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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Metabolite Annotation By Chromatographic Behavior · holobiomicslab

   Use when when you have an untargeted metabolomics dataset from HPLC–MS (e.g., mzML, NetCDF) with detected peaks of unknown identity, and you need to disambiguate or validate tentative compound annotations by comparing observed retention time against machine-learning predicted retention time.
   0 installs
2. ▌
   Metabolomics Peak Data Normalization And Handling · holobiomicslab

   Use when when you have raw peak intensity matrices from metabolomics LC-MS/MS experiments with zero values (missing peaks or undetected compounds) and need to prepare data for pathway-level analysis using PLAGE, ORA, or GSEA.
   0 installs
3. ▌
   Missing Value Imputation In Quantification Tables · holobiomicslab

   Use when after feature alignment across multiple LC-MS/MS runs, when the unified feature list contains zeros or nulls for specific feature–sample pairs because peaks were not detected in those individual runs, but the feature was detected in other samples in the cohort.
   0 installs
4. ▌
   Nearest Neighbor Clustering For Mass Spectrometry · holobiomicslab

   Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
   0 installs
5. ▌
   Negative Adduct Tokenization In Mass Spectrometry · holobiomicslab

   Use when you have negative-mode MS/MS spectra with annotated molecular formulas and negative adducts (from repositories like MassIVE or MetaboLights), and your current formula inference model is restricted to positive mode only.
   0 installs
6. ▌
   Neural Network Inference And Embedding Extraction · holobiomicslab

   Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to generate low-dimensional embeddings for spectral visualization, clustering, or retrieval tasks.
   0 installs
7. ▌
   Outlier Detection And Downweighting In Regression · holobiomicslab

   Use when when fitting a nonlinear regression (GAM spline) through retention time anchor points derived from feature pair alignments in LC-MS metabolomics, and you suspect some anchor points are measurement errors or misaligned features that could bias the smooth curve.
   0 installs
8. ▌
   Receiver Operator Characteristic Curve Generation · holobiomicslab

   Use when when you have computed similarity scores (cosine, modified cosine, Spec2Vec, or other metrics) between a set of query spectra and a reference library with known structural annotations (InChIKey), and you need to evaluate how well each scoring method distinguishes true structural matches.
   0 installs
9. ▌
   Reference Based Vs Global Coordinate Registration · holobiomicslab

   Use when you have detected feature tables from multiple LC-IMS-MS/MS samples (each with mz, drift_time, retention_time, and intensity columns) and need to match corresponding features across datasets to enable cross-sample quantitation or cohort analysis.
   0 installs
10. ▌
    Smiles Identifier Assignment From Structure Files · holobiomicslab

    Use when when you have a mass spectral library (MSP format) that lacks SMILES annotations but is paired with a folder of MOL structure files (from Lib2NIST export or similar source).
    0 installs
11. ▌
    Spectral Data Object Construction And Integration · holobiomicslab

    Use when you have centroided mzML files from LC–MS experiments and need to perform targeted metabolomics or lipidomics analysis. Specifically, use it when you require polarity filtering, QC-sample stratification, or batch-aware peak detection—all of which depend on sampleData$type annotations (e.
    0 installs
12. ▌
    Tandem Mass Spectrometry Fragmentation Simulation · holobiomicslab

    Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to evaluate without access to real mass spectrometry hardware.
    0 installs
13. ▌
    Tandem Mass Spectrometry Metadata Standardization · holobiomicslab

    Use when you have raw MS/MS spectra from public repositories (e.
    0 installs
14. ▌
    Tandem Mass Spectrometry Mirror Plot Construction · holobiomicslab

    Use when when you have raw LC-MS or LC-IMS-MS data in instrument format (Agilent .d, Thermo .raw, Bruker .
    0 installs
15. ▌
    Uncertainty Quantification From Model Predictions · holobiomicslab

    Use when when you have a trained neural network (e.g., a Siamese model predicting molecular structural similarity) and need to identify and filter unreliable predictions before using them in downstream analysis. Apply this skill when raw model performance is suboptimal (~0.
    0 installs
16. ▌
    Metabolite Identification From Transformation Rules · holobiomicslab

    Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological compartment (e.g., soil/aquatic microbiota, mammalian liver, or gut microbiota).
    0 installs
17. ▌
    Performance Degradation Quantification And Analysis · holobiomicslab

    Use when you have a pretrained model with documented performance on a bounded input domain (e.g., molecules ≤19 heavy atoms, sequences <1000 bp) and you need to establish whether and how much accuracy drops on held-out test cases outside that domain boundary.
    0 installs
18. ▌
    Sample Prioritization Through Structural Clustering · holobiomicslab

    Use when you have 2D NMR spectral data (HSQC, HMBC, COSY) from multiple samples in a natural products screening campaign and need to rank samples by structural novelty or identify which samples share common molecular scaffolds.
    0 installs
19. ▌
    Unknown Chemical Identification In Complex Mixtures · holobiomicslab

    Use when you have experimental LC–QTOF mass spectra from complex environmental samples (e.
    0 installs
20. ▌
    Cluster Umap Layout Reproducibility Benchmarking · holobiomicslab

    Use when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10k_multiome dataset (or a similar single-cell ATAC-seq dataset with a published reference) and need to validate that spectral embedding, Leiden clustering, and UMAP layout have converged to expected cluster identities and.
    0 installs
21. ▌
    Contact Frequency Aggregation By Genomic Feature · holobiomicslab

    Use when you have a cooler Hi-C contact matrix, a set of genomic features (e.g., CTCF peaks, enhancers, or TAD boundaries defined in BED format), and want to quantify average contact patterns around those features to detect local organization principles.
    0 installs
22. ▌
    Genome Alignment And Contact Matrix Construction · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a kilobase-resolution Hi-C experiment and need to produce a processed Hi-C contact map (.hic file) for visualization, loop calling, or chromatin structure analysis. This is the entry point for any Hi-C dataset that has not yet been aligned and normalized.
    0 installs
23. ▌
    Genome Sequence Matching For Nucleotide Patterns · holobiomicslab

    Use when you have filtered peak or chromatin accessibility counts and need to annotate each peak with the presence or absence of specific DNA sequence patterns—either predefined motifs (e.
    0 installs
24. ▌
    Background Distribution Null Hypothesis Testing · holobiomicslab

    Use when when predicting one data modality (e.g., metabolite abundances) from another (e.g., microbiome composition) and you need to distinguish genuine microbe–metabolite associations from false positives driven by data compositionality, sample size artifacts, or confounding variation.
    0 installs
25. ▌
    Compound Reliability Filtering By Rsd Threshold · holobiomicslab

    Use when apply this filter after batch correction of compound/internal-standard ratios when you have pooled study quality control (SQC) samples and need to determine which compounds are sufficiently reproducible for downstream reporting. Use it specifically when the nonReportableRSD threshold (e.
    0 installs
26. ▌
    Containerized Application Deployment Validation · holobiomicslab

    Use when when deploying containerized versions of a multi-variant application (e.g., CLI, development, Linux, and Windows flavors) and you need to verify that each built image meets documented size constraints before registry push or production release.
    0 installs
27. ▌
    Derivatizing Matrix Ionization Rule Application · holobiomicslab

    Use when when working with mass spectrometry imaging data from metabolites treated with derivatizing matrices (e.
    0 installs
28. ▌
    Mass Difference Calculation From Spectral Peaks · holobiomicslab

    Use when you have a list of detected masses (m/z peaks) from MALDI-MS imaging data and want to systematically search for adduct relationships. Apply this skill when you suspect that observed peaks include not just parent metabolites but also their adducts with matrix ions (e.
    0 installs
29. ▌
    Mass Spectrometry Data Structure Interpretation · holobiomicslab

    Use when you have received an mzPeak archive (a ZIP file containing Parquet tables) and need to understand its internal structure, validate that spectrum metadata aligns with signal data, reconstruct m/z and intensity arrays (especially when null marking or zero-run stripping is present), or verify.
    0 installs
30. ▌
    Metabolite Candidate Ranking Likelihood Scoring · holobiomicslab

    Use when you have a query mass spectrum matched to multiple candidate metabolites (by accurate mass, database lookup, or spectral similarity), and you possess or can train a DNN model for retention time prediction on your target chromatographic method.
    0 installs
31. ▌
    Metabolite Concentration Stoichiometric Mapping · holobiomicslab

    Use when you have intracellular metabolomics abundance data (absolute or relative concentrations) for multiple cell lines or conditions, a constraint-based stoichiometric metabolic model with reaction-metabolite associations, and you need to disentangle how differences in substrate concentration.
    0 installs
32. ▌
    Molecular Duplicate Detection And Deduplication · holobiomicslab

    Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
    0 installs
33. ▌
    R Package Installation And Runtime Verification · holobiomicslab

    Use when before running any R function that wraps compiled C# methods or system executables (e.g., rawrr::readSpectrum), especially when the package depends on language runtimes (.NET, Mono) or proprietary third-party assemblies that must be downloaded and configured separately.
    0 installs
34. ▌
    Wine Windows Runtime Initialization Diagnostics · holobiomicslab

    Use when you are deploying a Windows .NET application (e.g., AirdPro CLI) inside a Docker container on a non-Windows host and need to understand whether Wine initialization completes, how long it takes (documented as >30 minutes), whether .
    0 installs
35. ▌
    Anndata Object Integration And Metadata Mapping · holobiomicslab

    Use when you have preprocessed and filtered ST and SM AnnData objects with spatial coordinates and features, and you need to establish spot-level correspondence between the two modalities to enable downstream joint analysis.
    0 installs
36. ▌
    Association Strength Normalization For Networks · holobiomicslab

    Use when after generating metabolite-disease correlations and protein association predictions from a deep learning module (e.g., DeepMSProfiler's feature extraction), before constructing a bipartite network graph for publication.
    0 installs
37. ▌
    Biotransformation Rule Extraction From Database · holobiomicslab

    Use when you need to populate or reconstruct a biotransformation prediction module and have access to a curated biotransformation database (such as EAWAG BBD) that documents empirically validated microbial degradation pathways, enzyme-substrate relationships, and reaction outcomes.
    0 installs
38. ▌
    Chemical Formula Deduplication Across Databases · holobiomicslab

    Use when you have retrieved chemical formulae and metadata from two or more of HMDB, ChEMBL, or PubChem and need to merge them into a single searchable database without formula duplication.
    0 installs
39. ▌
    Chemical Identifier Standardization And Mapping · holobiomicslab

    Use when you have structure-organism pairs originating from multiple open databases (e.g., ChEMBL, PubChem, Wikidata) with disparate identifier schemes, file formats (TSV, JSON, XML, proprietary schemas), and taxonomic rank naming conventions.
    0 installs
40. ▌
    Chromatographic Peak Detection Gradient Descent · holobiomicslab

    Use when you have LC-HRMS profile-mode data (retention time × m/z matrix format) and need to automatically identify chromatographic peak locations and boundaries prior to feature extraction, reference matching, or training a peak-classification CNN model.
    0 installs
41. ▌
    Controlled Vocabulary Lookup Table Construction · holobiomicslab

    Use when after ingesting and parsing multiple external databases with diverse identifier schemes and nomenclatures. Trigger conditions: (1) you have interim standardized tables with local identifiers (structure_id, organism_name, reference_doi) that lack semantic normalization;
    0 installs
42. ▌
    Coordinate System Normalization 1based Indexing · holobiomicslab

    Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
    0 installs
43. ▌
    Core Spectra Variable Definition And Population · holobiomicslab

    Use when when implementing a custom MsBackend class for the Spectra package, you must define these two methods to satisfy the MsBackend virtual class API contract.
    0 installs
44. ▌
    Elution Profile Normalization And Preprocessing · holobiomicslab

    Use when when you have raw co-fractionation/mass-spectrometry elution intensity profiles and plan to train a CNN or semi-supervised learning model (Label Spreading) directly on unengineered elution data.
    0 installs
45. ▌
    Extracted Ion Chromatogram Parameter Extraction · holobiomicslab

    Use when after isolating TIC peak regions via sliding window analysis and peak expansion (isolatePeaks), apply this skill when you need dataset-specific XCMS parameter estimates.
    0 installs
46. ▌
    Hierarchical Clustering Dendrogram Construction · holobiomicslab

    Use when when you have a Metaboprep object after quality control filtering and need to visualize metabolite correlation structure to: (1) identify clusters of co-regulated features that may represent the same biological pathway or measurement artifact, (2) set tree-cutting height thresholds for.
    0 installs
47. ▌
    High Dimensional Similarity Search Optimization · holobiomicslab

    Use when when you have a large spectral library (thousands to millions of spectra) represented as high-dimensional vectors and need to match unknown query spectra against it, but exhaustive pairwise comparison is computationally prohibitive.
    0 installs
48. ▌
    Internal Standard Ion Selection And Application · holobiomicslab

    Use when after isotope correction has been applied to MSI ion images, when you have sprayed or identified a reference lipid standard of known amount (pmol/mm²) and need to normalize target lipid intensities against this standard to remove matrix effects and enable cross-pixel and cross-sample.
    0 installs
49. ▌
    Lchrms Chromatographic Peak Boundary Extraction · holobiomicslab

    Use when you have a set of target molecules with known molecular formula, main adduct, and experimentally determined retention time boundaries, and you want to extract their chromatographic peaks and isotopologues from LC-HRMS mzML files to generate a ground-truth benchmark for validating.
    0 installs
50. ▌
    Machine Learning Model Selection And Comparison · holobiomicslab

    Use when when you have a preprocessed metabolomics feature matrix with labeled samples and need to determine which classifier (traditional ML vs. deep learning) predicts the phenotype of interest.
    0 installs
51. ▌
    Mass Offset Scanning For Modification Detection · holobiomicslab

    Use when you have a query mass spectrum of unknown modification status and need to search a spectral library to identify the peptide and its post-translational modifications.
    0 installs
52. ▌
    Mass Spectrometry Imaging Vendor Format Support · holobiomicslab

    Use when your input mass spectrometry imaging data is in a proprietary vendor format (Bruker .d/.baf, or other binary formats not natively supported by MSIGen) and you need to convert it to an open, readable format (mzML or processed binary) compatible with MSIGen's msigen() function.
    0 installs
53. ▌
    Mass Spectrometry Peak Detection And Extraction · holobiomicslab

    Use when you have raw high-resolution mass-spectrometry data in mzML or mzXML format from breath analysis and need to identify individual volatile organic compounds before sample-to-sample alignment or comparative analysis.
    0 installs
54. ▌
    Metabolite Feature Visualization Across Batches · holobiomicslab

    Use when after applying batch-effect correction methods (parametric ComBat, non-parametric ComBat, ber, or ber-bagging) to log-transformed metabolomics abundance matrices, use this skill when you need to visually inspect whether technical heterogeneity (drift across batch, signal shift) has been.
    0 installs
55. ▌
    Metabolite Prediction Cyp450 Enzyme Specificity · holobiomicslab

    Use when you have a small-molecule query (acetaminophen, drug candidate, xenobiotic, or other compound as SMILES or SDF) and need to predict which metabolites would be formed if that molecule were metabolized by a defined subset of the nine major human CYP450 isoforms (1A2, 2A6, 2B6, 2C8, 2C9.
    0 installs
56. ▌
    Metabolomic Data Normalization Post Integration · holobiomicslab

    Use when immediately after integrating multiple metabolomic datasets from different analytical experiments into a unified feature-by-sample matrix. Batch effects manifest as systematic unwanted variations correlated with analytical batch rather than biological sample groups;
    0 installs
57. ▌
    Metabolomics Analyte Stability Characterization · holobiomicslab

    Use when you are designing a blood sampling protocol for metabolomics or lipidomics analysis and need to predict whether specific analytes (polar metabolites or lipids) will degrade under planned pre-analytical conditions (e.
    0 installs
58. ▌
    Metabolomics Data Exclusion Criteria Validation · holobiomicslab

    Use when you have received or published a claim about the number of metabolites excluded by a missingness-based quality filter (e.g., 'cutoff=0.
    0 installs
59. ▌
    Multi Tool Result Integration And Harmonization · holobiomicslab

    Use when when you have completed parallel or sequential tool runs (e.g., CPAT, signalP, Pfam, fimo) on the same set of sequences and need to create a unified functional annotation table, summary statistics, or cross-tool comparison report.
    0 installs
60. ▌
    Network Topology Analysis For Bgc Deduplication · holobiomicslab

    Use when when you have a collection of tokenised BGCs (each gene represented as Pfam domain tokens) and need to remove near-duplicate or highly similar clusters before detecting biosynthetic sub-clusters.
    0 installs
61. ▌
    Python Bracket Notation Protocol Implementation · holobiomicslab

    Use when you have a blockwise-indexed compressed file (e.g., indexed gzip with chapter or spectrum identifiers) and need to retrieve individual logical blocks by key using Python bracket notation (e.g., `handler['chapter_1']` or `handler[0]`) rather than sequential iteration.
    0 installs
62. ▌
    Python Class Implementation With Dunder Methods · holobiomicslab

    Use when you have mzML spectral data stored in a non-standard format (SQLite database, custom binary store, or indexed archive) and need pymzML's Reader to parse and iterate over spectra as if they were in native mzML files. Specifically, when FileInterface.
    0 installs
63. ▌
    Sciex Multiquant Data Export Format Recognition · holobiomicslab

    Use when you have txt files exported from Sciex MultiQuant (>v3.0.3) containing QCpool samples measured at regular intervals during mass spectrometry sequences, and you need to validate whether the file structure is compatible with the QComics package before parsing and quality assessment.
    0 installs
64. ▌
    Smarts Pattern Design For Microbial Degradation · holobiomicslab

    Use when you need to predict small molecule metabolism in soil or aquatic microbiota and must translate published biotransformation rules (reaction types, enzyme families, substrate patterns) from EAWAG or similar biodegradation databases into executable chemical pattern-matching rules compatible.
    0 installs
65. ▌
    Spatial Transcriptome Metabolome Coregistration · holobiomicslab

    Use when you have paired spatial transcriptome and metabolome datasets (both as h5ad files with .obsm['spatial'] coordinate matrices and .
    0 installs
66. ▌
    Spectral Data Compression By Frame And Mobility · holobiomicslab

    Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you need to reduce data volume while preserving signal integrity for subsequent HRdm demultiplexing and peak deconvolution.
    0 installs
67. ▌
    Structure Similarity Search Across Repositories · holobiomicslab

    Use when you have a SMILES string or chemical structure and need to determine whether it exists in public chemical repositories, or locate reference identifiers and metadata for the same compound across multiple authoritative sources.
    0 installs
68. ▌
    Transcript Abundance Quantification With Salmon · holobiomicslab

    Use when you have adapter-trimmed FASTQ files and need to obtain transcript-level abundance estimates without performing full genomic alignment.
    0 installs
69. ▌
    Unit Test Design For Cheminformatics Algorithms · holobiomicslab

    Use when you have implemented a custom Filter subclass (e.g., Tanimoto sampling, metabolomics matching, or target filtering) in minedatabase/filters.py and need to verify that similarity scoring, scaling transformations (e.
    0 installs
70. ▌
    Univariate Statistical Testing For Metabolomics · holobiomicslab

    Use when you have paired metabolomics count data (metabolite abundance matrix) and sample metadata with categorical treatment or experimental factor assignments, and you need to test for statistically significant differences in individual metabolite abundances between exactly two groups (t-test) or.
    0 installs
71. ▌
    Euclidean Distance Computation Approximation · holobiomicslab

    Use when when constructing k-nearest neighbor graphs from spatial coordinates (e.g., microscopy x,y positions or tissue section coordinates) and exact neighbor discovery is computationally prohibitive;
    0 installs
72. ▌
    Pearson Correlation Computation Across Tools · holobiomicslab

    Use when you have quantification results from two or more independent implementations, versions, or variants of the same analysis tool (e.g. C++ salmon 1.11.
    0 installs
73. ▌
    Spatial Neighbor Graph Properties Validation · holobiomicslab

    Use when after calling squidpy.gr.spatial_neighbors on an AnnData object containing spatial coordinates in obsm.
    0 installs
74. ▌
    Spectral Coverage And Intensity Metric Computation · holobiomicslab

    Use when you have completed a ViMMS simulation run or processed real LC-MS/MS data and need to quantitatively assess whether one DDA controller (e.g., WeightedDEWController with exclusion) outperforms another (e.g., TopNController) in terms of spectral coverage and signal recovery.
    0 installs
75. ▌
    Spectral Similarity Scoring And Reference Matching · holobiomicslab

    Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from Metlin or GNPS).
    0 installs
76. ▌
    Exact Mass Utilization For Compound Identification · holobiomicslab

    Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query chemicals are present in your samples and retrieve their -match factors (scoring the confidence of the spectral match) and.
    0 installs
77. ▌
    Biosynthetic Gene Cluster Mining With Genomic Data · holobiomicslab

    Use when you have LC-MS/MS spectra (MGF, mzXML, mzML, or mzData format) from a bacterial or fungal strain and corresponding genomic sequence data (FASTA, antiSMASH .final.gbk, or BOA .annotated.
    0 installs
78. ▌
    Cascade Search Strategy For Peptide Identification · holobiomicslab

    Use when use this strategy when analyzing tandem mass spectrometry data where you expect both unmodified and modified peptide identifications and require high confidence assignments with controlled false discovery rates.
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79. ▌
    Expressionset Construction And Metadata Annotation · holobiomicslab

    Use when after validating a peak table (either standardized format or software tool–generated format) and its corresponding label file, before applying any NOREVA assessment functions (normulticlassqcall, nortimecourseqcall, etc.).
    0 installs
80. ▌
    Feature Matrix Preparation For Supervised Learning · holobiomicslab

    Use when you have preprocessed metabolomics feature abundance data and want to train multiple classifiers (traditional ML or deep learning) to predict sample phenotype or disease status.
    0 installs
81. ▌
    Mass Spectrometry Workflow Orchestration Snakemake · holobiomicslab

    Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
    0 installs
82. ▌
    Metabolite Annotation Integration Across Databases · holobiomicslab

    Use when you have MZmine-aligned features with m/z and retention time, and you have generated spectral annotations from two or more database sources (e.g., GNPS/ISDB spectral matching and SIRIUS in silico structure elucidation).
    0 installs
83. ▌
    Metabolomic Feature Statistical Hypothesis Testing · holobiomicslab

    Use when when you have a normalized and batch-corrected feature abundance matrix from non-targeted LC-MS/MS metabolomics (e.
    0 installs
84. ▌
    Metabolomics Chemical Mixture Generation From Hmdb · holobiomicslab

    Use when you need to create realistic, diverse chemical populations for simulating LC-MS/MS acquisition strategies in a virtual environment. It is essential when you lack real metabolomics data but want to prototype and compare fragmentation strategies (e.
    0 installs
85. ▌
    Molecular Fingerprint Extraction And Vectorization · holobiomicslab

    Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
    0 installs
86. ▌
    Molecular Structure Reconstruction From Embeddings · holobiomicslab

    Use when you have a pretrained encoder that produces fixed-size embeddings from MS/MS spectra (or other molecular data modalities) and you need to recover the corresponding molecular structure as a SMILES string.
    0 installs
87. ▌
    Neutral Loss Extraction From Fragmentation Spectra · holobiomicslab

    Use when preparing MS/MS spectra for bag-of-fragments conversion and LDA-based motif discovery. You have raw spectra in supported formats (.mgf, .mzML, or .
    0 installs
88. ▌
    Parameter Range Filtering For Chromatographic Data · holobiomicslab

    Use when you have raw MS data in instrument-native or mzML format (Agilent .d, Thermo .raw, Bruker .d) and need to isolate specific analyte regions defined by precise m/z windows, RT windows (in seconds or minutes), and/or ion mobility arrival-time windows.
    0 installs
89. ▌
    Peak Boundary Identification In Extracted Ion Data · holobiomicslab

    Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
    0 installs
90. ▌
    Spectral Embedding Extraction From Neural Networks · holobiomicslab

    Use when you have a set of preprocessed MS/MS spectra (binned to 10,000 m/z bins with intensities square-root transformed) and a trained MS2DeepScore Siamese neural network model, and you need to compute 200-dimensional spectral embeddings for dimensionality reduction, clustering, or chemical space.
    0 installs
91. ▌
    Structural Clustering Validation In Chemical Space · holobiomicslab

    Use when you have trained or loaded a deep learning model that produces high-dimensional spectral embeddings (e.g., 200-dimensional vectors from MS2DeepScore base network) and need to validate that these embeddings capture chemical structure information rather than learning spurious patterns.
    0 installs
92. ▌
    Unknown Pollutant Identification Mass Spectrometry · holobiomicslab

    Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a Windows environment with ≥16 GB RAM and ≥2 GB NVIDIA GPU, and you need compound identification with confidence scores and.
    0 installs
93. ▌
    Metabolite Phenotype Association Partial Correlation · holobiomicslab

    Use when you have a SummarizedExperiment object containing NMR or MS metabolomic data with aligned phenotype information (BMI, disease status, age, gender), and you need to identify metabolites associated with a continuous or categorical outcome while controlling for known confounders that might.
    0 installs
94. ▌
    Nmr Inadequate Spectra Acquisition And Preprocessing · holobiomicslab

    Use when when you have raw INADEQUATE NMR spectral data (e.g., from a query sample or library) and need to extract peak coordinates and intensities as a first step toward identifying metabolite peak networks or comparing against a metabolite database.
    0 installs
95. ▌
    Pytest Unit Test Execution And Coverage Reporting · holobiomicslab

    Use when after implementing or modifying Python library functions (such as utility functions in cooltools.lib subpackages) to verify correctness and identify gaps in test coverage before merging changes or releasing code.
    0 installs
96. ▌
    Spectral Embedding Dimension Reduction Parameters · holobiomicslab

    Use when after generating a tile matrix or feature count matrix from single-cell ATAC-seq, RNA-seq, Hi-C, or methylation data, before clustering or UMAP visualization, when you need unsupervised dimension reduction that scales to millions of cells and is agnostic to the underlying data modality.
    0 installs
97. ▌
    Artifact Size Measurement And Range Verification · holobiomicslab

    Use when you have built multiple Docker image variants (e.g., cli, dev, linux, windows) from a multi-stage Dockerfile and need to verify that their uncompressed and compressed storage footprints fall within documented acceptable ranges (e.
    0 installs
98. ▌
    Confidence Score Extraction From Neural Networks · holobiomicslab

    Use when when you have a trained deep learning model (e.g., PS2MS) and an evaluation dataset of compounds, and you need to assess how prediction confidence varies across structural novelty classes (e.g., training-similar vs. structurally novel NPS analogues).
    0 installs
99. ▌
    Github Actions Workflow Inspection And Execution · holobiomicslab

    Use when a GitHub repository displays a CI workflow badge (e.g., passing/failing status in README) and you need to verify that the reported status is accurate, reproduce the CI environment locally, or debug workflow failures.
    0 installs
100. ▌
     Graph Neural Network Architecture Implementation · holobiomicslab

     Use when you have a baseline GNN model trained on a molecular property prediction task (e.
     0 installs