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HolobiomicsLab

@holobiomicslab source repo

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1. ▌
   Pytorch Tensor Shape Validation · holobiomicslab

   Use when after implementing a transformer encoder backbone with masking mechanisms in PyTorch, before training on mass spectra data.
   0 installs
2. ▌
   Random Forest Regression Tuning · holobiomicslab

   Use when your MetaboSet object contains missing values (marked as NA) in the expression matrix after quality flagging, but you need complete data for multivariate analysis.
   0 installs
3. ▌
   Ranked Candidate Prioritization · holobiomicslab

   Use when you have a feature quantification table (m/z, retention time, peak areas) and candidate metabolite annotations (chemical identifiers, MS/MS spectra matches, or SIRIUS/GNPS predictions) linked to a sample organism or taxon, and you need to prioritize which candidates are most biochemically.
   0 installs
4. ▌
   Retention Order Prediction Rplc · holobiomicslab

   Use when when you have a set of small molecules (as SMILES or structures) that need to be identified or ranked by their elution order in RPLC systems with acidic pH (~2.7), and you want to assess model confidence in retention predictions.
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5. ▌
   Retention Time Window Filtering · holobiomicslab

   Use when you have mzML/mzXML chromatogram files from Thermo, Waters, or Bruker instruments and need to extract MS1 and MS2 scans matching both a target m/z value AND a known or suspected retention time range.
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6. ▌
   Roc Curve Auc Metric Evaluation · holobiomicslab

   Use when after training a NeatMS CNN model on labeled MS1 peaks and generating predictions on a held-out test set, compute ROC-AUC to assess whether the model achieves the target discrimination threshold (AUC ≥ 0.9) without evidence of overfitting.
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7. ▌
   Sample Partitioning By Metadata · holobiomicslab

   Use when you have a merged MGF file (e.g., from MZmine output) containing MS/MS spectra from multiple biological or environmental samples, and you need to process each sample independently through annotation pipelines (e.
   0 installs
8. ▌
   Scikit Learn Metric Computation · holobiomicslab

   Use when you have prediction arrays (model outputs) and ground-truth label arrays from a classification task and need to compute confusion matrices, accuracy scores, or other performance metrics for visualization or quantitative evaluation.
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9. ▌
   Separation Metric Normalization · holobiomicslab

   Use when you have extracted retention times from top MS1 features across an LC-MS run and need a single, comparable metric to evaluate how effectively a gradient spreads compounds across the chromatographic window.
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10. ▌
    Simulation Output Serialization · holobiomicslab

    Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans, and fragmentation events in memory.
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11. ▌
    Spectral Alignment Optimization · holobiomicslab

    Use when when you have two MS/MS fragmentation spectra (with precursor m/z values and fragment ion lists) and need to establish correspondence between their fragment ions beyond simple pairwise comparison.
    0 installs
12. ▌
    Spectral Data Format Conversion · holobiomicslab

    Use when you have raw tandem mass spectrometry data in one or more of the vendor formats (MGF, mzML, or msp) and need to apply unsupervised topic modeling (LDA-based motif discovery) or comparative fragmentation analysis.
    0 installs
13. ▌
    Spectral Data Import Validation · holobiomicslab

    Use when when you have raw mass spectrometry data in one or more of the six supported file formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to transform it into matchms spectrum objects for processing, cleaning, or similarity comparisons.
    0 installs
14. ▌
    Spectral Data Normalization Tic · holobiomicslab

    Use when apply TIC normalization when you have raw, unprocessed mass spectrometry data (Cardinal objects or imaging matrices with 10,000+ m/z features and 1,000+ spectra) where signal intensity varies across spatial locations or samples due to instrumental drift, uneven sample preparation, or.
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15. ▌
    Spectral Data Quality Assurance · holobiomicslab

    Use when when importing raw mass spectrometry data in formats like mzML, mzXML, msp, MGF, or JSON and you need to ensure spectral data quality before proceeding to similarity comparisons or other downstream analyses.
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16. ▌
    Spectral File Format Conversion · holobiomicslab

    Use when when you have a GNPS molecular networking job archive (downloaded as a .zip or compressed archive) and need to prepare metabolomics spectra and molecular family data for NPLinker integration.
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17. ▌
    Spectral Metadata Schema Design · holobiomicslab

    Use when you are implementing a file parser or data ingestion module that must read .raw (Thermo) and .mzml files from heterogeneous LC-MS instruments and pass structured data to downstream tools (e.
    0 installs
18. ▌
    Spectral Peak Fragment Matching · holobiomicslab

    Use when you have MS/MS spectral data (mzML, mzXML format) and a parent mass or molecular formula, and you need to identify the metabolite(s) responsible for the observed fragmentation pattern by scoring candidates against their theoretical fragmentation profiles.
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19. ▌
    Spectral Precursor Peak Removal · holobiomicslab

    Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry experiment (e.g., via USI) and before intensity filtering or scaling.
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20. ▌
    Spectral Scan Metadata Matching · holobiomicslab

    Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name, molecular weight, and annotation fields), and you need to pair each scan set with its corresponding chemical record to build.
    0 installs
21. ▌
    Spectral Similarity Computation · holobiomicslab

    Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
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22. ▌
    Statistical Enrichment Analysis · holobiomicslab

    Use when you have ranked GCF-MF (Gene Cluster Family–Molecular Family) links using two or more independent scoring functions and a set of experimentally validated links.
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23. ▌
    Statistical Result Reproduction · holobiomicslab

    Use when you have downloaded a Jupyter notebook from a published metabolomics workflow repository (e.
    0 installs
24. ▌
    Strain Spectrum Mapping Linkage · holobiomicslab

    Use when when you have downloaded and extracted a GNPS archive (from GNPS1 or GNPS2 workflows) and need to establish which spectral records (from spectra.mgf) were generated from which bacterial strains or samples. The file_mappings.tsv or file_mappings.
    0 installs
25. ▌
    Swath Ms Spectrum Deconvolution · holobiomicslab

    Use when you have SWATH-MS raw data (mzML or vendor format) from an untargeted metabolomics experiment and need to identify metabolites.
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26. ▌
    Tandem Mass Spectrum Clustering · holobiomicslab

    Use when you have a large collection of tandem mass spectra (mzML, mzXML, or MGF format) and want to group similar spectra into clusters to identify redundancy, discover novel peptides or metabolites, or prepare data for downstream annotation.
    0 installs
27. ▌
    Tandem Ms Output Interpretation · holobiomicslab

    Use when you have received spectrum predictions (fragment masses and intensities) from a neural model (ICEBERG, SCARF, or similar) and need to extract structural information, rank candidate molecules, or validate predictions against experimental spectra.
    0 installs
28. ▌
    Tanimoto Similarity Computation · holobiomicslab

    Use when you have a trained MS2DeepScore neural network and a set of MS/MS spectra (52 binned peaks per spectrum after preprocessing) for which you need to compute pairwise structural similarity predictions.
    0 installs
29. ▌
    Tcn Encoder Input Preprocessing · holobiomicslab

    Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z (env[:, 0]) has been removed from the feature vector to avoid leakage of mass information into the model's learned.
    0 installs
30. ▌
    Theoretical Spectrum Generation · holobiomicslab

    Use when you have a defined set of lipid species (identified by class and fatty acid composition) and need to create a high-throughput spectral library for mass spectrometry-based lipid identification.
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31. ▌
    Tracer Metabolite Pair Matching · holobiomicslab

    Use when you have acquired LC-MS peak tables from both unlabeled (12C) and isotope-labeled (13C) samples from a stable isotope tracing experiment, paired with sample metadata distinguishing case and control groups, and you need to systematically identify which unlabeled features correspond to.
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32. ▌
    Transformer Input Preprocessing · holobiomicslab

    Use when preparing chemical formulae (e.g., 'C6H12O6') as inputs to a transformer-based neural network for MS/MS spectrum scoring. Use it specifically when the transformer must rank multiple candidate formulae against an observed mass spectrum and element composition constraints are important;
    0 installs
33. ▌
    Untargeted Lcms Peak Annotation · holobiomicslab

    Use when you have a peak-intensity matrix from untargeted LC-MS analysis (raw detected peaks with m/z and intensity values) and need to assign putative metabolite identities.
    0 installs
34. ▌
    Usi Spectrum Identifier Parsing · holobiomicslab

    Use when when you have a USI string (e.g., mzspec:MTBLS1124:QC07.
    0 installs
35. ▌
    Vendor Instrument Data Handling · holobiomicslab

    Use when you have acquired raw mass spectrometry data in vendor-proprietary formats (ThermoFisher, Agilent, or equivalent) and need to analyze it using MSThunder for unknown organic pollutant identification.
    0 installs
36. ▌
    Workflow Branching Logic Design · holobiomicslab

    Use when when a spectral matching tool produces mixed output containing both exact library matches and analog search results, and your analysis or publication requires separate handling, interpretation, or reporting of these two match classes.
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37. ▌
    Chemical Shift Reference Matching · holobiomicslab

    Use when when preparing an input spectral peak list for NMRformer or similar Transformer-based peak assignment models, and you have observed peaks whose chemical shifts do not align with known metabolite signatures.
    0 installs
38. ▌
    Command Line Interface Invocation · holobiomicslab

    Use when when you have installed a Python package and need to verify that its command-line entry point is accessible, or when you need to discover available commands and options for NMR data processing workflows without consulting external documentation.
    0 installs
39. ▌
    Emd Spectral Distance Computation · 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 in the mixture and their abundances.
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40. ▌
    Endianness Detection And Handling · holobiomicslab

    Use when when reading a binary file format with a magic integer or fixed checksum field at a known offset, and endianness is not explicitly declared in file metadata or header comments.
    0 installs
41. ▌
    Mass Spectrometry Data Processing · holobiomicslab

    Use when you have raw mass spectrometry data in vendor-specific formats (Thermo RAW, Waters RAW, or open formats like mzML/jcamp) that need to be ingested, validated, and converted to a standardized representation for downstream peak detection, quantification, or integration with other NMR/IR/MS.
    0 installs
42. ▌
    Metabolic Parameter Visualization · holobiomicslab

    Use when when you have paired NMR metabolite measurements and corresponding processing metadata (pre-centrifugation delay, post-centrifugation delay, sample type, cohort) for a blood sample cohort and need to determine which metabolites remain stable across the expected or observed delay range, or.
    0 installs
43. ▌
    Metabolite Signal Drift Detection · holobiomicslab

    Use when when you have multi-batch metabolomics data (SummarizedExperiment object with raw or log-transformed assays) and need to assess whether specific metabolites exhibit systematic signal drift across experimental run order or strong batch effects that would justify hierarchical normalisation.
    0 installs
44. ▌
    Metabolomics Data Standardization · holobiomicslab

    Use when you have raw 1D NMR spectral data (urine, worm, or other biological samples) that needs to be converted into peak tables for metabolite identification and quantification.
    0 installs
45. ▌
    Metadata Structure Transformation · holobiomicslab

    Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be deposited into a structured online repository like Metabolomics Workbench, but the raw format does not conform to the.
    0 installs
46. ▌
    Multi Database Structure Querying · holobiomicslab

    Use when after cleaning and clustering LC-MS features in MS-CleanR, when you need to assign putative compound identities to a feature set with MS/MS spectra, and when candidate compounds may exist across multiple specialized databases (e.g., natural products, pharmaceuticals, contaminants).
    0 installs
47. ▌
    Mzmine Quantitative Table Parsing · holobiomicslab

    Use when you have LC–MS/MS data processed through MZmine2 or MZmine3 and need to construct a feature quantification table for natural product discovery pipelines (e.g., INVENTA prioritization, GNPS networking, or metabolite annotation).
    0 installs
48. ▌
    Nmr Spectral Comparative Analysis · holobiomicslab

    Use when you have 2D NMR spectral data (heteronuclear and/or homonuclear experiments) from multiple samples in a natural products library or mixture, and you need to identify common structural scaffolds, correlate features across samples, or prioritize samples for further structural annotation.
    0 installs
49. ▌
    Small Molecule Structure Matching · holobiomicslab

    Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the observed compounds by matching their experimental features (mass-to-charge ratio, retention time, spectral signature) to.
    0 installs
50. ▌
    Structure Prediction From Spectra · holobiomicslab

    Use when you have experimental mass spectrometry spectra (LC–QTOF or similar format) from unknown compounds and need to predict their molecular structures.
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51. ▌
    Virtual Environment Configuration · holobiomicslab

    Use when you have a Python application (e.g., ROIAL-NMR) with documented dependencies and version constraints, and you need to install it on a fresh machine or verify that the environment can be reconstructed without import or runtime errors.
    0 installs
52. ▌
    Bead Count Threshold Filtering · holobiomicslab

    Use when apply this filter after loading raw .idat files or beta-valued matrices from HumanMethylation450 or EPIC methylation arrays when you need to remove probes with insufficient bead counts that may introduce measurement noise or bias into downstream differential methylation or enrichment.
    0 installs
53. ▌
    Chip Seq Peak Calling Workflow · holobiomicslab

    Use when when you have aligned ChIP-Seq reads (single-end BED or paired-end BEDPE format) and need to identify enriched genomic regions by comparing ChIP signal against control background, with the ability to customize fragment length estimation, local bias calculation, and peak score thresholds.
    0 installs
54. ▌
    Cis Contact Frequency Analysis · holobiomicslab

    Use when when you have loaded a cooler file containing Hi-C contact matrices and need to quantify how contact probability decays with genomic distance within a single chromosome.
    0 installs
55. ▌
    Slingshot Trajectory Embedding · holobiomicslab

    Use when you have an ArchR project with clustered single-cell ATAC-seq cells and want to reconstruct developmental or cellular transition trajectories. Use this skill when your research question requires ordering cells along a developmental continuum (e.
    0 installs
56. ▌
    Tf Binding Site Classification · holobiomicslab

    Use when you have aligned ATAC-seq BAM files, corrected Tn5 insertion bias and computed footprint scores (via TOBIAS ATACorrect and ScoreBigwig), a motif database in JASPAR or compatible format, and you need to assign occupancy states (bound/unbound) and confidence scores at specific TF binding.
    0 installs
57. ▌
    Bioconda Package Installation · holobiomicslab

    Use when you have identified a package available in the Bioconda channel (indicated by a conda version badge or Bioconda recipe URL) and need to verify that installation succeeds and that the package's critical modules are importable in the target Python environment, especially before integrating.
    0 installs
58. ▌
    Conditional Record Resolution · holobiomicslab

    Use when converting JSON metadata and you need to populate a target field by selecting or iterating over records only when they satisfy a logical test condition (e.g., 'include this record only if a specific field has a particular value').
    0 installs
59. ▌
    Configuration File Generation · holobiomicslab

    Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5 and need version-specific parameter defaults (e.g., column names and scaling factors that differ between versions).
    0 installs
60. ▌
    Database Metadata Enumeration · holobiomicslab

    Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) and need to verify the reported counts of unique entities (source databases, organisms, structures, and their pairs) to confirm dataset integrity, assess data coverage, or reproduce published statistics in a.
    0 installs
61. ▌
    Deep Learning Model Inference · holobiomicslab

    Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to classify unknown compounds or generate prediction confidence scores for structural novelty analysis.
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62. ▌
    Development Environment Setup · holobiomicslab

    Use when when you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution. Specifically when the package declares dev dependencies in setup.py or pyproject.toml and maintains a pytest test suite in a tests/ directory.
    0 installs
63. ▌
    Flat File Parsing And Loading · holobiomicslab

    Use when when you have published LOTUS flat files (TSV or compressed TSV.GZ) containing structure-organism pairs and need to enumerate unique structures, group by organism prevalence, or validate record counts against gold-standard benchmarks.
    0 installs
64. ▌
    Injection Sequence Annotation · holobiomicslab

    Use when you have a Sciex Multiquant TXT export file containing a metabolomics or lipidomics analytical sequence and need to locate QCpool samples that were injected at regular intervals, validate their spacing matches study design expectations, and compile structured metadata for downstream.
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65. ▌
    Ion Image Augmentation Design · holobiomicslab

    Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that reflect either co-localization relationships between different molecular ions (COL mode) or isotopic relationships.
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66. ▌
    Lexical Analysis Tokenization · holobiomicslab

    Use when you have a mass-spectrometry query string written in MassQL (or similar domain-specific SQL-inspired syntax) that must be converted into structured form for execution. The input is raw, unparsed text containing SQL keywords, MS-specific operators (e.
    0 installs
67. ▌
    Mass Spectrometry Data Import · holobiomicslab

    Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.
    0 installs
68. ▌
    Mass2motif Annotation Mapping · holobiomicslab

    Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
    0 installs
69. ▌
    Ms Backend API Implementation · holobiomicslab

    Use when you have MS data in a new format or storage system (e.g., a custom database, HDF5 file, or proprietary raw file) and need to make it accessible to Spectra-based analysis workflows without forking the Spectra package itself.
    0 installs
70. ▌
    Ms Dial Version Compatibility · holobiomicslab

    Use when you are preparing to run LipoCLEAN on MS-DIAL output and need to create or update a configuration file, or you have switched between MS-DIAL 4 and MS-DIAL 5 data and need to verify that your options file and trained model are compatible with the current version's column naming and scaling.
    0 installs
71. ▌
    Mzml File Parsing And Loading · holobiomicslab

    Use when when you have real LC-MS/MS experimental data in mzML format (e.
    0 installs
72. ▌
    Package Dependency Management · holobiomicslab

    Use when you need to set up a cloned or downloaded scientific Python package for local development, testing, or execution. Specifically, use it when: (1) you have a package repository with a pyproject.toml or setup.py that declares dev dependencies;
    0 installs
73. ▌
    Ppm Error Tolerance Filtering · holobiomicslab

    Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to chemodiversity analysis, transformation network generation, or multivariate statistics.
    0 installs
74. ▌
    Reproducibility Gap Detection · holobiomicslab

    Use when evaluating whether a published computational method can be independently executed: (1) source code is claimed to be available but repository structure, build instructions, or dependency specifications are incomplete;
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75. ▌
    Runtime Performance Profiling · holobiomicslab

    Use when when you need to empirically validate that one mass spectrometry data processing library achieves higher throughput than competing alternatives. Specifically: you have multiple candidate libraries (e.
    0 installs
76. ▌
    Smiles Canonicalization Rdkit · holobiomicslab

    Use when when preprocessing raw SMILES strings from external chemistry databases (e.g., CCSBase, METLIN-CCS, or custom compound libraries) that may contain multiple valid but non-canonical notations for the same molecular structure.
    0 installs
77. ▌
    Smiles Parsing And Validation · holobiomicslab

    Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing descriptors, generating mass spectra, or calculating chemical fingerprints.
    0 installs
78. ▌
    Smiles Sdf Parsing Validation · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
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79. ▌
    Tabular Data Field Comparison · holobiomicslab

    Use when you have multiple independent implementations of the same data format reader (e.g., Rust, Python, R versions) and need to verify they produce identical or equivalent output.
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80. ▌
    Tensor Encoding Deep Learning · holobiomicslab

    Use when when you have validated SMILES strings or RDKit molecule objects representing chemical structures and need to feed them into a pre-trained deep learning model (such as PS2MS, NEIMS, or DeepEI) that expects fixed-size numerical tensor inputs.
    0 installs
81. ▌
    Web Service Health Monitoring · holobiomicslab

    Use when your annotation pipeline depends on multiple external web converters and you need to diagnose why annotation jobs are failing, slow, or incomplete. Use it if you observe missing metadata fields in output .
    0 installs
82. ▌
    Annotation Table Construction · holobiomicslab

    Use when when you have access to multiple public metabolomics databases and need to build a unified reference table for metabolite annotation in untargeted mass spectrometry analysis.
    0 installs
83. ▌
    Aromaticity Index Computation · holobiomicslab

    Use when after molecular formula assignment from FT-ICR MS peaks and elemental composition tabulation (C, H, O, N, S, P counts), when you need to quantify the degree of aromaticity and carbon-skeleton unsaturation for each detected compound to support Van Krevelen classification, chemodiversity.
    0 installs
84. ▌
    Autotuner Object Manipulation · holobiomicslab

    Use when after AutoTuner has completed EICparams extraction and parameter estimation on raw untargeted metabolomics data (mzML, mzXML, or CDF format), and you need to pass those estimates into XCMS or MZmine2 for full dataset processing.
    0 installs
85. ▌
    Biomolecular Class Annotation · holobiomicslab

    Use when you have raw or processed TWIM-MS data with arrival time and m/z dimensions, and you need to label experimental features by biomolecular class before performing CCS calibration or validation.
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86. ▌
    Biomolecule Metadata Handling · holobiomicslab

    Use when initiating a proteomics or panomics analysis with peptide- or protein-level expression data. The trigger is the simultaneous availability of: (1) a quantification matrix (rows = biomolecules, columns = samples), (2) sample metadata (e.
    0 installs
87. ▌
    Biotransformation Enumeration · holobiomicslab

    Use when you have a known parent drug chemical formula and aim to predict its metabolite landscape prior to or during high-resolution mass spectrometry analysis (mzML).
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88. ▌
    Bruker Solarix Format Parsing · holobiomicslab

    Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d) and need to programmatically access the transient time-domain signal and metadata for zero-filling, apodization windowing (e.g., Hanning), or mass calibration.
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89. ▌
    Bubble Plot Aesthetic Mapping · holobiomicslab

    Use when you have parsed GO enrichment results (GO term identifiers, p-values or adjusted p-values, gene ratios, gene counts) into CSV format and need to render them as interactive bubble plots.
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90. ▌
    Ccs Prediction Model Training · holobiomicslab

    Use when you have a dataset of SMILES strings with corresponding experimental CCS measurements and want to build a predictive model that can rapidly generate CCS values for new molecules without running expensive ion-mobility spectrometry experiments.
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91. ▌
    Ccs Reference Data Extraction · holobiomicslab

    Use when you have obtained or need to prepare a DTCCS_N2 reference library for U13C-labeled lipids (typically provided as part of a lipidomics tool distribution) and need to extract, validate, and normalize its contents into a machine-readable table format before using it for CCS bias calculation.
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92. ▌
    Chemical Descriptor Retrieval · holobiomicslab

    Use when after harmonizing compound identifiers to PubChem IDs (e.g., via check_names function).
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93. ▌
    Chemical Formula Manipulation · holobiomicslab

    Use when when you have a parent drug's raw chemical formula and need to predict its potential metabolites in mass spectrometry data (mzML format) to match against observed peaks.
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94. ▌
    Chemical Structure Validation · holobiomicslab

    Use when after compound database dereplication with SIRIUS or MetFrag has produced candidate annotations (CSV or JSON format), and you need to filter implausible structures, compute standardized molecular descriptors, and rank candidates by confidence before reporting final metabolite.
    0 installs
95. ▌
    Chromatographic Peak Labeling · holobiomicslab

    Use when you have a user-defined reference list of isolated, high-confidence chromatographic peaks (ground-truth) matched across multiple LC-HRMS samples, and you need to produce a labelled training dataset large enough to train a CNN model that discriminates true peaks from background noise and.
    0 installs
96. ▌
    Compound Set Filtering Python · holobiomicslab

    Use when when running Pickaxe reaction network expansion and you need to reduce the candidate compound set before each generation using criteria not covered by built-in filters (e.g., similarity thresholds, metabolomics matching, or target-based selection).
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97. ▌
    Compound Structure Processing · holobiomicslab

    Use when you have a collection of DNA adduct or small-molecule compound structures stored in SDF format and need to prepare them for computational workflows like CFM-ID fragment prediction, or when integrating new compounds into a structured compound database.
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98. ▌
    Conformer Ensemble Processing · holobiomicslab

    Use when you have a set of conformers that have already been filtered by ASE-ANI neural network potentials and need to extract quantum-mechanical electronic properties (polarizability tensor, dipole moment) required for collision cross section calculation.
    0 installs
99. ▌
    Conversion Graph Construction · holobiomicslab

    Use when when integrating MSMetaEnhancer into Galaxy or another workflow platform and you need to dynamically populate conversion option menus without hardcoding service-specific logic.
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100. ▌
     Costes Threshold Segmentation · holobiomicslab

     Use when when you have two or more co-registered LA-ICP-MS element channel images and need to compute colocalization coefficients (especially Manders) that require reproducible, bias-free segmentation.
     0 installs