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HolobiomicsLab

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1. ▌
   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
2. ▌
   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
3. ▌
   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
4. ▌
   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
5. ▌
   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
6. ▌
   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
7. ▌
   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
8. ▌
   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
9. ▌
   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.
   1 install
10. ▌
    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
11. ▌
    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
12. ▌
    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.
    2 installs
13. ▌
    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.
    2 installs
14. ▌
    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
15. ▌
    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
16. ▌
    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.
    2 installs
17. ▌
    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
18. ▌
    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
19. ▌
    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.
    2 installs
20. ▌
    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.
    0 installs
21. ▌
    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
22. ▌
    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.
    2 installs
23. ▌
    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.
    0 installs
24. ▌
    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.
    2 installs
25. ▌
    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
26. ▌
    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.
    1 install
27. ▌
    Mass2motif Annotation Mapping · holobiomicslab

    Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
    0 installs
28. ▌
    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
29. ▌
    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
30. ▌
    Mzml File Parsing And Loading · holobiomicslab

    Use when when you have real LC-MS/MS experimental data in mzML format (e.
    0 installs
31. ▌
    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
32. ▌
    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
33. ▌
    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;
    0 installs
34. ▌
    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
35. ▌
    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
36. ▌
    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.
    1 install
37. ▌
    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.
    0 installs
38. ▌
    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.
    2 installs
39. ▌
    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
40. ▌
    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
41. ▌
    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.
    1 install
42. ▌
    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
43. ▌
    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
44. ▌
    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.
    2 installs
45. ▌
    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
46. ▌
    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).
    0 installs
47. ▌
    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.
    0 installs
48. ▌
    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.
    0 installs
49. ▌
    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.
    0 installs
50. ▌
    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.
    0 installs
51. ▌
    Chemical Descriptor Retrieval · holobiomicslab

    Use when after harmonizing compound identifiers to PubChem IDs (e.g., via check_names function).
    0 installs
52. ▌
    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.
    2 installs
53. ▌
    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
54. ▌
    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
55. ▌
    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).
    2 installs
56. ▌
    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.
    0 installs
57. ▌
    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
58. ▌
    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.
    0 installs
59. ▌
    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.
    2 installs
60. ▌
    Cross Dataset Entry Filtering · holobiomicslab

    Use when you have received MSBERT-preprocessed spectral data from GNPS, MoNA, or MTBLS1572 and need to ensure data integrity before training a spectral embedding model.
    0 installs
61. ▌
    Cross Omics Feature Alignment · holobiomicslab

    Use when you have preprocessed multiomics datasets from distinct biomolecular classes (e.
    2 installs
62. ▌
    Database Repository Retrieval · holobiomicslab

    Use when when you need to obtain a specific curated database (e.g., DNA adduct compounds) that is published in a GitLab or GitHub repository and available in structured formats (SDF, Excel, Word).
    0 installs
63. ▌
    Development Mode Installation · holobiomicslab

    Use when you need to run a local test suite, contribute code changes to a repository, or iterate rapidly on package modifications.
    0 installs
64. ▌
    Directed Edge Weight Encoding · holobiomicslab

    Use when after computing a Jacobian matrix from covariance data and extracting directed edges representing metabolite interactions, use this skill when you need to communicate the magnitude and direction of metabolite-to-metabolite influences in a single integrated visualization.
    0 installs
65. ▌
    Elemental Composition Parsing · holobiomicslab

    Use when when you have FT-ICR MS peak data with assigned molecular formulas (e.g., from CoreMS, Formularity, or similar formula assignment tools) and need to compute thermodynamic indices (DBE, GFE, AImod, NOSC) or classify peaks by elemental composition.
    0 installs
66. ▌
    Embedding Similarity Matching · holobiomicslab

    Use when after a CNN model has generated predicted molecular embeddings from mass spectrometry data, and you need to identify the most likely candidate molecules from a reference database.
    0 installs
67. ▌
    Entry Point Script Validation · holobiomicslab

    Use when after installing a Python package or cloning its repository, to verify that the primary command-line interface is functional and discoverable before attempting analysis workflows.
    0 installs
68. ▌
    Fingerprint Generation Morgan · holobiomicslab

    Use when you have parsed molecular structures from the SMRT dataset or similar small molecule collections and need to create a vectorized molecular representation suitable for neural network input alongside molecular graph representations.
    0 installs
69. ▌
    Fisher Exact Test Application · holobiomicslab

    Use when you have a list of metabolites or lipids with associated p-values (e.
    2 installs
70. ▌
    Fisher Exact Test Computation · holobiomicslab

    Use when you have partitioned genomic-metabolomic links into discrete categories (e.
    0 installs
71. ▌
    Git Feature Branch Management · holobiomicslab

    Use when when contributing a new feature, bug fix, or documentation update to a shared repository (like iomega/ms2query), and you need to isolate your changes from the main development branch to allow for testing, review, and conditional integration without disrupting the primary codebase.
    2 installs
72. ▌
    Gpu Environment Configuration · holobiomicslab

    Use when you need to run a PyTorch model that was trained on GPU (e.g., JESTR with released NPLIB1 weights) and require verified GPU availability (torch.cuda.is_available() returns True). Apply this skill when you have a requirements.
    0 installs
73. ▌
    Hdf5 File Structure Traversal · holobiomicslab

    Use when when you have converted multidimensional mass spectrometry data (or other complex data) into MZA HDF5 format and need to understand the file hierarchy, validate the conversion output, extract metadata tables and array structure, or access spectra across different programming environments.
    0 installs
74. ▌
    Hmm Profile Database Querying · holobiomicslab

    Use when when you have BGC sequences (FASTA or GenBank format) or protein sequences and need to annotate them with biosynthetic or functional domains from a curated pHMM database (e.g., PFAM 35.0).
    2 installs
75. ▌
    Imputation Quality Validation · holobiomicslab

    Use when after applying BPCA imputation to a filtered metabolite matrix (with metabolites having >80% missingness already removed) and before proceeding to median normalization.
    0 installs
76. ▌
    Imzml File Loading And Import · holobiomicslab

    Use when when you have one or more imzML files containing mass spectrometry imaging data and need to import them into LipidQMap for ion image extraction, isotopic correction, and quantitative analysis.
    0 installs
77. ▌
    Ionomics Data Format Handling · holobiomicslab

    Use when you have raw ICP-MS ion concentration measurements (e.g., Ca44, Cd111, Fe56, Zn66 in ppm) organized as a data frame with multiple replicates per sample and batch identifiers, and you need to prepare this for ionomics analysis in Galaxy or the IonFlow R package.
    0 installs
78. ▌
    Irreversible Model Conversion · holobiomicslab

    Use when you have a constraint-based metabolic model in SBML or similar format with reversible reactions and need to sample the feasible steady-state flux region using optGpSampler or other samplers that require an irreversible stoichiometric matrix.
    0 installs
79. ▌
    Isotopic Envelope Calculation · holobiomicslab

    Use when when you have one or more peptide sequences (as strings) and need to predict their theoretical isotopic distribution for comparison against experimental MS peaks, validation of mass calibration, or simulation of expected peptide signals in a mass spectrometry assay.
    0 installs
80. ▌
    Iterative Fitting Convergence · holobiomicslab

    Use when you have 1D mass spectrometry signal data (e.
    2 installs
81. ▌
    Java Static Method Invocation · holobiomicslab

    Use when you have a Java application or standalone tool that needs to predict CYP450-catalyzed metabolites for one or more molecules and you require the option to compare predictions with and without CypReact filtering applied.
    0 installs
82. ▌
    Joint Embedding Space Scoring · holobiomicslab

    Use when you have a mass spectrum from an untargeted metabolomics experiment and a set of candidate molecules (e.g., downloaded from PubChem) that may explain that spectrum. You want to rank these candidates by likelihood of correctness to prioritize manual annotation or further validation.
    0 installs
83. ▌
    JSON Spectral Data Processing · holobiomicslab

    Use when you have raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize field names, validate chemical identifiers (SMILES, InChI, InChIKey), remove duplicates, filter by quality criteria.
    0 installs
84. ▌
    Archive Extraction And File Mapping · holobiomicslab

    Use when when you have downloaded a GNPS molecular networking job archive (from GNPS1 or GNPS2 workflows: METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING, classical_networking_workflow, or feature_based_molecular_networking_workflow) and need to extract and standardize.
    0 installs
85. ▌
    Batch Aware Normalization Workflows · holobiomicslab

    Use when your LC-MS feature table exhibits intensity variations across samples that correlate with technical batches (e.
    0 installs
86. ▌
    Batch Correction Quality Assessment · holobiomicslab

    Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have been attenuated without loss of data dimensionality or sample information.
    2 installs
87. ▌
    Bgc Spectrum Iokr Score Computation · holobiomicslab

    Use when when you have a collection of microbial genomes with predicted BGCs (via antiSMASH), a set of MS/MS spectra (e.g. from GNPS), and you want to score potential BGC-spectrum associations based on the presence of conserved molecular substructures inferred from the BGC's closest MIBiG homolog.
    2 installs
88. ▌
    Binary And XML Data Deserialization · holobiomicslab

    Use when you have raw LC-MS data in .mzML (XML-based) or Thermo .raw (proprietary binary) format and need to load it into memory for visualization, querying, or downstream analysis.
    0 installs
89. ▌
    Charge State Specific Peak Matching · holobiomicslab

    Use when you have peak-picked features with m/z, drift_time, retention_time, and intensity columns, and you need to identify monoisotopic peaks and their charge-state-specific isotopologue members (e.g., singly charged C13-substituted species).
    0 installs
90. ▌
    Chemical Class Metadata Integration · holobiomicslab

    Use when you have generated a GNPS molecular network (classical or feature-based workflow) and possess chemical class annotations (from GNPS library matching, ClassyFire, or other structural classifiers) that you wish to propagate onto network nodes and edges to enable chemical family-level.
    0 installs
91. ▌
    Chemical Formula Ranking Evaluation · holobiomicslab

    Use when after running formula inference on a benchmark dataset with known formula and adduct ground truth (e.g., NPLIB1, NIST20, or CASMI 2022). Apply this skill when you need to quantify ranking performance, isolate the contribution of specific model features (e.
    0 installs
92. ▌
    Chromatographic Coelution Detection · holobiomicslab

    Use when after feature detection when you have a feature table with m/z, retention time, and intensity columns, and you need to group features into empirical compounds (putative metabolites) that account for isotopologue patterns and multiple adduct forms arising from a single underlying analyte.
    0 installs
93. ▌
    Classification Metric Visualization · holobiomicslab

    Use when after training or evaluating a classification model (e.g., a Siamese neural network for spectrum similarity prediction) and obtaining a prediction array and corresponding ground-truth label array.
    0 installs
94. ▌
    Coefficient Of Variation Comparison · holobiomicslab

    Use when after normalization of a metabolomic feature matrix but before statistical testing, when you have both QC (technical replicate) and non-QC (study) samples and need to remove features with unstable or poorly reproducible signal patterns.
    0 installs
95. ▌
    Cohen Kappa Inter Rater Reliability · holobiomicslab

    Use when when you have two independent predictions of categorical outcomes (up/down/no-change variation signs) across multiple sample pairs and need to measure agreement beyond what would be expected by chance.
    0 installs
96. ▌
    Collision Cross Section Calibration · holobiomicslab

    Use when you have LC-IMS-MS/MS data with drift_time measurements and need to convert raw drift times into calibrated CCS values for structural annotation.
    0 installs
97. ▌
    Collision Cross Section Computation · holobiomicslab

    Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
    2 installs
98. ▌
    Comparative Omics Report Generation · holobiomicslab

    Use when when you have feature lists (in CSV format) from two or more different MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), different processing software (e.
    0 installs
99. ▌
    Container Image Building Conversion · holobiomicslab

    Use when your Nextflow metabolomics workflow has been validated with Docker locally, but you need to deploy it on an HPC cluster that mandates Singularity containerization (e.g., Red Hat Enterprise Linux 8.
    0 installs
100. ▌
     Cross Domain Metadata Harmonization · holobiomicslab

     Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate cross-domain summary statistics.
     0 installs