together genes with correlated domain compositions.
    0 installs
53. ▌
    Graph Neural Network Model Loading · holobiomicslab

    Use when when you need to evaluate GNN performance on collision cross section prediction using the enveda/ccs-prediction repository, either by loading an existing pre-trained model checkpoint or by retraining from scratch using deposited datasets and published hyperparameters.
    0 installs
54. ▌
    Graphical Interface Error Handling · holobiomicslab

    Use when when building a standalone desktop application with a graphical user interface that depends on external binary tools or libraries, and you need to prevent user confusion from cryptic runtime errors. Specifically: when your GUI framework (e.
    0 installs
55. ▌
    Group Specification And Subsetting · holobiomicslab

    Use when when implementing a fold-change filter or similar feature-level metric that requires comparison across sample groups, and the analysis goal requires including or excluding specific groups (e.g., comparing only treated vs. control samples, or excluding low-quality replicates).
    0 installs
56. ▌
    Harmonized Metadata Schema Mapping · holobiomicslab

    Use when you have imported mass spectrometry spectra from multiple file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to standardize their metadata fields before performing spectral comparisons, similarity scoring, or library construction.
    2 installs
57. ▌
    Histogram Peak Occurrence Analysis · holobiomicslab

    Use when after you have computed a histogram of pairwise mass differences from MSI peak data and want to identify which mass shifts occur most frequently and whether they correspond to known chemical adducts.
    0 installs
58. ▌
    Imaging Data Workspace Integration · holobiomicslab

    Use when you have paired cdf files (raw mass spectrometry imaging data) and Matlab workspace (.mat) files for the same root sample, and you need to reproduce published linear-axis imaging analysis results (e.g., per-root mass spectrometry imaging metrics along a developmental or spatial axis).
    0 installs
59. ▌
    Interactive Plot Axis Selection UI · holobiomicslab

    Use when when you have a high-resolution mass spectrometry dataset with m/z values and need to generate Kendrick mass plots where users should choose between plotting raw m/z or computed Normalized Kendrick Mass (NKM) on the x-axis.
    0 installs
60. ▌
    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
61. ▌
    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
62. ▌
    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
63. ▌
    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
64. ▌
    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
65. ▌
    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
66. ▌
    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.
    2 installs
67. ▌
    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
68. ▌
    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
69. ▌
    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
70. ▌
    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
71. ▌
    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.
    1 install
72. ▌
    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
73. ▌
    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
74. ▌
    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).
    1 install
75. ▌
    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
76. ▌
    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
77. ▌
    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.
    2 installs
78. ▌
    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.
    2 installs
79. ▌
    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
80. ▌
    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
81. ▌
    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
82. ▌
    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.
    2 installs
83. ▌
    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
84. ▌
    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.
    2 installs
85. ▌
    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
86. ▌
    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
87. ▌
    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
88. ▌
    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
89. ▌
    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
90. ▌
    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
91. ▌
    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.
    1 install
92. ▌
    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
93. ▌
    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
94. ▌
    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
95. ▌
    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
96. ▌
    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
97. ▌
    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
98. ▌
    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.
    2 installs
99. ▌
    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
100. ▌
     Frame Metadata Extraction And Export · holobiomicslab

     Use when after completing multidimensional smoothing and saturation repair on Agilent MassHunter (.
     0 installs