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HolobiomicsLab

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1. ▌
   Quality Assurance Contamination Removal · holobiomicslab

   Use when you have a feature quantification table exported from MZmine3 processing of non-targeted LC-MS/MS data that includes both biological samples and blank/control samples, and you need to identify and exclude features whose intensity is driven by contamination in blanks rather than true.
   2 installs
2. ▌
   Quantum Chemistry Structure Preparation · holobiomicslab

   Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for LC-IM-MS/MS analysis.
   0 installs
3. ▌
   Quantum Mechanical Property Calculation · holobiomicslab

   Use when when you have interpolated or optimized molecular geometries (from geodesic_interpolate or CREST conformer ensembles) and need to compute ab initio electronic energies, orbital properties, or transition state characteristics to populate a fragmentation reaction network or validate.
   0 installs
4. ▌
   Retention Time Correction And Alignment · holobiomicslab

   Use when you have multiple LC-MS runs with the same set of targets (compounds) and observe or expect retention time drift or jitter between runs.
   0 installs
5. ▌
   Roi Tensor Formatting For Deep Learning · holobiomicslab

   Use when after segmenting raw profile LC-MS data into candidate ROIs containing potential peaks, and before feeding ROI data to a CNN-Transformer peak detection network.
   0 installs
6. ▌
   Rt Transformation Parameter Calculation · holobiomicslab

   Use when you have centroided mzML or mzXML LC-MS files from a single batch run that exhibit systematic retention-time drift between samples, one or more designated QC reference file(s), and you need to harmonize RT coordinates across all samples before feature detection to reduce false positive and.
   2 installs
7. ▌
   S4 Class Definition And Slot Management · holobiomicslab

   Use when you are extending the MsBackend virtual class to create a new backend for storing MS spectra data and need to define the internal data structure. Specifically: when you have multiple types of spectra variables (e.
   2 installs
8. ▌
   Siamese Architecture Module Integration · holobiomicslab

   Use when when refactoring a mass-spectrometry formula-prediction codebase that has deprecated a monolithic scoring function (FDRNet) and requires a modular, symmetric Siamese design to independently embed spectrum and molecular-formula features before combining them.
   0 installs
9. ▌
   Signal To Noise Ratio Calculation Peaks · holobiomicslab

   Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence detection, before reporting features in the final feature table.
   0 installs
10. ▌
    Sparse Vs Dense Vector Format Selection · holobiomicslab

    Use when when converting high-resolution tandem mass spectra to vectors for clustering or similarity searching, you must decide whether to output sparse or dense vectors. Use this decision point after binning spectra into mass bins but before constructing nearest-neighbor indexes.
    0 installs
11. ▌
    Spatial Metabolomics Feature Annotation · holobiomicslab

    Use when your spatial metabolomics dataset contains raw m/z features (e.g., from MALDI-MS imaging or LC-MS/MS) without metabolite annotations, and you have selected a reference database and adduct type appropriate for your ionization mode and biological sample.
    0 installs
12. ▌
    Spectral Data Input Handling Mgf Format · holobiomicslab

    Use when when you have raw MS/MS mass spectrometry data and need to submit it to the Mass2SMILES Docker inference container for structure and functional group prediction.
    1 install
13. ▌
    Spectral Data Normalization And Merging · holobiomicslab

    Use when you have acquired multiple MS1 spectra over a defined acquisition time range (e.g., 0–30 s in FIA-MS) and need to combine them into a unified spectrum before feature detection.
    2 installs
14. ▌
    Spectral Data Processing And Annotation · holobiomicslab

    Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular features, build a molecular network from fragmentation spectra, and annotate those features using both spectral.
    2 installs
15. ▌
    Spectral Entropy Similarity Computation · holobiomicslab

    Use when you need to measure the similarity between two MS/MS spectra as a continuous value that reflects both peak presence/absence and intensity patterns, particularly when comparing noisy versus denoised spectrum variants, or when ranking candidate reference library matches during compound.
    0 installs
16. ▌
    Spectral Feature Scrambling Permutation · holobiomicslab

    Use when when performing large-scale untargeted metabolomics annotations where you need to assess the false discovery rate of metabolite identifications but lack sufficient negative control samples or decoy compound databases.
    2 installs
17. ▌
    Spectral Library Matching With Taxonomy · holobiomicslab

    Use when you have MS/MS spectra (.mgf) and candidate metabolite annotations (with m/z, retention time, chemical identifiers) linked to a known organism or taxon, and you want to rank annotations by both spectral similarity AND biochemical likelihood in that organism's lineage.
    0 installs
18. ▌
    Spectral Motif Inference And Extraction · holobiomicslab

    Use when you have preprocessed MS/MS spectral data (converted to bag-of-fragments format with neutral losses extracted and noise filtered) and seek to identify recurring fragmentation patterns indicative of molecular substructures across a spectral cohort.
    2 installs
19. ▌
    Spectral Overlay Rendering Multi Sample · holobiomicslab

    Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment quality metrics) and need to visualize and interactively filter peaks across multiple spectra to support comparative mass.
    2 installs
20. ▌
    Spectral Peak Annotation Using Proforma · holobiomicslab

    Use when you have a tandem mass spectrum with observed m/z peaks and a known peptide sequence (as a ProForma string, optionally with post-translational modifications), and you want to determine which observed peaks correspond to expected fragment ions (b-type, y-type, a-type) within a specified.
    0 installs
21. ▌
    Spectral Peak Binning And Vectorization · holobiomicslab

    Use when you have raw MS/MS spectra with variable numbers of peaks at continuous m/z values and need to feed them to a neural network (e.g., Siamese network for similarity prediction) that requires fixed-size vector input.
    0 installs
22. ▌
    Spectral Similarity Matching Algorithms · holobiomicslab

    Use when when you have experimental MS/MS spectra (from mzML or .rda preprocessed format) and need to annotate them against a reference fragmentation library.
    0 installs
23. ▌
    Spectral Similarity Scoring And Ranking · holobiomicslab

    Use when after discovering Mass2Motifs via LDA topic modeling on MS/MS data, when you need to assign putative structural annotations to those motifs by comparing their fragmentation signatures (weighted fragment and neutral loss distributions) to a curated reference database of known motifs and.
    2 installs
24. ▌
    Spectrum Feature Engineering Validation · holobiomicslab

    Use when when implementing or auditing a deep learning pipeline for MS/MS-based molecular formula prediction, verify that precursor m/z values in the input feature array are zeroed before they reach the spectrum encoder (e.g., TCN).
    0 installs
25. ▌
    Structural Cluster Network Construction · holobiomicslab

    Use when after you have identified statistically significant LC-MS features and run MamsiStructSearch to generate structural clusters (isotopologue groups, adduct groups, cross-assay links) and computed correlation cluster assignments.
    0 installs
26. ▌
    Tab Delimited Metabolomics File Parsing · holobiomicslab

    Use when when you have raw metabolomics measurements in tab-delimited text format (e.g., from Sciex OS exports) and need to load them into R for quality control analysis.
    0 installs
27. ▌
    Targeted Peak Integration Configuration · holobiomicslab

    Use when when performing targeted quantification of known compounds in LC-MS data using TARDIS, especially when the instrument acquired data with multiple overlapping m/z scan windows.
    0 installs
28. ▌
    Tensorflow Cpu Runtime Parameter Tuning · holobiomicslab

    Use when deploying Mass2SMILES on a TensorFlow-CPU build and you need to optimize inference throughput on multi-core systems. This is particularly necessary when GPU inference is unavailable due to CUDA driver incompatibility, or when inference hardware has variable core counts (e.
    2 installs
29. ▌
    Tof Ms Signal Enhancement Low Abundance · holobiomicslab

    Use when your raw TOF-MS data (Agilent MassHunter .d format) exhibits jagged, artifact-prone peaks in low-abundance ions that compromise peak quality assessment or when you need to improve signal-to-noise before ion mobility demultiplexing or peak deconvolution.
    0 installs
30. ▌
    Training Data Loading And Preprocessing · holobiomicslab

    Use when you have downloaded raw LC-MS spectral peak data from a public repository (e.g., DOI 10.25345/C5FD2F) and need to ingest it into memory and prepare it in the format expected by a TensorFlow/Keras neural network classifier.
    0 installs
31. ▌
    Training Validation Test Set Allocation · holobiomicslab

    Use when after labeling a representative subset of peaks (typically 10–20 pooled samples with corresponding feature tables) and before neural network training, when you need to split labeled data into independent subsets for model training, hyperparameter tuning, and unbiased performance evaluation.
    0 installs
32. ▌
    Transformer Architecture Implementation · holobiomicslab

    Use when when building a neural network to map between mass spectrometry spectra and molecular properties (e.g., fingerprints, SMILES, or fragment ions) where sequential or spectral feature dependencies must be captured.
    0 installs
33. ▌
    Transformer Encoder Architecture Design · holobiomicslab

    Use when when you need to learn chemical-rational embeddings of tandem MS/MS spectra for library matching or molecular property prediction, and you want to leverage self-supervised learning through masking.
    0 installs
34. ▌
    Tsne Embedding Dimensionality Reduction · holobiomicslab

    Use when when you have a precomputed similarity matrix of mass spectra (e.
    2 installs
35. ▌
    Untargeted Metabolomics Data Processing · holobiomicslab

    Use when you have untargeted MS2 spectral data (from LC-MS/MS or similar instruments) and need to assign metabolic pathway context to detected compounds when standard spectral library matching is unavailable or insufficient.
    0 installs
36. ▌
    Virtual Mass Spectrometer Configuration · holobiomicslab

    Use when when you have generated or extracted a chemical mixture (via DatabaseFormulaSampler, ChemicalMixtureCreator, or ChemicalMixtureFromMZML) and need to establish a virtual instrument to simulate scan acquisition.
    0 installs
37. ▌
    Block Layout Analysis For Io Optimization · holobiomicslab

    Use when when preparing NMR datasets for processing in NMRFx and the Dataset.createDataFile() method must choose among competing storage backends.
    0 installs
38. ▌
    Convolutional Neural Network Layer Design · holobiomicslab

    Use when you have 1H NMR spectral tensors as input and need to extract local features (e.g., peak patterns, signal neighborhoods) before applying attention-based or sequence-level processing.
    0 installs
39. ▌
    Fragment Ion Theoretical Mass Calculation · holobiomicslab

    Use when when building a comprehensive lipid fragment ion library covering all chain composition and positional isomer variants (e.g., 168.6 million entries).
    0 installs
40. ▌
    Graph Neural Network Design For Chemistry · holobiomicslab

    Use when you have 1D or 2D NMR spectra (1H and/or 13C) and need to predict unknown molecular structure (formula and connectivity) up to ~19 heavy atoms; or you have a set of molecular fragment-structure pairs and need to model how fragments assemble into complete structures.
    2 installs
41. ▌
    JSON Payload Construction For Nmr Spectra · holobiomicslab

    Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification. Use this skill before making API calls to ensure peak data conforms to the expected JSON schema.
    0 installs
42. ▌
    Molecular Network Clustering And Analysis · holobiomicslab

    Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative molecular families.
    0 installs
43. ▌
    Molecular Structure Prediction Evaluation · holobiomicslab

    Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
    2 installs
44. ▌
    Molecular Structure Prediction Validation · holobiomicslab

    Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular structures, and you need to assess prediction accuracy and structural correctness against ground-truth or reference.
    2 installs
45. ▌
    Nmr Metabolomic Quality Control Reporting · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of plasma or serum samples, and you need to assess how processing delays affect metabolite concentrations and.
    0 installs
46. ▌
    Nmr Spectrum Tiling Format Interpretation · holobiomicslab

    Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile) and the system must decide between multiple storage backends (SubMatrixFile, BigMappedMatrixFile, MappedSubMatrixFile, MappedMatrixFile). Triggers include: (1) dataset metadata specifies a cache-file flag;
    1 install
47. ▌
    Spectral Peak Data Validation And Parsing · holobiomicslab

    Use when when you have received POST requests containing peaks data as form parameters (chemical shift, multiplicity, integration values) and need to accept, validate, and normalize those values before formatting them into a query compatible with an external NMR prediction service such as.
    0 installs
48. ▌
    Structural Similarity Scoring Metabolites · holobiomicslab

    Use when when you have paired MS/MS spectra from unknown metabolites and a reference database of known metabolites, and you want to rank candidate structures for unknown compounds by their predicted structural similarity rather than exact spectral matching.
    0 installs
49. ▌
    Atac Seq Bam Read Alignment Processing · holobiomicslab

    Use when when you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites, peaks, regulatory regions) to detect transcription factor occupancy footprints or compare chromatin accessibility between bound and unbound.
    0 installs
50. ▌
    Bedgraph Format Parsing And Validation · holobiomicslab

    Use when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC bedGraph format before passing them to peak-calling tools like SEACR.
    0 installs
51. ▌
    Bin Level Sequencing Depth Calculation · holobiomicslab

    Use when you have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each genomic bin to assess coverage uniformity, identify poorly-sequenced regions, or prepare bin-level weights for downstream normalization.
    2 installs
52. ▌
    Chromatin Accessibility Quantification · holobiomicslab

    Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .
    1 install
53. ▌
    Fragment Based Count Matrix Generation · holobiomicslab

    Use when you have a backed AnnData object containing processed fragment data (stored in .obsm['fragment_paired'] or .
    0 installs
54. ▌
    Hi C Normalization And Bias Correction · holobiomicslab

    Use when after generating raw Hi-C contact matrices from aligned reads (post-merge, pre-analysis).
    2 installs
55. ▌
    Hierarchical Dendrogram Interpretation · holobiomicslab

    Use when you have a methylBase object containing aligned methylation calls across multiple samples and need to verify whether samples cluster by expected experimental condition (e.g., test vs. control) or identify unexpected sample relationships.
    0 installs
56. ▌
    Iterative Lsi Dimensionality Reduction · holobiomicslab

    Use when when you have aligned paired scATAC-seq and scRNA-seq data from the same cells (multiome data) and need to create a single reduced-dimension coordinate space that integrates both chromatin accessibility and gene expression signals for joint clustering, trajectory analysis, or visualization.
    2 installs
57. ▌
    Large Scale Single Cell Matrix Loading · holobiomicslab

    Use when you have a single-cell count matrix with 10 million or more cells that must be processed through dimension reduction, clustering, or integration pipelines. Use it specifically before executing matrix-free spectral embedding (tl.
    0 installs
58. ▌
    Poisson Statistical Enrichment Testing · holobiomicslab

    Use when after extending ChIP sample reads to their predicted fragment length and constructing local lambda bias tracks (incorporating d-scaled, 1 kb, 10 kb, and genome-wide backgrounds).
    0 installs
59. ▌
    Single Cell Chromatin Sample Filtering · holobiomicslab

    Use when after loading fragment counts into a SummarizedExperiment object (e.g., via getCounts) but before motif matching or deviation computation.
    0 installs
60. ▌
    Transcription Factor Footprint Scoring · holobiomicslab

    Use when after bias-corrected ATAC-seq signal tracks (bigWig files) have been generated and you need to quantify transcription factor binding strength within open chromatin regions.
    0 installs
61. ▌
    Backend Performance Tradeoff Analysis · holobiomicslab

    Use when you are designing or optimizing an MsBackend implementation and need to decide whether to pre-populate the @spectraVars slot with all core spectra variable columns (mz, intensity, rtime, scanIndex, precursorMz, precursorIntensity, acquisitionNum, msLevel) at initialization time, or defer.
    0 installs
62. ▌
    Batch Script Execution And Automation · holobiomicslab

    Use when you have generated a peak table or feature list output file from an external peak-picking tool (MZmine, XCMS, MS-DIAL, or Compound Discoverer) in its native export format and need to ingest it into LipidMatch for lipid identification without manual column remapping or format conversion.
    0 installs
63. ▌
    Combination Function Parameterisation · holobiomicslab

    Use when you have two or more independent, standardised scoring functions that rank the same set of candidate pairs (e.
    0 installs
64. ▌
    Compositional Data Transformation Clr · holobiomicslab

    Use when apply CLR transformation when you have microbiome or metabolomic count data that sums to a constant across samples (relative abundance or compositional data) and intend to train supervised or unsupervised machine learning models (especially neural networks) that assume unbounded, linear.
    2 installs
65. ▌
    Converter Job Enumeration And Mapping · holobiomicslab

    Use when building a multi-source metadata annotation pipeline where converters are organized as dynamically discoverable subclasses in separate packages (e.g., MSMetaEnhancer.libs.converters.web and MSMetaEnhancer.libs.converters.
    0 installs
66. ▌
    Convolutional Neural Network Encoding · holobiomicslab

    Use when you have pairs of augmented ion images from mass spectrometry imaging data and need to generate low-dimensional representation vectors that maximize similarity between augmentations of the same image while avoiding representation collapse.
    0 installs
67. ▌
    Cross Script Consistency Verification · holobiomicslab

    Use when when a deep learning pipeline processes mass spectrometry spectra through multiple independent scripts (e.g., train_rescore.py, run_fiddle.py, test_caffeine.py) and a specific feature must be removed or masked to prevent the model from learning directly from a protected input (e.
    0 installs
68. ▌
    Cross Validation Benchmark Evaluation · holobiomicslab

    Use when you have developed a predictive model and need to compare its performance against established baselines (e.g., linear regression, Random Forest, Canonical Correlation Analysis) across multiple datasets with paired input-output features.
    0 installs
69. ▌
    Distribution Statistics Summarization · holobiomicslab

    Use when you have loaded a collection of molecular fingerprint vectors (such as biosynfoni fingerprints from a deposited dataset) and need to characterize their statistical and distributional properties before using them for machine learning, similarity searching, or method validation.
    0 installs
70. ▌
    Domain Context To Application Routing · holobiomicslab

    Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the search must be executed against the appropriate domain-curated spectral library.
    0 installs
71. ▌
    Feature Normalization Standardization · holobiomicslab

    Use when after extracting and encoding molecular descriptors and structural features (atom types, bond connectivity, graph topology) from SMILES strings into a fixed-size numerical tensor, before passing the feature matrix to the PS2MS deep learning model for NPS prediction.
    1 install
72. ▌
    Github Actions Workflow Configuration · holobiomicslab

    Use when when you have a Python package repository on GitHub and need to automatically verify that pull requests and commits pass unit tests and meet code quality standards before merge.
    0 installs
73. ▌
    Intensity To Concentration Conversion · holobiomicslab

    Use when you have raw MS intensity data paired with measurements from known concentration standards, and you need to produce absolute quantified concentration values rather than relative intensity measurements.
    0 installs
74. ▌
    Ion Mobility Mobilogram Visualization · holobiomicslab

    Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across the ion mobility axis.
    2 installs
75. ▌
    Mass Spectrometry Data Column Mapping · holobiomicslab

    Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer in its native export format and need to ingest it into LipidMatch for lipid identification.
    0 installs
76. ▌
    Mass Spectrometry Image Preprocessing · holobiomicslab

    Use when when preparing raw mass spectrometry imaging (MSI) ion images for deep learning–based representation learning, especially when you need to generate augmented image pairs that preserve domain-specific artifacts (photon counting noise, missing pixels) while varying appearance.
    2 installs
77. ▌
    Matrix Directive Collation Validation · holobiomicslab

    Use when you have IC-FTMS measurement records in JSON format with multiple samples per metabolite assignment and you need to verify that a matrix directive with collate='assignment' correctly groups records by assignment identifier and merges sample intensity values into a single dictionary per.
    2 installs
78. ▌
    Metabolic Model Consensus Integration · holobiomicslab

    Use when you have draft metabolic reconstructions in SBML or standard format for multiple organisms in a microbial community (e.
    0 installs
79. ▌
    Metabolite Set Composition Validation · holobiomicslab

    Use when after constructing a background set for ORA in metabolomics: you have loaded an experimental detection list and a metabolomics pathway database, applied background-set construction logic, and need to confirm that the resulting background set has the correct size, composition, pathway.
    2 installs
80. ▌
    Multi Stage Dockerfile Interpretation · holobiomicslab

    Use when you need to validate that Docker image builds for multiple deployment variants (e.g., cli, dev, linux, windows) meet documented compressed size ranges, or when you must audit storage footprint across a multi-target build pipeline without pre-computed metrics.
    2 installs
81. ▌
    Networkx Object Generation And Export · holobiomicslab

    Use when after identifying statistically significant features and assigning them to structural clusters (isotopologue groups, adduct groups, cross-assay links) and correlation clusters via MamsiStructSearch.
    2 installs
82. ▌
    Neural Network Architecture Extension · holobiomicslab

    Use when you have a working base MPNN model (e.g., chemprop) and need to add task-specific feature processing layers (spectral, electronic, or domain features) to improve predictions on a specialized molecular property or spectrum.
    0 installs
83. ▌
    Ora Statistical Background Definition · holobiomicslab

    Use when you are implementing ORA for metabolomics pathway analysis and must decide which metabolites constitute the statistical background against which to test your experimental detection list.
    2 installs
84. ▌
    Python Struct Packing For Binary Data · holobiomicslab

    Use when you need to serialize heterogeneous data (e.g., index integers and file offsets of different byte widths) into a compact binary format, or parse a binary file format specification that includes fixed-width field encodings.
    2 installs
85. ▌
    Quality Control Threshold Application · holobiomicslab

    Use when you have a feature table with intensity values across study (unknown) and blank control samples, and you need to remove features that may represent instrument artifacts, contamination, or noise rather than true biological signal.
    0 installs
86. ▌
    Spectral Library Matching And Ranking · holobiomicslab

    Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a reference library.
    0 installs
87. ▌
    Spectral Library Matching And Scoring · holobiomicslab

    Use when when you have MS/MS fragment spectra (in .mgf format) acquired from unknown metabolite features and need to annotate them against known compounds.
    0 installs
88. ▌
    Spectrum Plot Generation Mz Intensity · holobiomicslab

    Use when you have mass spectrometry spectral data loaded into a Pandas DataFrame with columns representing m/z (mass-to-charge ratio) and intensity values, and you need to visualize the spectrum to inspect peak patterns, identify high-abundance ions, or compare spectral profiles across samples or.
    0 installs
89. ▌
    Summary Statistics Table Construction · holobiomicslab

    Use when when you need to quantify and compare the effect of multiple filtering thresholds (e.g., Match.Factor ≥65, ≥80, ≥90) on the size of a retained compound set.
    0 installs
90. ▌
    Workflow Definition Schema Validation · holobiomicslab

    Use when you have located a workflow definition file (YAML or JSON) in a versioned release or commit and need to verify that it conforms to the schema specification for that release version (e.g., v1.0.0).
    2 installs
91. ▌
    Annotation Candidate Ranking Tp Score · holobiomicslab

    Use when after generating TP candidates from annotation algorithms (ann_comp for structure-based, ann_form for formula-based), when you need to filter and rank candidates to focus on the most credible identifications.
    0 installs
92. ▌
    Arrival Time To Drift Time Conversion · holobiomicslab

    Use when when processing raw TWIM-MS experimental data that contains arrival time measurements but you need drift times for CCS calibration or class-specific CCS calculations.
    1 install
93. ▌
    Background Reference Set Construction · holobiomicslab

    Use when when preparing to perform pathway enrichment analysis on metabolomics data, you need a background-reference file that maps metabolic pathways to their constituent metabolites.
    2 installs
94. ▌
    Batch Effect Removal Metabolomic Data · holobiomicslab

    Use when after integrating feature matrices from multiple analytical experiments or batches (e.g., n=3 or more batches). Use it when batch-related systematic variations are present in the integrated dataset before proceeding to sample separation, marker identification, or annotation steps.
    0 installs
95. ▌
    Biodegradation Pathway Interpretation · holobiomicslab

    Use when you have a small-molecule chemical structure (as SMILES, MOL, or SDF) and need to predict how soil or aquatic microbiota will degrade or biotransform it.
    0 installs
96. ▌
    Biosynformatic Descriptor Computation · holobiomicslab

    Use when when you have a natural product structure (as a molecule object, SMILES string, or InChI string) and need to generate a biosynformatic descriptor for downstream machine learning tasks such as biosynthetic class prediction, structure-activity correlation, or natural product database.
    2 installs
97. ▌
    Bruker Baf Data Import And Conversion · holobiomicslab

    Use when you have Bruker .d/.baf format mass spectrometry imaging data and need to ingest it into MSIGen for conversion to visualizable ion images. This skill applies when your raw data originates from Bruker TIMSTOF or similar instruments and you lack direct .
    2 installs
98. ▌
    Chemical Space Similarity Computation · holobiomicslab

    Use when you have retrieved multiple candidate structures from a molecular structure database (e.g., PubChem, HMDB) for an unknown compound, and you have predictions of structurally related metabolites from a deep-learning mass spectral model (e.g., DeepMASS2).
    0 installs
99. ▌
    Cheminformatic Feature Representation · holobiomicslab

    Use when when you have natural product structures in SMILES, InChI, or SDF format and need to convert them into numerical feature vectors for downstream tasks such as biosynthetic class prediction, molecular similarity analysis, or machine learning-based natural product classification.
    0 installs
100. ▌
     Chemodiversity Descriptor Calculation · holobiomicslab

     Use when you have a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify the molecular chemodiversity, elemental composition diversity, or complexity of environmental organic samples for cross-sample comparison or.
     0 installs