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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Peak Quality Assessment By Selectivity And Snr Metrics · holobiomicslab

   Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence thresholds, and before mapping detected features back to individual samples or performing pre-annotation.
   0 installs
2. ▌
   Chromatographic Peak Detection With Prominence Control · holobiomicslab

   Use when after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature extraction in LC-MS or GC-MS metabolomics workflows.
   0 installs
3. ▌
   Ensemble Model Weight Learning For Spectral Prediction · holobiomicslab

   Use when you have pre-trained MLP and GNN models that generate different spectral predictions for the same metabolite candidates, and you want to combine them to improve ranking performance (average rank, Rank@K metrics) without retraining the base models.
   0 installs
4. ▌
   Multiway Principal Component Analysis Score Extraction · holobiomicslab

   Use when after preprocessing and aligning 2D chromatogram data (baseline correction, smoothing, peak alignment) and after running m_prcomp multiway PCA on the joined chromatogram matrix.
   0 installs
5. ▌
   Word2vec Vocabulary Matching And Unknown Peak Handling · holobiomicslab

   Use when converting MS/MS spectra into Spec2Vec embeddings using a pre-trained Word2Vec model that was trained on reference data (e.g., a subset of GNPS or MassBank).
   0 installs
6. ▌
   Candidate Neighbourhood Analysis For Spectral Matching · holobiomicslab

   Use when you have a query MS/MS spectrum matched against a library and need to re-rank the top 2000 candidate spectra by combining spectral similarity (MS2Deepscore) with structural neighbourhood information.
   0 installs
7. ▌
   Categorical Numerical Feature Concatenation For Graphs · holobiomicslab

   Use when when preparing heterogeneous column-metadata inputs for a graph transformer model that operates on molecular graphs. Specifically: (1) you have both categorical metadata (e.
   0 installs
8. ▌
   Connected Component Decomposition In Mass Spectrometry · holobiomicslab

   Use when you have a feature list from LC-MS preprocessing (e.g., asari output) and have already identified all pairwise feature matches to isotope and adduct patterns. Apply this skill when you need to separate feature matches into disjoint empirical compounds—i.
   0 installs
9. ▌
   Diagnostic Quality Assessment Of Chromatographic Peaks · holobiomicslab

   Use when after running targeted peak detection in TARDIS (screening_mode = FALSE) on centroided .mzML LC–MS files, apply this skill to verify that integrated peaks for your target compounds exhibit acceptable quality.
   0 installs
10. ▌
    Generalized Additive Model Hyperparameter Optimization · holobiomicslab

    Use when when fitting a nonlinear retention time (RT) mapping spline to anchor feature pairs (m/z and RT values) from two LC-MS datasets acquired under different conditions, you need to determine both the optimal B-spline basis dimension and identify which anchor points are outliers.
    0 installs
11. ▌
    Input Output Kernel Regression For Metabolite Matching · holobiomicslab

    Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links using metabolite structure information rather than genomic or strain-based features alone.
    0 installs
12. ▌
    Mass2motif Annotation Guidance Via Spectral Embeddings · holobiomicslab

    Use when after discovering Mass2Motifs through LDA topic modeling of MS/MS fragmentation data, when you need to assign chemical meaning (substructure classes, candidate annotations) to motifs by leveraging pre-trained spectral embeddings and a reference motif database.
    0 installs
13. ▌
    Metabolomics Functional Prediction Workflow Validation · holobiomicslab

    Use when a Python-based metabolomics analysis package has been relocated to a new GitHub organization (e.g., metabolomics-cloud) and you need to confirm that the migration preserved package integrity, installation, and runtime correctness.
    0 installs
14. ▌
    Method Equivalence Verification Across API Invocations · holobiomicslab

    Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode diagnostic outputs (e.g., EIC plots, peak detection metrics) are identical regardless of which invocation pattern is used.
    0 installs
15. ▌
    Ms2 Spectrum Peak Filtering By Training Set Membership · holobiomicslab

    Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a training dataset of known spectra (e.g., GNPS library spectra with structural annotations).
    0 installs
16. ▌
    Neutral Loss Calculation From Precursor Fragment Pairs · holobiomicslab

    Use when during MS/MS spectral preprocessing when converting raw spectra from .mgf, .msp, or .mzML formats into a bag-of-fragments corpus for LDA modeling. Use it after fragment ion masses have been extracted and normalized within each spectrum, and before noise filtering and corpus generation.
    0 installs
17. ▌
    Precursor Region Handling And M Z Tolerance Management · holobiomicslab

    Use when when computing entropy_similarity() between experimental (noisy or denoised) MS/MS spectra and reference library spectra, if the precursor m/z value is known and available.
    0 installs
18. ▌
    Quality Metric Computation From Mass Spectrometry Data · holobiomicslab

    Use when you have raw DIA mass spectrometry files (.raw, .d, or .wiff format) from timsTOF, TripleTOF, or Orbitrap instruments and need to assess their quality before downstream proteomics analysis.
    0 installs
19. ▌
    Receiver Operating Characteristic Curve Interpretation · holobiomicslab

    Use when you have a trained NeatMS neural network model and labelled peak validation data, and need to select an operational classification threshold or understand how TPR and FPR vary across probability thresholds (e.g., 0.00–0.99).
    0 installs
20. ▌
    Separation Efficiency Calculation From Retention Times · holobiomicslab

    Use when you have extracted retention times from MS1 spectra for top signals in a single LC-MS/MS run and need to evaluate whether that gradient's separation performance is sufficient, or when you are building the objective function for an iterative gradient optimization loop where each candidate.
    0 installs
21. ▌
    Strain Identifier Mapping Across Genomics Metabolomics · holobiomicslab

    Use when when preparing multiomics datasets for NPLinker that combine GNPS metabolomics, AntiSMASH genomics, and MIBiG reference data, and you need to establish which strain IDs or sample identifiers appear in both genomic and metabolomic experiments.
    0 installs
22. ▌
    Molecular Fragment Assembly From Transformer Predictions · holobiomicslab

    Use when when you have encoded spectral features (from a CNN featurizer applied to 1D 1H and/or 13C NMR spectra) and a set of candidate molecular fragments predicted for a molecule with ≤19 heavy atoms, and you need to determine the correct connectivity and assembly order to recover the.
    0 installs
23. ▌
    Chromatin Accessibility Binding Status Classification · holobiomicslab

    Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually occupied by proteins in your cell type or condition.
    0 installs
24. ▌
    Transcription Factor Binding Depletion Quantification · holobiomicslab

    Use when after bias-correcting ATAC-seq cutsite signal (using ATACorrect or equivalent) when you have a set of genomic regions of interest (e.
    0 installs
25. ▌
    Python Workflow Execution And Orchestration · holobiomicslab

    Use when you have raw LC/MS data in mzML format and need to execute a complete non-targeted screening workflow to extract and annotate chemical features.
    0 installs
26. ▌
    Replicate Spectrum Aggregation Sample Level · holobiomicslab

    Use when after frequency-based denoising has been applied to individual replicate spectra within each feature (via generate_denoised_spectra), you have a collection of denoised fragment ion lists per feature per scan.
    0 installs
27. ▌
    Repository Cloning And Structure Navigation · holobiomicslab

    Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.
    0 installs
28. ▌
    Retention Time Indexed Spectral Aggregation · holobiomicslab

    Use when you have Thermo Fisher Scientific .raw files from an LC-MS experiment and need to extract spectral features (base-peak m/z, intensity, scan-level properties) indexed by retention time for downstream statistical analysis, method optimization, or diagnostic visualization.
    0 installs
29. ▌
    Ripp Peptide Sequence Database Construction · holobiomicslab

    Use when when you have genomic sequences (assembled contigs or antiSMASH/BOA mining results) and want to match experimental tandem mass spectra against predicted RiPP structures.
    0 installs
30. ▌
    Scan Number Mapping Dictionary Construction · holobiomicslab

    Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable, memory-efficient lookup table that can be applied during feature alignment without recomputing the regression for every sample.
    0 installs
31. ▌
    Score Standardisation Z Score Normalization · holobiomicslab

    Use when when comparing raw link scores (strain correlation or IOKR) across different GCF-MF or BGC-spectrum pairs and you need to distinguish true positive links from background noise. Raw scores depend on overlap size and are incomparable across links with different cluster sizes;
    0 installs
32. ▌
    Search Result Aggregation And Normalization · holobiomicslab

    Use when you have executed batch searches across two or more domain-specific MASST tools and obtained separate output files (_microbe.json, _plant.json, _tissue.
    0 installs
33. ▌
    Similarity Ranking And Retrieval Evaluation · holobiomicslab

    Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
    0 installs
34. ▌
    Spectral Embedding Rationality Verification · holobiomicslab

    Use when after training a transformer-encoder-based mass spectrometry embedding model (e.
    0 installs
35. ▌
    Spectral Preprocessing For Machine Learning · holobiomicslab

    Use when when preparing raw MS2 spectra (m/z and intensity pairs) for kernel-based scoring methods such as IOKR, especially when the training dataset is large and represents diverse ion types.
    0 installs
36. ▌
    Spectrum Alignment Performance Benchmarking · holobiomicslab

    Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a spectral library search.
    0 installs
37. ▌
    Spectrum Visualization And Figure Rendering · holobiomicslab

    Use when when you have a processed or annotated MsmsSpectrum object (from USI loading or direct instantiation) and need to generate a figure showing observed peaks, their intensities, and assigned fragment ions (e.g., b/y ions) for publication or presentation.
    0 installs
38. ▌
    Structure Annotation Via Similarity Ranking · holobiomicslab

    Use when you have an unknown tandem MS spectrum and seek to assign a chemical structure by matching against a curated reference database (e.g., NIST, GNPS, or custom metabolite libraries) without requiring an exact spectral match.
    0 installs
39. ▌
    Structured Molecule Relationship Evaluation · holobiomicslab

    Use when when you have tandem mass spectra (MSMS) from related or candidate molecules and need to determine which similarity metric—cosine, modified cosine, or neutral loss— ranks structurally similar compounds in your dataset. Particularly useful when structural relationships are known a priori (e.
    0 installs
40. ▌
    Subformula Enumeration And Mass Calculation · holobiomicslab

    Use when when performing chemical denoising of MS/MS spectra: after modifying a master formula based on SMILES and adduct information, enumerate all possible subformulas to establish the set of chemically valid neutral losses.
    0 installs
41. ▌
    Thread Utilization Profiling And Validation · holobiomicslab

    Use when when deploying Mass2SMILES inference on CPU-only hardware (e.g., when GPU/CUDA support is unavailable), you need to verify that the InferenceModel cpu_threads parameter (e.g., cpu_threads=128) actually controls thread allocation during execution.
    0 installs
42. ▌
    Untargeted Metabolomics Dataset Integration · holobiomicslab

    Use when you have two LC-MS feature tables (each with m/z, retention time, and intensity columns) from independent untargeted metabolomic experiments or replicates and need to establish one-to-one feature correspondence across them to compare abundances, detect shared metabolites, or merge datasets.
    0 installs
43. ▌
    Workflow Configuration And Parameterization · holobiomicslab

    Use when when preparing to execute the Nextflow4MS-DIAL workflow on raw LC-HRMS metabolomics data (.mzML or .
    0 installs
44. ▌
    Y Ion Signal Detection And Noise Assessment · holobiomicslab

    Use when you have extracted a centroided MS/MS spectrum from a Thermo Orbitrap raw file (via rawrr::readSpectrum or equivalent) and need to verify that the observed y-ion fragments for a known peptide precursor exhibit signal-to-noise ratios consistent with high-quality fragmentation.
    0 installs
45. ▌
    Metadata Extraction From Fixed Offset Records · holobiomicslab

    Use when you have a binary file (e.g., NV format) with a known fixed-size header block (e.
    0 installs
46. ▌
    Multimodal Tensor Construction And Validation · holobiomicslab

    Use when when you have downloaded raw spectroscopic datasets from multiple sources (NMR, HSQC, COSY, IR files) and need to combine them into a single coherent training corpus where each molecule is represented by all four modalities.
    0 installs
47. ▌
    Peaklist Metabolite Assignment Prioritization · holobiomicslab

    Use when you have extracted m/z and retention time (m/z-RT) information for peaks from untargeted LC/HRMS data (using tools like IDSL.IPA) and need to assign molecular formula identities to those peaks.
    0 installs
48. ▌
    Pfas Characteristic Mass Difference Detection · holobiomicslab

    Use when you have centroided MS2 spectra (ddMS2 data in mzML format) from HRMS analysis and need to identify potential PFAS compounds among thousands of features.
    0 installs
49. ▌
    Spectral Data Format Parsing Nmr Hsqc Cosy Ir · holobiomicslab

    Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert them into aligned, standardized tensors for multimodal machine learning.
    0 installs
50. ▌
    Bioinformatics Tool Binary Path Resolution · holobiomicslab

    Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all required tools are installed, executable, meet version requirements (e.g., samtools ≥1.
    0 installs
51. ▌
    Duplicate Read Filtering And Normalization · holobiomicslab

    Use when you have raw ChIP-Seq and control BED files with potential PCR duplicates or unequal sequencing depths. Duplicate filtering is mandatory before estimating fragment length (predictd) or generating coverage pileups.
    0 installs
52. ▌
    End To End Bioinformatics Pipeline Testing · holobiomicslab

    Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.
    0 installs
53. ▌
    Fragment Length Estimation From Read Pairs · holobiomicslab

    Use when you have paired-end ChIP-Seq data (BEDPE format) and need to determine the empirical fragment length (insertion length) before peak calling. This is mandatory for paired-end ChIP-Seq workflows to ensure MACS3 correctly extends coverage tracks and calculates local bias;
    0 installs
54. ▌
    Principal Component Analysis Visualization · holobiomicslab

    Use when after merging methylation call files from multiple samples using unite() to create a methylBase object, apply PCA when you need to visualize sample-level relationships based on overall methylation similarity across all covered bases, or when you want to determine which principal components.
    0 installs
55. ▌
    Simulation Dataset Validation Benchmarking · holobiomicslab

    Use when when you have installed or updated a DNA methylation analysis tool (e.g., ChAMP) and need to verify that it produces documented expected outputs on a reference simulation dataset before applying it to real experimental data.
    0 installs
56. ▌
    Analytical Pipeline Feature Documentation · holobiomicslab

    Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses it supports—particularly when the pipeline is positioned as an alternative to or improvement over established tools.
    0 installs
57. ▌
    Call Graph Construction And Visualization · holobiomicslab

    Use when when you need to understand the computational structure of a modular scientific application (especially one with multiple subprojects or plug-in architectures) and static code inspection alone does not reveal algorithm entry points, parameter propagation, or intermediate data.
    0 installs
58. ▌
    Chemo Informatics Workflow Reconstruction · holobiomicslab

    Use when when you have access to the source code of a chemo-informatics tool (e.
    0 installs
59. ▌
    Constraint Based Model Output Integration · holobiomicslab

    Use when when you have (1) transcriptomics data and a metabolic network model with GPR rules to compute RAS scores; (2) constraint-based model predictions (RPS from optGpSampler or similar) quantifying how gene expression differences translate to flux differences;
    0 installs
60. ▌
    Contrastive Learning Encoder Construction · holobiomicslab

    Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or isotope discovery.
    0 installs
61. ▌
    Database Schema Design And Implementation · holobiomicslab

    Use when when you have an mzML file that you want to store persistently in a queryable format for repeated access, or when memory constraints prevent loading entire mzML files into memory;
    0 installs
62. ▌
    Deep Learning Architecture Implementation · holobiomicslab

    Use when you have two augmented versions of the same ion image (from mass spectrometry imaging data) and need to extract learnable 512-dimensional feature representations using a shared-weight encoder for contrastive loss optimization.
    0 installs
63. ▌
    Error State Tracking Across Microservices · holobiomicslab

    Use when building or maintaining a system that fetches metadata from multiple independent external web services and needs to diagnose why annotation runs fail or slow down. Use it specifically when you need to distinguish between service-level failures (e.
    0 installs
64. ▌
    Fold Change Sign Determination Statistics · holobiomicslab

    Use when you have paired measurements (e.g., gene expression counts, protein abundance, or sampled flux distributions) from two cell lines or conditions and need to assign a directional sign to each reaction or gene for downstream concordance analysis.
    0 installs
65. ▌
    Instrument Platform Compatibility Mapping · holobiomicslab

    Use when when adopting a mass spectrometry data processing tool (e.g., LipidMatch) and needing to verify whether your specific instrument platform (vendor + model) and acquisition mode combination (targeted, ddMS2-topN, AIF, direct infusion, imaging) have been formally validated.
    0 installs
66. ▌
    Interactive HTML Figure Generation Plotly · holobiomicslab

    Use when your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration, web-based presentation, or interactive supplementary material.
    0 installs
67. ▌
    Ionization Mode Peak Retention Comparison · holobiomicslab

    Use when when you have loaded a raw mass spectrum (e.g. ESI_NEG_SRFA.
    0 installs
68. ▌
    Matplotlib Bokeh Plotly Backend Switching · holobiomicslab

    Use when when you have mass spectrometry data (chromatograms, spectra, mobilograms, or peak maps) in a Pandas DataFrame and need to generate the same visualization in multiple formats—e.
    0 installs
69. ▌
    Microbial Genome Annotation Harmonization · holobiomicslab

    Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single consensus model per organism that reflects only metabolic capabilities agreed upon across the input reconstructions, or when.
    0 installs
70. ▌
    Molecular Structure Input Format Handling · holobiomicslab

    Use when you are receiving molecular structures from external sources (COCONUT database, ZINC database, user-provided chemical data) in varying formats (SMILES strings, InChI identifiers, SDF files), and you need to unify them into a single canonical representation before computing biosynfoni.
    0 installs
71. ▌
    Multivariate Ordination Analysis Nmds Pca · holobiomicslab

    Use when after peak filtering and normalization, when you have a peak-abundance matrix (samples × assigned molecular formulas) and need to visualize and test for differences in overall molecular composition across experimental conditions or sample groups.
    0 installs
72. ▌
    Nmds Ordination Distance Metric Selection · holobiomicslab

    Use when when you have normalized peak intensity matrices from FT-ICR MS data or other high-resolution metabolomics experiments and need to visualize sample relationships and assess whether categorical grouping factors (e.
    0 installs
73. ▌
    Optional Dependency Extra Specifier Usage · holobiomicslab

    Use when when a Python package provides optional support for specialized data formats or functionality (e.
    0 installs
74. ▌
    Record Field Transformation And Collation · holobiomicslab

    Use when you have extracted tabular data into an intermediate JSON form and need to restructure records by mapping input fields to output dictionary keys, collating multiple records under a single grouping field, filtering records by test conditions or exclusion rules, or applying custom.
    0 installs
75. ▌
    Regression Metric Computation Rmse Mae R2 · holobiomicslab

    Use when you have model predictions and ground-truth labels for a test set and need to assess how well the trained model generalizes to unseen data. Typical triggers: after executing inference on a held-out test partition, after cross-dataset evaluation (e.
    0 installs
76. ▌
    Smiles Structure Annotation From Molfiles · holobiomicslab

    Use when you have a mass spectral library in MSP format (e.g., from NIST, SWGDRUG, or other sources) exported alongside a folder of MOL files, and you need to populate the SMILES field in each library record to enable structure-based filtering, annotation, or downstream MS-DIAL analysis.
    0 installs
77. ▌
    Spearman Correlation Statistical Analysis · holobiomicslab

    Use when you have paired predicted and observed metabolite abundance vectors from a predictive model (e.
    0 installs
78. ▌
    Summary Visualization Artifact Generation · holobiomicslab

    Use when you have completed batch spectral searches against multiple domain-specific MASST tools (via Fast Search API or individual domain searches) and need to combine and visualize the aggregated match results in a format compatible with metadataMASST web interface or downstream analysis.
    0 installs
79. ▌
    Test Output Parsing And Status Validation · holobiomicslab

    Use when you need to verify whether a GitHub Actions workflow badge (e.g., main.yml) accurately reports the CI pipeline's true pass/fail status.
    0 installs
80. ▌
    Transcriptomics Reaction Activity Scoring · holobiomicslab

    Use when you have RNA-seq read counts (FPKM or similar) for multiple cell lines or biological samples, a genome-scale metabolic model with GPR associations, and you need to constrain or weight metabolic reactions based on transcriptional regulation.
    0 installs
81. ▌
    Version Control Feature Branch Management · holobiomicslab

    Use when when you have modifications to propose for a shared codebase (e.g., bug fixes, new features, or documentation updates) and need to integrate them without disrupting the main development branch.
    0 installs
82. ▌
    Association Ranking Statistical Filtering · holobiomicslab

    Use when you have identified co-occurring metabolite–genomic variant associations from a network-driven over-representation analysis and need to rank them by confidence and control the family-wise error rate.
    0 installs
83. ▌
    Build System Configuration Identification · holobiomicslab

    Use when you have cloned a source repository and need to compile it on a supported operating system (Windows 10, Ubuntu 22.04, macOS 12+ ARM64) but do not know what build tools, dependencies, or compilation commands are required.
    0 installs
84. ▌
    Chemical Structure Integrity Verification · holobiomicslab

    Use when you have received or downloaded an SDF-formatted compound database file and need to confirm it is not corrupted, contains the expected number of molecular records, and that each record is structurally valid before using it in compound identification, library matching, or database.
    0 installs
85. ▌
    Chromatogram Retention Time Visualization · holobiomicslab

    Use when you have mass spectrometry data loaded as a pandas DataFrame with at minimum two numeric columns representing retention time and intensity values, and you need to generate a chromatogram visualization for exploratory analysis, quality control, or publication.
    0 installs
86. ▌
    Chromatographic Peak Detection Validation · holobiomicslab

    Use when you have centroided mzML data and a curated set of target molecules with known retention time (RT) boundaries, and you need to establish ground-truth peak detection performance metrics (e.
    0 installs
87. ▌
    Cnn Architecture Design For Spectral Data · holobiomicslab

    Use when when you have mass-spectrometry data (m/z and intensity pairs or spectral matrices) paired with ground-truth molecular fingerprints or InChIKeys, and you need to learn a non-linear mapping from spectral patterns to structural fingerprints for downstream metabolite ranking or annotation.
    0 installs
88. ▌
    Composite Map Data Structure Construction · holobiomicslab

    Use when after mass track extraction and alignment across samples, when you have a MassGrid structure (m/z-aligned mass tracks) and corresponding retention time calibration dictionaries for each sample, and need to prepare input for composite peak detection rather than per-sample peak detection.
    0 installs
89. ▌
    Concordance Score Calculation Cohen Kappa · holobiomicslab

    Use when you have paired quantitative variation patterns for the same set of reactions across multiple biological samples (cell lines) and need to discriminate whether flux variations correlate monotonically with substrate abundance changes (metabolic control) versus gene expression changes.
    0 installs
90. ▌
    Conditional Dispatch Logic Implementation · holobiomicslab

    Use when when accepting a file path as input in an MSI data processing pipeline and you need to determine which data reader module to instantiate before calling get_image_data() or load_pixels(). This arises when building a multi-vendor instrument workflow (e.
    0 installs
91. ▌
    Confidence Score Assignment And Filtering · holobiomicslab

    Use when after matching MRM transitions against a lipid reference database, when you have candidate lipid identities for each transition and need to rank them by quality and select a single match per transition for export to the labelled lipid-identity table.
    0 installs
92. ▌
    Cosine Annealing Learning Rate Scheduling · holobiomicslab

    Use when when training a heavily regularized deep neural network on large molecular datasets (e.
    0 installs
93. ▌
    Dataframe Construction And Column Merging · holobiomicslab

    Use when when implementing a new MsBackend subclass and need to return complete spectra data as a single DataFrame object that combines required core variables with backend-specific metadata columns, while avoiding cyclic function calls between spectraData() and spectraVariables().
    0 installs
94. ▌
    Deep Learning Neural Network Optimization · holobiomicslab

    Use when you have a preprocessed metabolomics expression matrix with labeled samples and need to compare deep learning performance against traditional classifiers (SVM, RF, GBM, LDA, LOG, Rpart, PAM), or when you need to build a prognosis model that incorporates non-linear interactions between.
    0 installs
95. ▌
    Dependency Installation And Configuration · holobiomicslab

    Use when when setting up a fresh clone of the ENPKG workflow repository or when onboarding to a new machine. Use this skill before attempting to run any workflow stages (data organization, taxonomical enhancement, MN generation, SIRIUS annotation, or graph building).
    0 installs
96. ▌
    Differential Metabolite Abundance Testing · holobiomicslab

    Use when you have preprocessed and normalized metabolite measurements from two or more distinct biological groups (e.
    0 installs
97. ▌
    Dockerfile Multi Stage Build Architecture · holobiomicslab

    Use when when you need to containerize a Windows-only .NET Framework GUI application (such as AirdPro V5/V6 written in C# for .NET Framework 4.8) for execution on macOS or Linux hosts, and you want to avoid shipping compile-time tooling (SDK) in the production image.
    0 installs
98. ▌
    Feature Matrix Aggregation Across Samples · holobiomicslab

    Use when after per-sample quantification is complete (e.g., salmon has produced quant.sf files for all samples in the cohort) and you need to prepare data for differential expression analysis, quality control comparisons, or multi-omics integration.
    0 installs
99. ▌
    Gene Level Volcano And Ma Plot Generation · holobiomicslab

    Use when after completing differential expression analysis (edgeR, DESeq2, or RankProduct) on count matrices to visualize fold-changes versus p-values and to assess the relationship between average expression levels and log2 fold-changes for gene-level omics data.
    0 installs
100. ▌
     Gnuplot Library Availability Verification · holobiomicslab

     Use when when deploying a Perl-based GUI application (such as LipidOne) on Microsoft Windows that depends on Gnuplot for visualization, and you need to ensure the application will not crash during dataset loading or plotting operations due to missing or inaccessible Gnuplot binaries.
     0 installs