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HolobiomicsLab

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1. ▌
   Lc Ms Data Pipeline Architecture · holobiomicslab

   Use when you have vendor-format LC-MS acquisition files (.raw, .d, .ms) from instrument runs and need to set up an end-to-end data quality control system that converts proprietary formats into open mzML, processes spectral data, and surfaces QC failures in real time.
   0 installs
2. ▌
   Lc Ms Feature Quality Assessment · holobiomicslab

   Use when you have generated feature tables from LC-MS data using different parameter combinations (e.g., varying Centwave, FeatureFinderMetabo, or ADAP peak picking settings) and need to objectively compare their outputs to select the -performing configuration for your dataset.
   0 installs
3. ▌
   Lc Ms Quality Metric Computation · holobiomicslab

   Use when after performing peak detection on centroided .mzML LC-MS data with screening_mode=FALSE in TARDIS.
   0 installs
4. ▌
   Lcms Feature Probability Scoring · holobiomicslab

   Use when you have an untargeted LC/MS feature table (m/z, retention time, intensity columns) and need to move beyond single-hit matching to probabilistic annotation.
   0 installs
5. ▌
   Lcms Feature Relationship Export · holobiomicslab

   Use when after ISFrag has completed identification of in-source fragment features (Part 4 output), when you need to serialize and inspect the hierarchical fragmentation relationships among identified ISF features, or when preparing data for visualization or external analysis of fragment lineage and.
   2 installs
6. ▌
   Lcms Target Visibility Screening · holobiomicslab

   Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.
   0 installs
7. ▌
   Lipid Library Annotation From Mz · holobiomicslab

   Use when you have experimental peaklist data (CSV or mzML-derived tables) from UHPLC-HRMS/MS instruments (Q-Exactive, Agilent/Bruker/SCIEX Q-TOF) with fragment m/z values and want to annotate them to known lipid identities.
   0 installs
8. ▌
   Machine Learning Model Inference · holobiomicslab

   Use when you have molecular descriptors or fingerprints for a set of compounds (e.g., from LC-MS metabolomics) and need to predict a continuous property—such as HPLC retention time—to support compound identification or filter out false positive annotations.
   0 installs
9. ▌
   Mahalanobis Distance Calculation · holobiomicslab

   Use when after data normalization (Box-Cox transformation) and before hypothesis testing in Step 9 of untargeted metabolomic workflows.
   0 installs
10. ▌
    Mass Difference Pattern Matching · holobiomicslab

    Use when after peak picking and sample alignment when you have an aligned feature table containing m/z and retention time coordinates. Use it when your untargeted LC-MS workflow needs to reduce feature redundancy caused by naturally occurring stable isotope patterns and common adduct formation.
    0 installs
11. ▌
    Mass Spectral Feature Annotation · holobiomicslab

    Use when you have m/z values from spatially-resolved mass spectrometry imaging (e.g., MALDI-MSI, DESI-MSI) and need to assign molecular formulae to thousands of features with higher precision than traditional LC-MS approaches.
    0 installs
12. ▌
    Mass Spectral Network Annotation · holobiomicslab

    Use when you have a GNPS molecular network (classical or feature-based) and MS2LDA LDA experiment output (Mass2Motif assignments with probability and overlap scores) from the same experiment, and you want to annotate network nodes with structural motifs and chemical classes to infer molecular.
    2 installs
13. ▌
    Mass Spectrum Similarity Scoring · holobiomicslab

    Use when when you have a query MS/MS spectrum (m/z and intensity pairs) that you need to match against a library of reference spectra, and you want to identify the -matching library entry while accounting for unmatched peaks that may indicate spectral contamination or chimerism.
    4 installs
14. ▌
    Mass Tolerance Optimization Hrms · holobiomicslab

    Use when you have experimental peak lists (m/z, retention time, intensity) from peak-picking software (MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to match them against a simulated lipid fragment library (500,000+ lipid species).
    2 installs
15. ▌
    Mass Track Consensus Computation · holobiomicslab

    Use when after mass tracks have been aligned across all samples (either via pairwise alignment for ≤10 samples or nearest-neighbor clustering for larger cohorts), and you need to generate a single representative m/z per aligned bin for downstream feature extraction and annotation.
    2 installs
16. ▌
    Metabolite Database Construction · holobiomicslab

    Use when when performing untargeted metabolomics annotation at scale and you need to estimate false discovery rates for candidate metabolite identifications.
    2 installs
17. ▌
    Metabolite Feature Normalization · holobiomicslab

    Use when you have loaded two or more nontargeted LCMS feature tables from the same analytical method that contain m/z, retention time, and intensity values, and these datasets exhibit differences in metadata scale, distribution, or format that could confound cross-dataset feature matching or.
    0 installs
18. ▌
    Metabolite Identifier Conversion · holobiomicslab

    Use when your metabolomics dataset contains metabolite identifiers in multiple formats (e.
    0 installs
19. ▌
    Metabolomics Classifier Training · holobiomicslab

    Use when you have a preprocessed metabolomics feature matrix (expression matrix with metabolite abundances as columns and samples as rows) with corresponding binary or multi-class sample labels, and you need to train and compare classifier performance to select the -performing model for disease.
    0 installs
20. ▌
    Molecular Fingerprint Generation · holobiomicslab

    Use when when you have annotated chemical structures (SMILES or InChI strings) from a curated MS/MS dataset and need to compute pairwise structural similarity scores (Tanimoto or other metrics) as training labels, or when preparing molecular representations for comparison against mass spectral data.
    2 installs
21. ▌
    Molecular Fingerprint Prediction · holobiomicslab

    Use when you have tandem MS/MS spectra paired with known molecular structures (for training) or unknown spectra requiring structure identification, and you want to predict dense molecular fingerprint vectors that encode structural similarity.
    0 installs
22. ▌
    Ms Peak Blank Signal Subtraction · holobiomicslab

    Use when you have an MS-DIAL feature table from DDA or DIA LC-MS analysis that includes blank injection samples (at least 3 recommended), and you need to eliminate features that are artifactual contamination rather than genuine metabolites.
    0 installs
23. ▌
    Ms Spectra Dataset Preprocessing · holobiomicslab

    Use when when you have a raw or partially processed MS/MS spectra collection (e.g., GNPS-sourced Orbitrap or Q-TOF spectra in MGF format) and need to (1) restrict to a specific instrument type (e.
    1 install
24. ▌
    Ms2 Diagnostic Fragment Matching · holobiomicslab

    Use when you have centroided MS2 spectra from data-dependent LC- or GC-HRMS measurements and need to rapidly prioritize potential PFAS features within a larger feature set.
    0 installs
25. ▌
    Ms2 Fragment Pattern Recognition · holobiomicslab

    Use when you have data-dependent acquisition (DDA) MS2 spectra from HRMS measurements (ESI or APCI ionization) and need to prioritize potential PFAS features from a large pool of detected ions.
    0 installs
26. ▌
    Msms Spectral Database Retrieval · holobiomicslab

    Use when when you have a target compound (modified or unmodified) and need to obtain its experimental MS/MS spectrum and metadata to serve as a known reference for ModiFinder analysis, or when benchmarking evaluation methods like average_distance scoring.
    0 installs
27. ▌
    Multiclass Metabolite Comparison · holobiomicslab

    Use when when you have a normalized metabolite abundance matrix with sample metadata assigning each sample to one of three or more distinct biological classes (e.
    1 install
28. ▌
    Network Diffusion Prioritization · holobiomicslab

    Use when after clustering and filtering KEGG candidates for LC-MS features, when you have a ranked set of candidate metabolites per feature and access to a metabolite interaction network (e.g., from FELLA).
    0 installs
29. ▌
    Neural Network Input Preparation · holobiomicslab

    Use when when you have annotated representative LCMS samples (raw mzML files + labeled feature tables in mzmine CSV format) and need to convert them into balanced or unbalanced peak matrix batches with fixed dimensions for neural network training.
    0 installs
30. ▌
    Neutral Loss Formula Computation · holobiomicslab

    Use when you have tandem mass spectra with precursor m/z and observed fragment peak m/z values (as mz/intensity pairs), and you need to construct interpretable feature vectors where each axis corresponds to a real chemical entity (peak or neutral loss) rather than a latent dimension.
    0 installs
31. ▌
    Neutral Loss Peak Interpretation · holobiomicslab

    Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.
    0 installs
32. ▌
    Numerical Method Scheme Analysis · holobiomicslab

    Use when when correcting LC-MS isotope labeling data and existing numerical schemes (e.
    0 installs
33. ▌
    Peak Deconvolution Preprocessing · holobiomicslab

    Use when you have raw IM-MS data in Agilent MassHunter (.d) or UIMF format from drift tube (DT) or SLIM instruments, and you intend to perform HRdm demultiplexing or peak deconvolution to resolve co-eluting or structurally similar ions.
    0 installs
34. ▌
    Peak Detection Mass Spectrometry · holobiomicslab

    Use when you have raw mass-spectrometry data files (mzML, mzXML, or vendor formats) from untargeted metabolomics experiments and need to extract differential metabolic ion peaks for downstream statistical or annotation analysis.
    0 installs
35. ▌
    Peak Detection Optimization Free · holobiomicslab

    Use when when processing raw untargeted LC/MS data in mzML or mzXML format and you need to detect peaks across mass-to-charge (m/z) and retention time (rt) dimensions without prior knowledge of optimal signal detection parameters, QC samples, or domain expertise in LC/MS preprocessing.
    2 installs
36. ▌
    Peak Detection Signal Processing · holobiomicslab

    Use when after feature extraction from mzML/mzXML breath analysis data when you have a numerical array or dataframe of feature intensities across retention time or m/z dimensions and need to identify which features represent genuine volatile organic compound (VOC) signals rather than noise or.
    0 installs
37. ▌
    Peak List Filtering And Cleaning · holobiomicslab

    Use when you have acquired MS/MS spectra containing suspect noise ions—either electronic noise (ions with identical intensities occurring >4 times in a single peak list, a signature of detector artifacts) or chemical noise (fragment ions chemically implausible given the precursor molecule's.
    0 installs
38. ▌
    Peak List Parsing And Validation · holobiomicslab

    Use when when importing raw mass spectrometry data from vendor or open formats (mzML, mzXML, msp, MGF, JSON, metabolomics-USI) and you need to extract peak m/z and intensity pairs into a standardized representation.
    0 installs
39. ▌
    Peak Matching And Mass Alignment · holobiomicslab

    Use when when you have raw MS2 spectra (m/z and intensity pairs) and a curated reference peak list from a large training dataset (e.
    0 installs
40. ▌
    Peak Picking Algorithm Selection · holobiomicslab

    Use when at the entry point of SLAW processing when you have centroided mzML or netCDF LC-MS files and need to decide which peak-picking algorithm to use. Trigger this skill when: (1) raw LC-MS data must be converted into a feature matrix;
    2 installs
41. ▌
    Peptide Mass Calculation Average · holobiomicslab

    Use when you have a list of polypeptide sequences (one per line or CSV format) and need to compute average mass (weighted by natural isotope abundances) to compare against experimental LC-MS or MS/MS data where the full isotopic distribution—not just the most abundant peak—is relevant for peptide.
    0 installs
42. ▌
    Pfas Homologous Series Detection · holobiomicslab

    Use when you have an m/z-resolved feature list from LC- or GC-HRMS analysis (either detected by pyOpenMS or provided as a custom Excel table) and need to prioritize potential PFAS compounds by identifying clusters of homologous structures.
    0 installs
43. ▌
    Proforma 2 0 Peptidoform Parsing · holobiomicslab

    Use when you have a ProForma 2.0 peptidoform string (e.
    0 installs
44. ▌
    Publication Figure Customization · holobiomicslab

    Use when after annotating a mass spectrometry spectrum with fragment ions (e.g., via ProForma 2.
    0 installs
45. ▌
    Qc Sample Reliability Evaluation · holobiomicslab

    Use when after drift correction has been applied to your LC-MS peak table and you need to identify low-quality metabolic features that exhibit high internal spread (RSD, RSD*) or excessive QC-versus-biological variation (D-ratio) before imputation and batch correction.
    0 installs
46. ▌
    Qr Code Generation And Embedding · holobiomicslab

    Use when you need to publish metabolomics spectra in static media (PDF, print, supplementary tables) and want readers or automated systems to access the corresponding interactive spectrum visualization without manual lookup.
    0 installs
47. ▌
    Quasi Molecular Adduct Filtering · holobiomicslab

    Use when after feature clustering has been applied to co-eluting LC-MS features and mass-to-charge ratio matching to KEGG has produced an annotated table with adduct assignments.
    0 installs
48. ▌
    R6 Class Object Mutation Testing · holobiomicslab

    Use when when applying a series of mpactr filter functions (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) with copy_object=FALSE to confirm that the original peak table object is mutated as intended, not silently copied.
    0 installs
49. ▌
    Ranked Annotation Prioritization · holobiomicslab

    Use when you have completed cluster-based filtering of KEGG candidate assignments in untargeted LC-MS metabolomics and need to rank those candidates by biological plausibility using a metabolite interaction network. Specifically, use it after `clusterBased.
    2 installs
50. ▌
    Raw File Data Extraction Via API · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or file-level headers programmatically—e.
    0 installs
51. ▌
    Reference Semantics Verification · holobiomicslab

    Use when when applying sequential filters to a large metabolomics peak table (e.g., mispicked ions, group, CV, or in-source filters) and you need to confirm that setting copy_object=FALSE actually modifies the input object in-place rather than creating a hidden copy.
    0 installs
52. ▌
    Relative Abundance Preprocessing · holobiomicslab

    Use when when you have raw count tables from 16S rRNA sequencing (microbiome) or LC-MS/MS metabolomics (metabolome) and need to train neural network or regression models for microbe-metabolite relationship prediction.
    0 installs
53. ▌
    Replicate Spectrum Concatenation · holobiomicslab

    Use when after extracting raw MS/MS spectra from mzML files for individual features (identified by precursor m/z and retention time) and you have multiple replicate spectra for the same feature that need to be pooled for consensus analysis.
    0 installs
54. ▌
    Retention Time Alignment Scoring · holobiomicslab

    Use when after feature m/z grouping and pairwise alignment detection have identified candidate feature pairs, and anchor points have been selected to establish retention time correspondence.
    0 installs
55. ▌
    Retention Time Index Calibration · holobiomicslab

    Use when you have acquired a bottom-up proteomics LC-MS/MS run (e.
    1 install
56. ▌
    Retention Time Window Clustering · holobiomicslab

    Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you need to link individual m/z features into structural clusters representing the same metabolite in different ionization states or isotopic forms.
    0 installs
57. ▌
    Retention Time Window Extraction · holobiomicslab

    Use when you have loaded sqMass files containing pre-extracted transition group chromatograms and need to isolate chromatographic traces within a specific retention time interval—either defined by OpenSwath feature metadata (apex retention time ± margin) or by manual user selection.
    0 installs
58. ▌
    Runtime Performance Benchmarking · holobiomicslab

    Use when when you have implemented or adopted a new clustering or analysis tool and need to validate that it meets stated runtime claims on a representative production-scale dataset. Particularly important when the tool uses hardware acceleration (GPU) and the claimed speedup is a core contribution;
    0 installs
59. ▌
    Scan Index Filtering By Ms Level · holobiomicslab

    Use when when you have generated a scan index from rawrr::readIndex() on a Thermo .
    0 installs
60. ▌
    Scan Index Parsing And Filtering · holobiomicslab

    Use when you have a Thermo Orbitrap .raw file and need to (1) verify that a targeted acquisition method (e.g., PRM) maintains consistent scan spacing across all cycles; (2) extract only scans matching a specific precursor ion and fragmentation method;
    0 installs
61. ▌
    Score Distribution Visualization · holobiomicslab

    Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient separation between validated links and the background population.
    0 installs
62. ▌
    Signal Apodization Configuration · holobiomicslab

    Use when when processing raw Bruker Solarix transient files (.d format) destined for FT-MS analysis, especially for ESI-negative or low-abundance natural organic matter samples where baseline noise and side-lobe artifacts around intense peaks degrade peak picking and formula assignment accuracy.
    0 installs
63. ▌
    Small Molecule Compound Indexing · holobiomicslab

    Use when when you have retention order predictions from multiple ensemble members (e.g., ROASMI_1 through ROASMI_5) for a set of candidate compounds and need to assign a per-compound uncertainty score that reflects how consistently the ensemble members rank that compound relative to others.
    0 installs
64. ▌
    Smoothing Spline Basis Selection · holobiomicslab

    Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction spline.
    0 installs
65. ▌
    Spectral Data Import And Parsing · holobiomicslab

    Use when you have raw mass spectrometry data in one or more supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, or JSON) and need to convert it into a standardized in-memory representation that can be processed, validated, and compared using matchms.
    0 installs
66. ▌
    Spectral Feature Standardization · holobiomicslab

    Use when after peak-picking stage completes on centroided mzML or netCDF raw LC-MS data via any of the three wrapped algorithms (Centwave, FeatureFinderMetabo, ADAP), when you need to pass the detected features to downstream SLAW stages (alignment, isotope/adduct grouping, gap-filling, MS2.
    0 installs
67. ▌
    Spectral Fragment Ion Annotation · holobiomicslab

    Use when you have an MS/MS spectrum (m/z and intensity arrays) and a known or hypothesized peptide sequence (optionally with post-translational modifications in ProForma 2.
    2 installs
68. ▌
    Spectral Intensity Normalisation · holobiomicslab

    Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
    0 installs
69. ▌
    Spectral Intensity Normalization · holobiomicslab

    Use when after removing precursor and noise peaks from an MsmsSpectrum object when the spectrum contains peaks with highly variable intensities (e.g., one or two dominant peaks with many weaker fragments).
    0 installs
70. ▌
    Spectral Peak Embedding Encoding · holobiomicslab

    Use when when you have variable-length MS/MS peak lists (m/z and intensity arrays) that must be fed into a transformer-based model for spectra analysis, and you need deterministic, normalized embeddings that preserve peak frequency information across multiple scales.
    2 installs
71. ▌
    Spectrum Annotation Augmentation · holobiomicslab

    Use when you have a TCN-predicted training set of MS/MS spectra with formula annotations and need to prepare it for Siamese rescore model training.
    0 installs
72. ▌
    Synthetic Lcmsms Data Generation · holobiomicslab

    Use when you need to create defined LC-MS/MS datasets with known molecular composition and fragmentation patterns for algorithm validation, method development, or evaluation of analytical challenges (e.g., co-elution prediction).
    0 installs
73. ▌
    System Environment Configuration · holobiomicslab

    Use when you need to execute a complex computational chemistry workflow (QCxMS2) that depends on multiple external semiempirical and ab initio quantum chemistry packages.
    0 installs
74. ▌
    Transformation Method Comparison · holobiomicslab

    Use when when you have paired microbiome (16S rRNA or functional) and metabolome (LC-MS/MS or similar) data and must decide between compositional transformations (CLR, RA, or others) before training a predictive model.
    0 installs
75. ▌
    Unsupervised Spectrum Clustering · holobiomicslab

    Use when when you have high-dimensional embedding vectors from pretrained models (e.g., MSBERT) and need to verify that the learned representation space groups spectra by chemical similarity without labeled training data.
    0 installs
76. ▌
    Usi Spectrum Identifier Encoding · holobiomicslab

    Use when you have a Universal Spectrum Identifier (USI) string referencing a spectrum in a supported metabolomics repository (GNPS, MassBank, MetaboLights, Metabolomics Workbench, MassIVE, or MS2LDA) and need to create an embeddable, scannable reference for publication or data integration that.
    2 installs
77. ▌
    Web Application Endpoint Mapping · holobiomicslab

    Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that spectrum to the appropriate domain-specific MASST application for searching.
    0 installs
78. ▌
    Xcms Grouped Object Manipulation · holobiomicslab

    Use when you have preprocessed LC-MS data with detected chromatographic peaks that need to be consolidated into feature groups representing putative compounds.
    0 installs
79. ▌
    Xcms Output Replacement Workflow · holobiomicslab

    Use when xCMS has produced aligned LC-MS features but alignment quality is suspected to be poor—especially when analyzing hundreds of samples, data acquired over extended periods (>1 week), or when individual m/z bins show inconsistent RT shifts.
    0 installs
80. ▌
    Bioassay Activity Data Integration · holobiomicslab

    Use when when you have (1) a molecular network graph from GNPS with node identifiers and edges, (2) LC-MS/MS features quantified across fractions in a feature table, and (3) bioassay measurements (e.
    0 installs
81. ▌
    In Silico Fragment M Z Calculation · holobiomicslab

    Use when when you have experimental UHPLC-HRMS/MS or direct infusion MS/MS data and need to identify lipid species by comparing observed fragment m/z values against a library of simulated fragments. Apply this skill when your lipid library is incomplete or specialized (e.
    0 installs
82. ▌
    In Silico Fragmentation Prediction · holobiomicslab

    Use when you have candidate metabolite structures (from database lookup or enumeration) and experimental MS/MS spectra (mzML, mzXML format), and need to rank candidates by how well their predicted fragments match observed peaks.
    1 install
83. ▌
    Inadequate Spectral Interpretation · holobiomicslab

    Use when you have clustered peak networks from INADEQUATE NMR spectra (output from the Clustering module) and need to assign metabolite identities by comparing them to known spectral signatures.
    0 installs
84. ▌
    Top K Retrieval Ranking Evaluation · holobiomicslab

    Use when when you have deployed a trained embedding or similarity model on a test set of tandem mass spectra and need to measure its ability to rank correct library compounds near the top of retrieved candidates.
    2 installs
85. ▌
    Transfer Learning Encoder Freezing · holobiomicslab

    Use when you have a pretrained spectrum encoder (e.g., TCN on mass spectrometry data) that has learned useful representations, and you need to train new components (e.g., a rescoring module) for a related but distinct task (e.
    1 install
86. ▌
    Treemap Visualization Construction · holobiomicslab

    Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, use this skill when you need to communicate the count and percentage breakdown of ions retained vs. rejected across filter status categories.
    0 installs
87. ▌
    Untargeted Metabolomics Annotation · holobiomicslab

    Use when you have authentic metabolite standards analyzed by LC-MS in both positive and negative ESI modes (converted to .
    0 installs
88. ▌
    Usi Spectrum Retrieval And Loading · holobiomicslab

    Use when you have a USI accession (e.g., 'mzspec:MSV000082283:f07074:scan:5475' or 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') pointing to a publicly deposited tandem mass spectrometry scan in a GNPS or ProteomeXchange repository, and you need to retrieve and instantiate.
    0 installs
89. ▌
    Vendor Raw File Format Recognition · holobiomicslab

    Use when you have a directory containing mass spectrometry data files from multiple instrument vendors (Thermo, AB Sciex, Agilent, Bruker, etc.) and need to convert them to a common format (Aird or mzML).
    0 installs
90. ▌
    2d Nmr Pulse Sequence Implementation · holobiomicslab

    Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and spin-system J-coupling data, and you want to simulate realistic peak patterns including indirect-dimension evolution and phase.
    0 installs
91. ▌
    Chemical Shift Coordinate Extraction · holobiomicslab

    Use when you have loaded an INADEQUATE NMR spectrum file and need to detect individual peaks (local maxima) across the chemical shift dimension with associated intensity values. This is the mandatory first processing step before filtering peaks into networks or matching against metabolite databases.
    0 installs
92. ▌
    Coefficient Of Variation Computation · holobiomicslab

    Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association modeling.
    0 installs
93. ▌
    Container Image Build And Deployment · holobiomicslab

    Use when you have a Dockerfile and source repository for a bioinformatics tool (e.g., CloMet) and need to verify that the tool can be containerized, deployed, and made executable in an isolated environment.
    0 installs
94. ▌
    Cross Assay Feature Linkage Analysis · holobiomicslab

    Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple parallel assays acquired in complementary ionization modes (e.
    0 installs
95. ▌
    Graph Based Molecular Representation · holobiomicslab

    Use when when you have 1D NMR spectra (¹H and/or ¹³C) as input and need to predict complete molecular structure (both molecular formula and bond connectivity) for molecules with up to 19 heavy atoms.
    0 installs
96. ▌
    Lineshape Convolution And Broadening · holobiomicslab

    Use when after generating theoretical spin multiplets for individual metabolites via first-order or density-matrix NMR simulation, but before combining spectra or applying Fourier transformation.
    0 installs
97. ▌
    Mass Difference Network Construction · holobiomicslab

    Use when you have a preprocessed peak list (m/z values and assigned molecular formulas) from direct injection FT-ICR MS of a complex organic mixture (e.
    0 installs
98. ▌
    Modality Contribution Quantification · holobiomicslab

    Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you need to understand their relative importance for the downstream prediction task (e.g., molecular structure elucidation).
    2 installs
99. ▌
    Nmr Chemical Shift Interval Matching · holobiomicslab

    Use when you have isolated one or more regions-of-interest (ROIs) from a proton NMR spectrum (defined as lower and upper chemical-shift bounds in ppm) and need to systematically generate a list of plausible metabolite assignments from a reference database.
    0 installs
100. ▌
     Nmr Metabolite Identity Confirmation · holobiomicslab

     Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
     0 installs