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HolobiomicsLab

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1. ▌
   Mass Spectrum Prediction Modeling · holobiomicslab

   Use when you have a collection of molecular structures (SMILES or chemical graphs) with paired experimental tandem mass spectra and want to build or benchmark a predictive model.
   2 installs
2. ▌
   Mass To Charge Tolerance Matching · holobiomicslab

   Use when you have statistically significant LC-MS features and need to group them into structural clusters. Specifically, use it after selecting features by p-value threshold (e.g., p < 0.
   0 installs
3. ▌
   Mass Tolerance Window Calibration · holobiomicslab

   Use when when implementing adduct detection in LC-MS metabolomics workflows, after defining theoretical adduct mass offsets (e.g., [M+NH4]+ at +17.0266 Da, [M+K]+ at +38.9815 Da), and before assigning adduct labels to a feature table.
   0 installs
4. ▌
   Mass Track Extraction And Binning · holobiomicslab

   Use when when you have centroid mzML files from LC-MS metabolomics acquisition and need to construct sample-level mass tracks before cross-sample alignment. Specifically: you are starting fresh with vendor-converted or pre-processed mzML input;
   0 installs
5. ▌
   Mass2motif Parameter Optimization · holobiomicslab

   Use when when you have a preprocessed bag-of-fragments corpus from tandem mass spectrometry spectra and need to train an MS2LDA model to discover Mass2Motifs.
   0 installs
6. ▌
   Mb Vip Feature Importance Ranking · holobiomicslab

   Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify which features drive model performance and warrant further statistical validation or biological interpretation.
   0 installs
7. ▌
   Metabcombiner Object Construction · holobiomicslab

   Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to identify overlapping <m/z, retention time> features across them.
   0 installs
8. ▌
   Metabolite Feature Anova Analysis · holobiomicslab

   Use when you have normalized abundance data from LC-MS/MS for multiple samples classified into three or more discrete groups (e.
   0 installs
9. ▌
   Metabolite Feature Column Mapping · holobiomicslab

   Use when you have peak-picked LC-MS metabolomics data in a tabular format (R data frame) with columns for mass-to-charge ratio, retention time, feature identifiers, adduct annotations, and sample measurements, but the column names do not follow a standard naming convention.
   0 installs
10. ▌
    Metabolite Mass Database Matching · holobiomicslab

    Use when after features have been grouped into empirical compounds (empCpds) with inferred molecular formulas and adduct assignments by khipu, and you need to assign putative metabolite identities at the formula level.
    0 installs
11. ▌
    Metabolite Ratio Batch Correction · holobiomicslab

    Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with measured ion areas for compounds and assigned internal standards.
    0 installs
12. ▌
    Metabolite Set Annotation Mapping · holobiomicslab

    Use when you have a metabolomics peak intensity matrix with feature IDs (m/z, retention time, or arbitrary peak identifiers) and need to assign these peaks to standardized metabolite databases or spectral groupings (KEGG compounds, ChEBI IDs, GNPS Molecular Families, or MS2LDA Mass2Motifs) before.
    2 installs
13. ▌
    Metabolomic Heatmap Visualization · holobiomicslab

    Use when after completing feature annotation and reaction assignment in an untargeted metabolomics workflow, specifically when you have a feature-by-sample intensity matrix aligned with metabolite identities and want to communicate cluster structure, reaction pathway groupings, and feature.
    0 installs
14. ▌
    Metabolomic Signal Quantification · holobiomicslab

    Use when you have raw untargeted LC/MS data in open mzML or mzXML format and need to extract a quantified feature matrix (m/z and retention time coordinates with sample intensities) without prior knowledge of optimal signal detection parameters, batch effects, or quality control samples.
    0 installs
15. ▌
    Metabolomics Data Format Handling · holobiomicslab

    Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into MetaboAnalystR 4.0 for unified LC-MS1 feature detection and MS/MS spectra processing.
    0 installs
16. ▌
    Metabolomics Data Quality Metrics · holobiomicslab

    Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high technical variability or signal degradation before proceeding to statistical analysis or interpretation of.
    0 installs
17. ▌
    Missing Peak Imputation Fillpeaks · holobiomicslab

    Use when apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection failures.
    0 installs
18. ▌
    Molecular Network Node Annotation · holobiomicslab

    Use when you have a GNPS-generated molecular network (classical or feature-based workflow) and corresponding MS2LDA LDA experiment results (Mass2Motif assignments and/or chemical class predictions), and you need to propagate those annotations to individual network nodes to support visual and.
    0 installs
19. ▌
    Molecular Networking Construction · holobiomicslab

    Use when you have LC-MS/MS DDA data from one or more samples and need to organize fragmentation spectra by similarity relationships to support compound annotation, enable cross-sample comparisons, and identify known and unknown metabolites sharing structural features.
    2 installs
20. ▌
    Molecular Representation Encoding · holobiomicslab

    Use when when you have a molecular target compound defined by SMILES, InChI, or chemical formula and need to feed it into a pretrained spectrum prediction model (ICEBERG or SCARF) to generate tandem mass spectra or conduct structural elucidation.
    2 installs
21. ▌
    Ms Dial Export File Specification · holobiomicslab

    Use when you have MS-DIAL 4 or MS-DIAL 5 alignment results and need to configure LipoCLEAN for quality filtering of lipid identifications. Use this skill at the start of a LipoCLEAN analysis when you need to specify which MS-DIAL export files to analyze and how to locate them.
    2 installs
22. ▌
    Ms Dial Peak Character Estimation · holobiomicslab

    Use when you have a filtered MS-DIAL peak list (post-generic filtering, containing m/z, retention time, and peak intensity metrics for each feature) and need to group features into clusters that represent true metabolite signals rather than instrumental or chemical artifacts.
    2 installs
23. ▌
    Ms Ms Spectral Data Preprocessing · holobiomicslab

    Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for MS/MS-to-structure inference.
    0 installs
24. ▌
    Ms1 Scan Extraction And Filtering · holobiomicslab

    Use when you have a Thermo Fisher Scientific .raw file from an Orbitrap instrument and need to programmatically retrieve MS1 spectral attributes (base-peak m/z, intensity, retention time) for downstream statistical analysis or quality control in R, rather than relying on external preprocessing.
    2 installs
25. ▌
    Ms2 Fingerprint Vector Generation · holobiomicslab

    Use when you have LC-MS/MS data in mzML, mzXML, or MGF format from one or more metabolomics samples and need to compare samples that may have poor overlap in detected features, strong retention time shifts between runs, or were acquired on different LC methods or MS technologies (e.
    2 installs
26. ▌
    Msconvert Parameter Configuration · holobiomicslab

    Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it for nontargeted analysis using MSThunder on a Linux system.
    0 installs
27. ▌
    Multi Instrument Data Integration · holobiomicslab

    Use when you have DIA mass spectrometry raw files from multiple instrument types (timsTOF, TripleTOF, Orbitrap) in their native formats (.raw, .d, .
    0 installs
28. ▌
    Mzml Format Export From Simulator · holobiomicslab

    Use when after running an Environment simulation in ViMMS that has generated MS1 and/or MS/MS scans from a virtual mass spectrometer and controller pair. Use this skill when you need to preserve the generated scans in a standard format compatible with existing metabolomics software (e.
    2 installs
29. ▌
    Mzml Mzxml File Format Processing · holobiomicslab

    Use when your raw LC-MS data are in vendor-specific binary formats (e.g., .raw, .d, .
    0 installs
30. ▌
    Neighbourhood Density Computation · holobiomicslab

    Use when after library-matching has produced ranked candidate spectra with MS2Deepscore embeddings.
    0 installs
31. ▌
    Network Graph Manipulation Python · holobiomicslab

    Use when you have a molecular network graph exported from GNPS (as GraphML, JSON, or adjacency format) and separate experimental data (bioassay activity matrix, feature quantification table, or MS/MS annotations) indexed by feature ID, retention time, or m/z.
    2 installs
32. ▌
    Network Node Attribute Assignment · holobiomicslab

    Use when you have constructed a NetworkX graph with LC-MS features as nodes and need to annotate each node with metadata derived from the MamsiStructSearch output (assay source, isotopologue group, adduct group, structural cluster ID, correlation cluster ID, and optional compound annotation).
    2 installs
33. ▌
    Neutral Loss Composition Matching · holobiomicslab

    Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries from a MotifDB reference database.
    0 installs
34. ▌
    Peak Detection And Mass Alignment · holobiomicslab

    Use when when you have raw LC-MS/MS data files (.mzML, .raw, or vendor formats) from multiple samples and need to identify reproducible molecular features across the cohort before annotation or statistical analysis.
    0 installs
35. ▌
    Peak Quality Label Stratification · holobiomicslab

    Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
    0 installs
36. ▌
    Peak Table Filtering Metabolomics · holobiomicslab

    Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples (SampleType='LQC') and you want to exclude noisy or unstable EICs before building a peak quality classifier.
    2 installs
37. ▌
    Peptide Spectrum Match Annotation · holobiomicslab

    Use when when you have a peptide sequence, observed MS2 spectrum peaks (m/z, intensity, charge state), and need to determine which theoretical fragment ions (B and Y ions) match the observed data—particularly in stable isotope probing (SIP) experiments where peptides carry heavy isotope labels (e.
    0 installs
38. ▌
    Peptidoform Scoring And Filtering · holobiomicslab

    Use when after a transformer-based de novo sequencing model (such as Casanovo) generates candidate peptide sequences from MS/MS spectra, before exporting results or using them in database matching or visualization workflows.
    0 installs
39. ▌
    Positive Mode Ionization Analysis · holobiomicslab

    Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
    0 installs
40. ▌
    Positive Negative Class Balancing · holobiomicslab

    Use when when training a formula rescoring model on MS/MS spectra where positive examples (correct molecular formulas) are unevenly distributed across molecular formula groups or vastly outnumbered by negative examples (incorrect candidates), resulting in class imbalance that degrades model.
    0 installs
41. ▌
    Ppm Tolerance Scoring And Ranking · holobiomicslab

    Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
    2 installs
42. ▌
    Precursor Ion Isolation Windowing · holobiomicslab

    Use when processing SWATH-MS (Sequential Windowed Acquisition of all Theoretical Mass-spectra) raw data files (mzML or vendor format) for untargeted metabolomics, specifically before attempting to deconvolute overlapping MS/MS spectra.
    0 installs
43. ▌
    Precursor List Formatting For Dda · holobiomicslab

    Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an Orbitrap instrument using Excalibur software.
    2 installs
44. ▌
    Probability Threshold Calibration · holobiomicslab

    Use when after training or loading a NeatMS neural network model, apply this skill when you have a labelled validation dataset and need to determine the optimal probability threshold that maximizes classification performance (true positives minus false positives).
    0 installs
45. ▌
    Proteomics Data Format Conversion · holobiomicslab

    Use when you have vendor raw files (e.g., .raw from Thermo, .d from Agilent, .wiff2 from Sciex) that need to be converted to a standard format for analysis pipelines, data sharing, or when you require the high compression rates and fast decoding provided by Aird format.
    0 installs
46. ▌
    Public Database Query Integration · holobiomicslab

    Use when you have an experimental MS/MS spectrum (m/z and intensity pairs with known precursor m/z) and need to identify the compound by searching against public repositories or a local reference library.
    2 installs
47. ▌
    Qc Sample Classification Labeling · holobiomicslab

    Use when when loading multiple LC-MS runs (mzML files) into an MsExperiment object and the injection sequence contains an interleaved or documented pattern of QC and sample runs (e.g., two QC, four sample, two QC, four sample, two QC).
    3 installs
48. ▌
    Quality Control Report Generation · holobiomicslab

    Use when after completing doAnalysis on an mzQuality SummarizedExperiment object with outlier detection, batch correction, and compound reliability filtering applied.
    0 installs
49. ▌
    Query Result Serialization To CSV · holobiomicslab

    Use when after executing a MassQL query against mzML mass spectrometry files and obtaining a tabulated result DataFrame in memory.
    2 installs
50. ▌
    R Script Validation And Execution · holobiomicslab

    Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
    0 installs
51. ▌
    R Statistical Model Serialization · holobiomicslab

    Use when after training a customized R statistical or machine learning model on annotated training data, you need to persist the trained model object for reuse in downstream analysis workflows without retraining.
    0 installs
52. ▌
    R6 Reference Semantics Comparison · holobiomicslab

    Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original data object in memory or preserve it.
    1 install
53. ▌
    Retention Time Prediction Scoring · holobiomicslab

    Use when you have a list of candidate metabolites for an unknown compound (from mass-to-structure search or library matching), experimental retention time(s) from one or more chromatographic methods, and access to a trained DNN RT predictor and meta-learned RT projection model.
    0 installs
54. ▌
    Rippp Structure Database Matching · holobiomicslab

    Use when you have: (1) tandem MS/MS spectra in MGF, mzXML, mzML, or mzData format from LC-MS/MS analysis; (2) a set of predicted RiPP precursor peptides derived from genomic biosynthetic gene cluster mining (via antiSMASH, BOA, or raw FASTA);
    0 installs
55. ▌
    Sample Relationship Visualization · holobiomicslab

    Use when after generating aligned MS2 fingerprints (sample-by-fingerprint matrices) from metabolomics data when you need to visually inspect sample clustering, identify sample similarities, or detect batch effects and RT shifts across different LC methods or mass spectrometer technologies.
    0 installs
56. ▌
    Search Results Loader Integration · holobiomicslab

    Use when you have search result files from one or more DIA-MS analysis tools and need to load them into a unified environment for Q-value filtering, cross-tool comparison (upset plots), and interactive visualization of identifications, quantifications, and coefficient of variation metrics across.
    0 installs
57. ▌
    Signal Noise Trade Off Evaluation · holobiomicslab

    Use when after generating consensus spectra with fragment recurrence frequencies, when you have replicate MS/MS spectra for features and need to choose a single frequency cutoff for denoising. Triggers include: (1) uncertainty about which frequency threshold to apply across all features;
    0 installs
58. ▌
    Signal To Noise Ratio Computation · holobiomicslab

    Use when after peak detection in nontargeted LC-MS workflows when you have a feature table with detected peaks and need to assign quality scores or filter low-confidence features.
    0 installs
59. ▌
    Spectral Candidate Classification · holobiomicslab

    Use when after performing spectral library matching of mass spectrometry peaks against a fragmentation library (e.
    0 installs
60. ▌
    Spectral Clustering Density Based · holobiomicslab

    Use when you have computed a sparse pairwise distance matrix from MS/MS spectra (via nearest neighbor indexing) and need to partition spectra into homogeneous clusters—typically when clustering bottom-up proteomics data with the goal of grouping spectra from the same peptide sequence or when you.
    2 installs
61. ▌
    Spectral Data Object Construction · holobiomicslab

    Use when you have a set of centroided .mzML LC-MS files from a targeted metabolomics or lipidomics experiment and need to represent them as a structured object that links raw spectra to sample-level metadata (e.
    0 installs
62. ▌
    Spectral Database Query Execution · holobiomicslab

    Use when when you have an unknown mass spectrum (query spectrum) and need to search it against a reference database of billions of spectra to find matching or structurally related compounds.
    2 installs
63. ▌
    Spectral Denoising Formula Method · holobiomicslab

    Use when you have a noisy MS/MS spectrum and need to identify and remove chemical noise ions (as opposed to electronic noise). You have the precursor compound's SMILES string or molecular formula and its adduct type.
    1 install
64. ▌
    Spectral Dimensionality Reduction · holobiomicslab

    Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
    2 installs
65. ▌
    Spectral Feature Table Generation · holobiomicslab

    Use when you have raw LC-MS data in mzXML format (or vendor formats convertible via MS-Convert) and need to identify and quantify metabolic features before multi-sample alignment. Use MS1 peak picking for full-scan or DDA data to extract Gaussian and non-Gaussian shaped peaks;
    0 installs
66. ▌
    Spectral Library Entry Generation · holobiomicslab

    Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for a known metabolite.
    0 installs
67. ▌
    Spectral Metadata Standardization · holobiomicslab

    Use when you have mass spectrometry spectra stored across multiple, disparate metabolomics repositories (GNPS, MassBank, MetaboLights, Metabolomics Workbench, ProteoXchange, MS2LDA) and need to retrieve them using a single identifier scheme, or you are publishing spectrum figures and need.
    2 installs
68. ▌
    Spectral Molecular Family Linking · holobiomicslab

    Use when when you have pre-processed genomic data (GCFs from AntiSMASH/BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to systematically score and rank putative relationships between biosynthetic gene clusters and their.
    2 installs
69. ▌
    Spectral Peak Annotation Proforma · holobiomicslab

    Use when you have an annotated or raw tandem mass spectrometry spectrum and need to identify which observed peaks correspond to expected peptide fragment ions from a known or predicted peptidoform. Use it before spectrum visualization if you want highlighted, labeled fragment matches;
    2 installs
70. ▌
    Spectrum Peak To Fragment Mapping · holobiomicslab

    Use when when you have a tandem mass spectrum (MS/MS) and a ProForma 2.0 peptidoform string (e.g., DLTDYLM[Oxidation]K) and need to identify which observed spectrum peaks correspond to expected b-ion and y-ion fragments, in order to validate peptide identification or annotate spectrum quality.
    1 install
71. ▌
    Spectrum Relevance Classification · holobiomicslab

    Use when you have a collection of MS/MS spectra from reference standards representing your compounds of interest (e.g., flavonoids, prenylated chalcones) and a set of MS/MS spectra from non-target or other compounds.
    0 installs
72. ▌
    Structural Annotation Integration · holobiomicslab

    Use when you have structural candidates from in silico tools (SIRIUS/CANOPUS) and library spectral matches from GNPS, but need to resolve conflicting or incomplete chemical classifications into a unified consensus.
    0 installs
73. ▌
    Taxonomic Weighting In Annotation · holobiomicslab

    Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) and MS/MS spectra, and you know the organism or taxon of origin for your samples.
    0 installs
74. ▌
    Thermo Raw Binary Data Extraction · holobiomicslab

    Use when you have acquired .raw files from a Thermo mass spectrometer (e.g., Q Exactive, Orbitrap) and need to expose their contents—scan numbers, retention times, m/z values, intensities, and precursor information—for downstream nontargeted LCMS feature detection and alignment.
    0 installs
75. ▌
    Topn Acquisition Parameter Tuning · holobiomicslab

    Use when when you have real LC-MS/MS data (mzML format) from an untargeted metabolomics experiment and want to test how variations in TopN DDA parameters affect which precursor ions are selected and fragmented, before deploying the optimized strategy on physical instruments.
    2 installs
76. ▌
    Transformation Product Prediction · holobiomicslab

    Use when after parent chemical suspects have been identified in a non-target screening workflow, use this skill when you need to screen for downstream products formed by chemical or biological transformation.
    0 installs
77. ▌
    Usi String Parsing And Resolution · holobiomicslab

    Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire dataset file.
    0 installs
78. ▌
    Workflow Output Validation And QA · holobiomicslab

    Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.
    0 installs
79. ▌
    Xcms Ramclustr Object Integration · holobiomicslab

    Use when you have centroid-mode LC–MS all-ion fragmentation (AIF) data already processed through xcms for feature detection and retention-time correction, and a corresponding RamClustR object that groups co-eluting fragment ions into putative spectral clusters.
    0 installs
80. ▌
    Compound Peak Association Inference · holobiomicslab

    Use when after peak picking on INADEQUATE NMR spectra when you have a set of peak coordinates and intensities and need to determine which peaks belong to the same molecular compound.
    0 installs
81. ▌
    Deep Learning Metabolite Annotation · holobiomicslab

    Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible format) from a water sample, a precursor m/z and retention time of interest, and want to annotate an unknown compound by predicting its molecular formula, structure, and name using deep learning scoring rather than.
    0 installs
82. ▌
    Dom Chemodiversity Characterization · holobiomicslab

    Use when you have a formula-assigned FT-ICR MS dataset (molecular formulas already assigned to individual mass features) and seek to understand the chemodiversity landscape and transformation relationships within DOM.
    0 installs
83. ▌
    Feature Table Consensus Aggregation · holobiomicslab

    Use when you have detected feature tables from multiple LC-IMS-MS/MS samples and need to establish a unified feature catalog in which each row represents a distinct molecular entity observed across one or more samples, with harmonized m/z, drift time, and retention time coordinates.
    1 install
84. ▌
    Hmdb Metabolite Query And Retrieval · holobiomicslab

    Use when you have identified one or more proton NMR spectral regions-of-interest (ROIs)—defined by lower and upper chemical-shift bounds in ppm—from complex biological samples (serum, saliva, urine, tissue, CSF) and need to generate a ranked list of plausible metabolite identities.
    0 installs
85. ▌
    Interactive Data Exploration Design · holobiomicslab

    Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs. serum, cohort identifiers) and need to interactively explore how variation in processing conditions drives changes in metabolic.
    2 installs
86. ▌
    Mass Spectrum Structure Elucidation · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision-induced dissociation, CID) and a known chemical formula (or narrow set of candidate formulas), and you need to identify the most likely structure(s) by ranking against a large candidate library such as PubChem.
    2 installs
87. ▌
    Metabolite Metadata Column Matching · holobiomicslab

    Use when validating mwTab files deposited to the Metabolomics Workbench and you need to verify that metadata columns match standard naming conventions and contain values in the expected format.
    0 installs
88. ▌
    Metabolite Peak Assignment From Nmr · holobiomicslab

    Use when you have a 1D ¹H NMR spectrum (as chemical shift vs. intensity) and a corresponding peak list (chemical shift values), and you need to identify which metabolites are responsible for each detected peak.
    0 installs
89. ▌
    Nightingale 1h Nmr Data Integration · holobiomicslab

    Use when you have newly assayed 1H-NMR metabolomics data from Nightingale Health (CSV or TSV format) and need to apply one or more published metabolic risk scores (Deelen et al. all-cause mortality, van den Akker MetaboAge, Würtz cardiovascular event risk, etc.).
    0 installs
90. ▌
    Nmr Spectrum To Structure Inference · holobiomicslab

    Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph without manual peak interpretation or exhaustive combinatorial search.
    0 installs
91. ▌
    Pre Analytical Delay Stratification · holobiomicslab

    Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect metabolic parameter stability within a plasma or serum sample cohort.
    0 installs
92. ▌
    Spectral Correlation Interpretation · holobiomicslab

    Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a prominent but structurally ambiguous peak.
    0 installs
93. ▌
    Spectral Peak Detection And Picking · holobiomicslab

    Use when you have raw INADEQUATE NMR spectra files and need to transition from continuous spectral data to discrete peak coordinates. Use it as the first signal-processing step before clustering peaks into networks or matching against metabolite databases.
    0 installs
94. ▌
    Transformer Based Fragment Assembly · holobiomicslab

    Use when when you have CNN-encoded spectral features (¹H and/or ¹³C NMR) and a set of predicted or candidate molecular fragments, and you need to determine which fragments are present and how they connect to form a valid molecular structure.
    0 installs
95. ▌
    Weighted Loss Function Optimization · holobiomicslab

    Use when when training a dual-encoder architecture (bi-encoder + cross-encoder) on NMR spectral data where independent encoding and joint pair processing produce competing or imbalanced gradient signals.
    0 installs
96. ▌
    Chip Seq Signal Pileup Extension · holobiomicslab

    Use when after duplicate filtering and fragment length prediction (d) in ChIP-Seq analysis, when you need to convert discrete read alignments into continuous coverage signal for comparison against control background.
    0 installs
97. ▌
    Cooler File Loading And Querying · holobiomicslab

    Use when your Hi-C data is stored in cooler format (a binary HDF5-based sparse matrix with associated genomic bins and genomic tracks); you need to programmatically access the contact matrix, bin coordinates, or track data (e.g., eigenvectors, GC content) for further analysis;
    0 installs
98. ▌
    Epigenetic Sample Stratification · holobiomicslab

    Use when after merging methylation call files into a unified methylBase object (covering all samples at common base positions), apply this skill to assess whether biological replicates cluster together, whether case/control or treatment groups separate as expected, and to identify potential sample.
    0 installs
99. ▌
    Genomic Loop Call Interpretation · holobiomicslab

    Use when you have a pre-generated .hic contact map file and need to identify and annotate chromatin loops or topologically associating domains (TADs) at high resolution.
    0 installs
100. ▌
     Local Background Bias Estimation · holobiomicslab

     Use when you have paired ChIP and control BED/BEDPE files and need to account for local sequencing bias before peak calling. Use it specifically when control signal varies across genomic regions at multiple spatial scales (e.
     0 installs