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HolobiomicsLab

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1. ▌
   Tic Based Intensity Scaling · holobiomicslab

   Use when after feature detection when you have a metabolomics feature table with intensity values across multiple samples and observe evidence of inter-sample intensity bias (e.g., batch effects, variable ionization efficiency, or instrument drift).
   5 installs
2. ▌
   Tree Based Model Validation · holobiomicslab

   Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to deploy predictions as executable queries or to validate that learned splits correspond to chemically meaningful.
   4 installs
3. ▌
   Uhplc Hrms Ms Data Matching · holobiomicslab

   Use when you have peak-picked UHPLC-HRMS/MS data (from Q-Exactive orbitrap, Agilent, Bruker, or SCIEX Q-TOF instruments) with both MS1 and MS/MS fragment spectra, and you need to assign lipid identities to detected features using in-silico fragmentation patterns.
   5 installs
4. ▌
   Web Service API Integration · holobiomicslab

   Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular fingerprint predictions, de-novo candidate structures, or chemical class annotations without maintaining local neural network.
   9 installs
5. ▌
   YAML Configuration Handling · holobiomicslab

   Use when when initializing a MolNotator project with user-defined parameters for ionization modes, adduct tables, database selections, output directories, and tool-specific thresholds.
   5 installs
6. ▌
   Annotation Confidence Scoring · holobiomicslab

   Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final annotated metabolite identities.
   4 installs
7. ▌
   API Request Response Handling · holobiomicslab

   Use when you have nuclear magnetic resonance (NMR) peak data (proton 1H and carbon-13 13C measurements) that you need to classify using a deployed deep learning model, and you have access to a TensorFlow Serving instance running the SMART 3 classification model.
   5 installs
8. ▌
   Array Of Objects Construction · holobiomicslab

   Use when you have tabular experimental data (e.g., sample metadata, mass spectrometry parameters, NMR acquisition details) in JSON table format and need to produce a list of structured objects for submission to a data repository (e.g., Metabolomics Workbench) or downstream format conversion.
   5 installs
9. ▌
   Dependency Version Management · holobiomicslab

   Use when when you need to document or reproduce a Python-based research application (or any package-dependent workflow) and discover that the original publication or repository specifies dependencies without versions, or when you want to verify that a documented set of pinned versions can be.
   10 installs
10. ▌
    Form Encoded Request Handling · holobiomicslab

    Use when when a web service must accept spectroscopic measurements (NMR peaks, IR/MS metadata) submitted as form-encoded POST parameters from a client, and those parameters need to be validated, reformatted into an external API query format, or passed to a downstream predictor service.
    7 installs
11. ▌
    Mass Spectral Data Validation · holobiomicslab

    Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
    5 installs
12. ▌
    Minimum Cost Flow Formulation · holobiomicslab

    Use when you have an NMR mixture spectrum and a library of single-compound reference spectra, and you need to identify which compounds are present and their relative abundances.
    7 installs
13. ▌
    Nmr Spectrum Phase Adjustment · holobiomicslab

    Use when you have acquired raw 1D NMR spectra (FID or processed spectra in NMRPipe format) that exhibit phase distortion—where peaks are not in pure absorption mode—and you need to prepare the spectrum for automatic deconvolution into peak tables.
    6 installs
14. ▌
    Nmrbox Environment Management · holobiomicslab

    Use when when you need to deploy SAND for 1D NMR spectrum deconvolution on a new machine or cluster, or when testing code changes before merging into production.
    5 installs
15. ▌
    Quality Metrics Summarization · holobiomicslab

    Use when after running QC analysis on NMR or MS metabolomic data and obtaining per-feature CV values, use this skill to validate that the dataset meets FDA thresholds (CV < 0.30 for discovery, CV < 0.15 for quantification) and to report the proportion of features meeting each threshold.
    8 installs
16. ▌
    Record Grouping And Collation · holobiomicslab

    Use when you have multiple rows in a table that describe the same logical entity (e.g., multiple measurements from the same sample, or repeated attributes under a common identifier) and need to merge them into a single dictionary entry keyed by that shared field.
    6 installs
17. ▌
    Spectral Graph Interpretation · holobiomicslab

    Use when after submitting MS/MS data and feature tables to GNPS and receiving a molecular networking job result.
    5 installs
18. ▌
    450k Array Data Processing · holobiomicslab

    Use when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical artifacts (batch effects, type-2 probe bias), and normalize the data before performing differential methylation analysis or DMR detection.
    5 installs
19. ▌
    Archr Project Manipulation · holobiomicslab

    Use when you have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality of the peak matrix via iterative LSI; (2) integrate multimodal data by combining ATAC and RNA dimensions;
    5 installs
20. ▌
    Atac Seq Footprint Scoring · holobiomicslab

    Use when you have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around TF-bound sites) across accessible chromatin regions before classifying individual TF binding sites.
    9 installs
21. ▌
    Methylbase Object Handling · holobiomicslab

    Use when after reading in per-sample methylation call files with methRead() and obtaining methylRawList objects, but before calculating differential methylation or performing annotation.
    5 installs
22. ▌
    Tsv File Io And Formatting · holobiomicslab

    Use when you have computed or received a precomputed expected contact frequency table (e.
    5 installs
23. ▌
    Arrow Table Serialization · holobiomicslab

    Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist them to disk in Parquet format for downstream analysis, interoperability with other languages (R, .
    5 installs
24. ▌
    CI CD Pipeline Monitoring · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a passing build status.
    4 installs
25. ▌
    CI CD Workflow Monitoring · holobiomicslab

    Use when when you need to verify that a continuous integration pipeline for a scientific software project (e.g., mzmine) completes successfully, produces expected build artifacts, or fails in a reproducible manner.
    8 installs
26. ▌
    CI CD Workflow Triggering · holobiomicslab

    Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that automated build infrastructure is functioning correctly.
    6 installs
27. ▌
    Descriptor Table Assembly · holobiomicslab

    Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification. Use this skill after descriptor calculation is complete and before invoking BitterPredict.m for bitter/non-bitter predictions.
    6 installs
28. ▌
    Expert Review Preparation · holobiomicslab

    Use when you have a published scientific article describing a computational method (e.g., natural products annotation, MS/MS data processing) and need to assess reproducibility before expert scrutiny.
    7 installs
29. ▌
    Feature Ablation Analysis · holobiomicslab

    Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic properties, bond types, or higher-order graph descriptors—are driving the model's predictions.
    7 installs
30. ▌
    Field Type Identification · holobiomicslab

    Use when when working with JSON project documents that must conform to a schema-defined structure, and you need to apply type-specific validation, sanitization, or transformation rules (e.g., URL whitespace detection, numeric range checking, mandatory field enforcement).
    7 installs
31. ▌
    JSON Structured Reporting · holobiomicslab

    Use when you need to persist and communicate the health status of multiple external web services queried during an annotation run.
    5 installs
32. ▌
    Model Metadata Validation · holobiomicslab

    Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm that input layers are named 'input_2048' and 'input_4096' and output layer is named 'output'.
    4 installs
33. ▌
    Motif Metadata Annotation · holobiomicslab

    Use when after LDA inference has produced a trained motifset (motifset.json or motifset_optimized.json) with Mass2Motif probability distributions over fragments and neutral losses.
    8 installs
34. ▌
    Mzpeak File Io Operations · holobiomicslab

    Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability across languages and tools; (2) load mzPeak spectrum or chromatogram data into memory as structured tables for analysis;
    5 installs
35. ▌
    Openapi Schema Generation · holobiomicslab

    Use when when you have a webservice codebase (Python, Java, etc.) with HTTP route definitions, parameter handling, and serialization logic, and you need to generate an OpenAPI 3.
    7 installs
36. ▌
    Organism Taxonomy Mapping · holobiomicslab

    Use when you have a cleaned organism table (with validated, deduplicated organism names from sources like NCBI, manual curation, or previous cleaning steps) and need to annotate each organism with Open Tree of Life identifiers, taxonomic lineage, and standardized taxonomic annotations.
    5 installs
37. ▌
    Otl Identifier Assignment · holobiomicslab

    Use when after organism name cleaning and taxonomy verification (4_cleaningTaxonomy.R) have been completed and you have a cleaned organism table with standardized names.
    6 installs
38. ▌
    Pathway Database Querying · holobiomicslab

    Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full pathway database should serve as the statistical background, and which pathways contain how many metabolites overall.
    8 installs
39. ▌
    Release Branch Management · holobiomicslab

    Use when you need to validate that a software project's release branch is stable and ready for distribution. Specifically, use it when: (1) a release tag has been created or code pushed to a release branch; (2) you need to confirm that CI/CD pipelines execute without failures;
    8 installs
40. ▌
    Repository Administration · holobiomicslab

    Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing new versions, after merging changes to release branches, or when troubleshooting build failures that block distribution of.
    6 installs
41. ▌
    Spectrum Array Validation · holobiomicslab

    Use when after applying any sequence of spectrum preprocessing operations (set_mz_range, remove_precursor_peak, filter_intensity, scale_intensity) to an MsmsSpectrum object, to confirm that the resulting arrays fall within specified m/z windows, intensity bounds, and peak count limits before.
    5 installs
42. ▌
    Anndata Object Annotation · holobiomicslab

    Use when after loading or merging spatial metabolomics data into an AnnData object (via read_sm_csv_as_anndata, read_sm_imzml_as_anndata, or merge_sm_pos_neg), and before filtering or normalization steps.
    6 installs
43. ▌
    Batch Name Reconciliation · holobiomicslab

    Use when when you have a metadata table with taxonomic annotations (species, genus, family columns) that may contain outdated, misspelled, or non-canonical taxon names, and you need to integrate these samples into a natural products analysis pipeline that requires standardized taxonomy (e.
    8 installs
44. ▌
    Build Artifact Validation · holobiomicslab

    Use when after completing a platform-specific build (e.g., mvn clean package, qmake6 && make, cmake && make) to confirm the generated artifact is not corrupted and can execute on the intended OS (Windows 10, Ubuntu 22.04, macOS 12+ ARM64, or other documented targets).
    4 installs
45. ▌
    Classifier Output Parsing · holobiomicslab

    Use when after a classifier (such as BitterPredict.m) has computed binary predictions (e.g., bitter vs. non-bitter) on a batch of molecular descriptors and you need to organize those predictions into a structured, labeled output file for downstream analysis, validation, or reporting.
    5 installs
46. ▌
    Command Sequence Ordering · holobiomicslab

    Use when you have a workflow.csv file co-located with sequence.csv in a session directory, and you need to initialize a reproducible, ordered chain of processing steps (e.
    9 installs
47. ▌
    Compound Query Formatting · holobiomicslab

    Use when you have a set of chemical compounds (identified by name, SMILES, InChI, or other standard identifier) that you need to classify using ClassyFire, and you must prepare them as a single batch query body for the submit_query POST request.
    4 installs
48. ▌
    Data Structure Validation · holobiomicslab

    Use when after converting or filtering objects (e.g., transformation products to suspect lists, feature groups through componentization) and before passing them to downstream functions like screenSuspects or generateComponents.
    7 installs
49. ▌
    Database Record Retrieval · holobiomicslab

    Use when you need to access a stored chemical structure, NRP sequence, or building-block annotation from the MassSpecBlocks database in order to export it to an external format (e.g., CycloBranch), transform it for mass spectra analysis, or integrate it with another chemical database query.
    4 installs
50. ▌
    Diagnostic Plot Rendering · holobiomicslab

    Use when when you have computed statistical or classification results (e.
    6 installs
51. ▌
    Dimple Pipeline Execution · holobiomicslab

    Use when when you have deposited mass spectrometry imaging data in NetCDF (CDF) format paired with MATLAB workspace files (.
    7 installs
52. ▌
    Eic Signal Peak Detection · holobiomicslab

    Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign retention time boundaries, apex intensities, and quality scores prior to peak annotation or cross-sample alignment.
    8 installs
53. ▌
    Field Exclusion Filtering · holobiomicslab

    Use when when transforming tabular data via the matrix directive and you need to copy most or all fields from input records into output dictionaries, but must explicitly exclude certain named fields (e.
    6 installs
54. ▌
    Graph Centrality Analysis · holobiomicslab

    Use when after constructing a network (adjacency matrix, edge list, or correlation network) when you need to identify which nodes are most central to network topology.
    8 installs
55. ▌
    Graph Community Detection · holobiomicslab

    Use when you have a sparse inverse covariance graph (GLASSO output) and multivariate PCA scores for the same samples/variables, and you need to partition the network into functionally or statistically coherent sub-networks rather than treating the graph as a monolithic structure.
    5 installs
56. ▌
    Image Intensity Jittering · holobiomicslab

    Use when when preparing ion images (single-channel 2D arrays or multi-channel spectral images) from mass spectrometry imaging for contrastive learning in DeepION's COL or ISO modes.
    4 installs
57. ▌
    Indexed Gzip File Parsing · holobiomicslab

    Use when you have compressed mzML.gz files and need to retrieve specific spectra by numeric identifier without decompressing the entire file.
    7 installs
58. ▌
    Isotope Pattern Detection · holobiomicslab

    Use when you have MS1-format mass spectrometry files and need to determine the isotope count for peptide features without manual inspection or expert parameter tuning.
    5 installs
59. ▌
    Jvm Dependency Resolution · holobiomicslab

    Use when when you have obtained source code for a Maven-based Java project and need to determine whether your local build environment can successfully compile it, or when preparing to reproduce a published CI/CD build workflow from a GitHub Actions or similar pipeline configuration.
    6 installs
60. ▌
    Kendrick Mass Calculation · holobiomicslab

    Use when you have uploaded m/z values from a high-resolution mass spectrometry analysis of a complex sample (e.g., crude oil, natural organic matter) and need to visualize homolog series trends.
    9 installs
61. ▌
    Keras Model Serialization · holobiomicslab

    Use when you have downloaded pre-trained Keras model files (via get_models.sh or similar) and need to prepare them for deployment in a TensorFlow Serving environment, particularly when the downstream inference system expects .h5 serialized models with explicit input/output layer naming conventions.
    7 installs
62. ▌
    La Icp Ms Image Denoising · holobiomicslab

    Use when raw LA-ICP-MS images contain isolated spike pixels (hot spots or cold spots) caused by instrumental noise, transient ablation artifacts, or detector glitches.
    9 installs
63. ▌
    M Z Intensity Calibration · holobiomicslab

    Use when you have raw or processed MS spectrum data (m/z and intensity pairs) from DI-MS, ASAP-MS, or other high-throughput mass spectrometry instruments that requires automated peak detection.
    9 installs
64. ▌
    Metadata Field Extraction · holobiomicslab

    Use when you have a directory of JSON-formatted annotation files and need to systematically extract a specific metadata field (such as curation status, entry identifier, or validation state) across all records.
    5 installs
65. ▌
    Metadata Field Validation · holobiomicslab

    Use when you have received new or updated MassBank records (in plain-text or structured format) that must be integrated into the MassBank-data repository and you need to ensure they conform to the MassBank format specification before acceptance.
    7 installs
66. ▌
    Mibig Metadata Extraction · holobiomicslab

    Use when when you need to audit, inventory, or report on the curation state of MIBiG entries; when cluster.status values must be validated or aggregated for quality control; when building a status index to support data governance or release workflows.
    5 installs
67. ▌
    Module Dependency Mapping · holobiomicslab

    Use when you need to understand or document the structural organization of an object-oriented codebase—specifically when developers require a map of which modules depend on others, where extension points (abstract classes, interfaces, factory patterns) exist, or when preparing to extend or refactor.
    7 installs
68. ▌
    Mrm Data Format Ingestion · holobiomicslab

    Use when you have raw MRM lipidomics export files in vendor-specific formats (e.g., TSV or CSV from a mass spectrometry instrument) and need to convert them into a standardized tabular format before performing lipid identification, statistical analysis, or visualization.
    5 installs
69. ▌
    Network Graph Pca Overlay · holobiomicslab

    Use when you have a sparse network graph generated by GLASSO and corresponding PCA scores from the same system, and you need to identify which regions or clusters of the network exhibit strong low-dimensional structure.
    5 installs
70. ▌
    Network Proximity Scoring · holobiomicslab

    Use when you have (1) metabolomic hits (DAMs or enriched metabolites) mapped to seed genes, (2) a protein–protein or gene interaction network (e.g., STRING), and (3) a set of candidate disease genes that need ranking by their functional proximity to metabolomic evidence.
    8 installs
71. ▌
    Overlapping Ion Detection · holobiomicslab

    Use when when annotating matrix-related ions in MSI datasets where two or more ions share identical or near-identical m/z values (isobaric ions) or exhibit overlapping spatial distributions across imaging pixels.
    5 installs
72. ▌
    Pep8 Standard Enforcement · holobiomicslab

    Use when preparing code for contribution to a Python project that mandates PEP8 compliance, or when setting up pre-commit quality gates for a codebase.
    8 installs
73. ▌
    Prediction Error Analysis · holobiomicslab

    Use when when you have trained multiple machine learning regressors on the same prediction task (e.
    6 installs
74. ▌
    Proforma Notation Parsing · holobiomicslab

    Use when when peptide identifications from a search engine (MaxQuant, MSGFPlus, Sage, etc.) contain custom or engine-specific modification notation that must be converted to a standardized format before rescoring, or when different search engines use incompatible modification label schemes that.
    7 installs
75. ▌
    Python Module Integration · holobiomicslab

    Use when when you have developed or obtained a new Python package that encapsulates domain-specific computational logic (e.
    8 installs
76. ▌
    Python R Interoperability · holobiomicslab

    Use when when a Shiny R application needs to use Python libraries that lack R equivalents or are more mature in Python (e.g., Kaleido for plot export), and users should not need to manually configure Python environments.
    6 installs
77. ▌
    R Package Function Export · holobiomicslab

    Use when you have built a reusable workflow function (e.g., a Shiny app launcher, automated analysis routine) within an R package and need to make it available to package users.
    7 installs
78. ▌
    Raw Spectral Data Reading · holobiomicslab

    Use when you have Thermo Orbitrap .raw files and need to extract specific spectral features (base-peak m/z, intensity values, chromatographic traces, scan-level metadata) for downstream statistical analysis or visualization in R. Use this skill when you want to avoid lossy format conversion (e.
    8 installs
79. ▌
    Rendering Speed Profiling · holobiomicslab

    Use when when you have implemented the same visualization (e.g., chromatogram, spectrum, peakmap, mobilogram) across multiple plotting backends in pyOpenMS-viz and need to determine which backend minimizes rendering latency.
    3 installs
80. ▌
    REST API Endpoint Routing · holobiomicslab

    Use when your input is a raw query string containing a chemical compound identifier and structural representation (e.g. tab-delimited compound ID + structure), and you need to submit it to the ClassyFire API for automatic structure-based classification.
    7 installs
81. ▌
    Retention Time Clustering · holobiomicslab

    Use when you have an XCMS CentWave feature extraction output table containing multiple features with near-identical m/z values and retention times (e.
    5 installs
82. ▌
    Runtime Output Validation · holobiomicslab

    Use when after invoking a Nextflow workflow via `make run` or equivalent command, to confirm the workflow executed without errors and generated expected output files.
    6 installs
83. ▌
    Smiles Format Preparation · holobiomicslab

    Use when you have molecular structures in raw or unstructured form and need to submit them to CypReact or similar command-line chemistry tools that accept CSV input.
    5 installs
84. ▌
    Smiles String Preparation · holobiomicslab

    Use when you have a target molecule (e.g., acetaminophen, a drug candidate, or a xenobiotic) whose structure you need to encode for metabolite prediction, reaction rule matching, or other structure-based cheminformatics workflow.
    6 installs
85. ▌
    Software Tool Enumeration · holobiomicslab

    Use when a software package claims to bundle or install a specific number of tools (documented or approximate) but the tool names, versions, and sources are not enumerated in the primary README or documentation.
    6 installs
86. ▌
    Spatial Feature Embedding · holobiomicslab

    Use when when analyzing imaging mass spectrometry datasets where you need to reduce high-dimensional peak intensity features while preserving spatial structure, and when automatic peak picking and marker ion identification are required.
    5 installs
87. ▌
    Spectral Library Indexing · holobiomicslab

    Use when you have large spectral libraries (thousands to millions of spectra) and need to search query spectra against them for peptide identification with tolerance for post-translational modifications.
    6 installs
88. ▌
    Spectral Signal Detection · holobiomicslab

    Use when you have mzML mass spectrometry data and a list of predicted candidate metabolites (with known mass-to-charge ratios and retention times) for a drug of interest, and you need to determine which candidates actually appear in the observed spectra rather than treating all predictions as.
    4 installs
89. ▌
    Threshold Based Filtering · holobiomicslab

    Use when after computing pairwise similarity scores between query molecular embeddings and a reference database, apply this skill when you need to distinguish high-confidence candidate matches from spurious matches.
    6 installs
90. ▌
    Training Dataset Assembly · holobiomicslab

    Use when when you have a large list of SMILES strings but lack corresponding experimental mass spectra, and you need to generate 30,000+ training pairs to train a deep learning model for molecular structure prediction.
    7 installs
91. ▌
    Virtual Screening Ranking · holobiomicslab

    Use when you have a library of natural product compounds (encoded as SMILES strings) and wish to rank them by predicted bioactivity or fitness for a downstream task.
    6 installs
92. ▌
    Xcms Parameter Estimation · holobiomicslab

    Use when you have raw untargeted metabolomics data (at least 3 samples in mzML, mzXML, or CDF format) from qTOF, orbitrap, or Fourier transform ion cyclotron resonance mass analyzers and need to obtain optimized XCMS processing parameters tailored to your specific instrument and dataset rather than.
    5 installs
93. ▌
    Paga Graph Abstraction · holobiomicslab

    Use when you have clustered single-cell RNA-seq data (via Leiden, Louvain, or equivalent) and a k-nearest neighbor graph computed in PCA space, and you want to abstract cell-level connectivity into cluster-level connectivity to infer developmental trajectories, lineage relationships, or.
    5 installs
94. ▌
    Msconvert Tool Configuration · holobiomicslab

    Use when you have vendor-specific raw mass spectrometry data files (e.g., from Orbitrap, Q-TOF, or other MS instruments) and need to feed them into IsoFusion or other tools that require MS1 format as input.
    8 installs
95. ▌
    Baseline Comparison Analysis · holobiomicslab

    Use when when you have trained a candidate model (e.g., an ensemble, a new architecture) and need to demonstrate its advantage over published or reference implementations on the same test data.
    8 installs
96. ▌
    Gc Ms Spectral Deconvolution · holobiomicslab

    Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be resolved by simple peak picking.
    3 installs
97. ▌
    Gc Ms Spectral Preprocessing · holobiomicslab

    Use when you have raw GC-MS data files containing overlapped peaks (unresolved components with coeluting retention times) and need to predict pure mass spectra for each individual component using a Transformer-based model.
    4 installs
98. ▌
    Metadata Coldata Integration · holobiomicslab

    Use when when you have generated a feature abundance matrix from mzrtsim() peak list simulation with known sample-level attributes (condition assignments, batch labels, sample identifiers) and need to package this into a SummarizedExperiment object for Bioconductor-compatible analysis pipelines.
    10 installs
99. ▌
    Model Checkpoint Persistence · holobiomicslab

    Use when training a Transformer or neural network model on a large dataset (e.g., 80,000+ training samples) where validation performance is monitored to prevent overfitting, and you need to halt training early or recover the -performing model checkpoint without re-executing the entire training loop.
    5 installs
100. ▌
     Ms Spectral Library Matching · holobiomicslab

     Use when when you have a GC-MS dataset (CSV with columns: Component.RT, Component.Area, Base.Peak.MZ, File.Name, Compound.Name, Match.Factor) and a known set of target chemicals you wish to locate and extract with their spectral match quality and quantitation.
     4 installs