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HolobiomicsLab

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1. ▌
   Nmr Spectrum Data Import And Parsing · holobiomicslab

   Use when you have raw 1D ¹H NMR spectroscopy output consisting of (1) a CSV file with chemical shift and intensity columns and (2) a TXT file listing detected peak chemical shifts, and you need to load and validate these into memory before passing them to a metabolite identification model like.
   0 installs
2. ▌
   Unannotated Feature Characterization · holobiomicslab

   Use when you have aligned feature tables from LC–MS/MS, corresponding in silico annotations (from GNPS/ISDB or SIRIUS), and metadata describing sample origin. Use it to rank extracts by the proportion of sample-specific, unannotated features—a proxy for structural novelty.
   0 installs
3. ▌
   Xcms Feature Extraction And Grouping · holobiomicslab

   Use when you have raw mzXML LC/MS files from replicated metabolomics experiments (e.g., 12 samples across labeled/unlabeled conditions) and need to extract, align, and group peaks before downstream feature filtering (e.g., fold-change or isotope enrichment analysis).
   0 installs
4. ▌
   Bedgraph File Format Manipulation · holobiomicslab

   Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for downstream statistical comparison or peak detection.
   2 installs
5. ▌
   Bisulfite Sequencing Data Loading · holobiomicslab

   Use when you have raw methylation call files from Bismark, MethylDackel, or similar bisulfite alignment tools (bedGraph, cytosine report, or tabix-indexed formats) and need to import them into R as methylRaw or methylRawListDB objects for downstream differential methylation analysis, quality.
   0 installs
6. ▌
   Chip Seq Read Alignment Filtering · holobiomicslab

   Use when when beginning peak calling on ChIP-Seq data: you have raw single-end or paired-end BED/BEDPE alignment files for both ChIP and control samples and need to remove duplicate reads before predicting fragment length and building local bias models.
   2 installs
7. ▌
   Cpg Island Feature Classification · holobiomicslab

   Use when you have a methylDiff object containing differentially methylated bases or regions from bisulfite sequencing, gene annotation in BED or similar format (RefSeq, Ensembl), and CpG island coordinate files, and need to understand what fraction of your differential methylation signal falls.
   0 installs
8. ▌
   Dna Methylation Array Data Import · holobiomicslab

   Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and downstream analysis.
   0 installs
9. ▌
   Hi C Insulation Score Calculation · holobiomicslab

   Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome. Use this skill when your research question requires quantifying local chromatin compartmentalization or annotating structural domain edges for downstream analysis (e.
   0 installs
10. ▌
    Methylation Region Identification · holobiomicslab

    Use when you have loaded normalized methylation beta-value matrices from Illumina EPIC or 450k arrays and need to move beyond single-CpG differential methylation testing to identify multi-CpG regions with coordinated differential methylation signals.
    0 installs
11. ▌
    Motif Database Query And Matching · holobiomicslab

    Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.
    2 installs
12. ▌
    Narrow Peak Coordinate Validation · holobiomicslab

    Use when after running macs3 callpeak with the -f BEDPE flag on paired-end ChIP-Seq data (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.
    2 installs
13. ▌
    Stream Trajectory Data Formatting · holobiomicslab

    Use when you have completed peak calling and cell annotation in ArchR and want to perform trajectory inference or visualization in STREAM. Apply it specifically when your analysis goal requires STREAM's specialized trajectory reconstruction methods (e.
    0 installs
14. ▌
    Z Score Based Statistical Testing · holobiomicslab

    Use when you have a sparse chromatin accessibility matrix (ATAC-seq or DNAse-seq counts per peak per sample), matched peak-annotation assignments (e.
    0 installs
15. ▌
    API Response Latency Measurement · holobiomicslab

    Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.
    0 installs
16. ▌
    Backend Performance Benchmarking · holobiomicslab

    Use when when you have execution time data for visualization scripts across multiple backends (matplotlib, Bokeh, Plotly) and need to determine which backend offers the fastest median performance for specific mass spectrometry plot types (chromatogram, mobilogram, peakmap, peakmap-marginals.
    0 installs
17. ▌
    Bit Vector Substructure Encoding · holobiomicslab

    Use when you need to represent natural product molecules as fixed-length bit vectors for downstream machine learning (e.
    2 installs
18. ▌
    Calibration Residual Calculation · holobiomicslab

    Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a given PPM tolerance window.
    2 installs
19. ▌
    Chemical Structure Deduplication · holobiomicslab

    Use when after applying biotransformation rules to generate candidate product structures from input molecules, when the same transformed structure can be produced via multiple transformation pathways or rule applications, and you need a single canonical representation while tracking which rules and.
    2 installs
20. ▌
    Chemical Structure Featurization · holobiomicslab

    Use when you have SMILES strings or molecular structure files (e.g., from a synthetic drug database) and need to feed them into a deep learning model like PS2MS, NEIMS, or DeepEI that expects numerical feature vectors.
    0 installs
21. ▌
    Cheminformatics Library Querying · holobiomicslab

    Use when you have a list of query chemicals (compound names or SMILES) and a reference library organized by chemical groups (e.g., Types A–E, GroupA/GroupB), and you need to assess which library compounds are structurally similar to your queries, retrieve their categorical annotations (e.
    0 installs
22. ▌
    Data Format Conformance Checking · holobiomicslab

    Use when you have retrieved a complete set of project JSON documents from a data platform and need to verify that each document's structure, field types, and required properties match a canonical JSON Schema definition (e.g., app/public/schema.json).
    0 installs
23. ▌
    Database Accessor Initialization · holobiomicslab

    Use when a Python module declares optional/conditional dependencies (e.g., sqlalchemy for database access) and you need to confirm that the module can be imported and instantiated without exceptions when those dependencies are present in the environment.
    0 installs
24. ▌
    Descriptor Subgroup Partitioning · holobiomicslab

    Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which descriptor categories (e.g., molecular weight, lipophilicity, topological, pharmacophoric) drive prediction decisions.
    0 installs
25. ▌
    Docker Image Registry Inspection · holobiomicslab

    Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's size falls within documented ranges (e.g., cli 6–7 GB, dev 9–11 GB, linux 8–10 GB, windows 4–5 GB).
    0 installs
26. ▌
    Field Mapping And Transformation · holobiomicslab

    Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.
    0 installs
27. ▌
    Ion Image Embedding Optimization · holobiomicslab

    Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions (representation collapse) during contrastive learning—specifically when optimizing for maximized similarity between augmentations.
    0 installs
28. ▌
    Lipid Species Abundance Counting · holobiomicslab

    Use when you have access to a lipidomics library repository (e.g., LipidMatch .csv files) and need to audit or report the total number of distinct lipid species and lipid-type categories present.
    0 installs
29. ▌
    Mass Action Kinetics Formulation · holobiomicslab

    Use when you have intracellular metabolomics concentration measurements across multiple cell lines or conditions, a stoichiometric metabolic network model with reaction-metabolite associations, and you need to predict how differences in substrate availability (independent of enzyme expression).
    2 installs
30. ▌
    Missing Data Simulation In Omics · holobiomicslab

    Use when when comparing the robustness of multiple pathway ranking methods (e.g., PLAGE, ORA, GSEA) on metabolomics or other omics data, and you need to establish which method is least sensitive to peak dropout, instrumental noise, or annotation uncertainty.
    0 installs
31. ▌
    Missing Value Imputation With Na · holobiomicslab

    Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which ones are explicitly stored in your backend.
    0 installs
32. ▌
    Molecular Descriptor Calculation · holobiomicslab

    Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
    2 installs
33. ▌
    Msi Data Format Interoperability · holobiomicslab

    Use when your MSI data is stored in a Cardinal imaging experiment object (version 2.2+) that has already been peak-binned with peakBin(), and you want to run mass2adduct's massdiff() and adductMatch() pipeline without manually exporting to CSV;
    0 installs
34. ▌
    Neural Network Weight Extraction · holobiomicslab

    Use when you have trained MLPNN models on paired microbiome-metabolome data (via 10-fold cross-validation repeated across multiple iterations) and need to derive interpretable microbe-metabolite interaction scores rather than treating the network as a black box.
    0 installs
35. ▌
    Orchestrator Architecture Design · holobiomicslab

    Use when when building a multi-backend visualization library where users specify both a plot type (spectrum, chromatogram, peakmap) and a backend (matplotlib for static output, Bokeh or Plotly for interactive), and you need to avoid code duplication across backends while keeping the user-facing API.
    2 installs
36. ▌
    Peak Quality Threshold Filtering · holobiomicslab

    Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
    0 installs
37. ▌
    Python Environment Configuration · holobiomicslab

    Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
    0 installs
38. ▌
    Qc Sample Variability Assessment · holobiomicslab

    Use when after batch correction of a metabolomics dataset using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to systematically evaluate which one produces the most stable compound quantification (lowest QC variability) for each compound.
    0 installs
39. ▌
    Qc Workflow Component Inspection · holobiomicslab

    Use when you have acquired a versioned QC workflow definition file (YAML or JSON) from a metabolomics QC system release (e.g., v1.0.
    3 installs
40. ▌
    R Parallel Backend Configuration · holobiomicslab

    Use when you have multiple MSP (mass spectrum) library files to read and merge in R, and your computational task is time-consuming (e.g., structure extraction, SMILES assignment, or RI assignment) and you have a multi-core system available.
    0 installs
41. ▌
    Raw Data Throughput Benchmarking · holobiomicslab

    Use when when you have a raw mass spectrometry file (e.g., Thermo Orbitrap .raw) and need to establish the measured throughput of a spectral reading function (e.
    0 installs
42. ▌
    S4 Class Object Memory Profiling · holobiomicslab

    Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures or defer initialization until data access.
    1 install
43. ▌
    Software Testing Unit Validation · holobiomicslab

    Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request. The skill is essential before pushing feature branches to the repository or merging changes into master.
    0 installs
44. ▌
    Spectra Variable Core Population · holobiomicslab

    Use when when implementing a custom MsBackend and the spectraData() method needs to return all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of which variables were explicitly stored during backend initialization.
    2 installs
45. ▌
    Spectral Data Quality Assessment · holobiomicslab

    Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type, precursor m/z, retention time), low-intensity noise peaks, or spectra with invalid or inconsistent metadata fields.
    0 installs
46. ▌
    Structured Data Element Checking · holobiomicslab

    Use when you have generated or received a mass spectrometry data file in a structured format (e.g., mzPeak, Parquet-based archive) and need to verify it conforms to the published specification before use in analysis pipelines, sharing with collaborators, or publishing.
    0 installs
47. ▌
    Structured Inventory Compilation · holobiomicslab

    Use when when you need to understand the modular composition of a multi-component research software project, particularly before onboarding, refactoring, or deploying it.
    0 installs
48. ▌
    Syntax Tree Construction Parsing · holobiomicslab

    Use when you have a domain-specific language (DSL) grammar specification and raw query strings that must be converted into structured intermediate representations for validation, transformation, or execution.
    0 installs
49. ▌
    Aggregate Statistics Computation · holobiomicslab

    Use when you have a validated or curated dataset (e.g., a TSV or gzip-compressed tabular file) and need to produce summary counts: unique curated structures (separately for 3D and 2D representations), unique organisms, and unique structure-organism pair combinations.
    0 installs
50. ▌
    Ancova Peak Association Analysis · holobiomicslab

    Use when when you have preprocessed metabolomics peak tables (feature matrix with samples × peaks) and sample metadata (phenotype/grouping information and optional continuous covariates), and your research question is to identify which peaks differ significantly between groups while accounting for.
    2 installs
51. ▌
    Bgc Feature Vector Normalization · holobiomicslab

    Use when when you have pre-computed BGC feature vectors (from domain architecture extraction) and need to cluster them into GCFs using BiG-SLiCE v2.
    0 installs
52. ▌
    Binary Representation Generation · holobiomicslab

    Use when you have raw mass spectra data (MGF format with m/z/intensity pairs) that need to be clustered rapidly, especially on large-scale proteomics datasets (millions of spectra).
    0 installs
53. ▌
    Biomarker Coefficient Extraction · holobiomicslab

    Use when after normalizing a log-transformed metabolomics featuredata matrix (with missing values imputed via knn or replacement) and encoding experimental factors into a design matrix (factormat), use this skill to fit a linear model and extract per-metabolite coefficients and p-values for each.
    0 installs
54. ▌
    Bruker Mass Spectrum Data Import · holobiomicslab

    Use when you have received a Bruker Solarix FT-ICR raw data directory (.d format, containing CompassXtract output or native ser/fid transients) and need to import it into a Python-based analysis workflow for FT-MS signal processing, calibration, or molecular formula search.
    2 installs
55. ▌
    Building Block Annotation Export · holobiomicslab

    Use when you have retrieved a user database entry (sequence or building-block structure record) from the MassSpecBlocks backend and need to generate a file in CycloBranch format for mass spectra analysis, interpretation, or sharing with collaborators using the CycloBranch software.
    2 installs
56. ▌
    Chemical Class Novelty Detection · holobiomicslab

    Use when when you have CANOPUS chemical class predictions for your samples and need to identify which extracts contain chemical classes absent from the literature for their species or genus.
    2 installs
57. ▌
    Chemical Structure Serialization · holobiomicslab

    Use when you need to export a stored chemical structure (sequence or building-block entry) from the MassSpecBlocks database to enable mass spectra analysis in CycloBranch or when preparing structures for import into other cheminformatics workflows that require a standardized structure interchange.
    0 installs
58. ▌
    Cheminformatics Table Generation · holobiomicslab

    Use when when you have standardized molecular structures (SMILES or SDF format) and need to compute molecular fingerprint bits and chemical property descriptors for downstream retention time prediction, molecular classification, or machine-learning-based identification tasks.
    0 installs
59. ▌
    Chromatographic Data Structuring · holobiomicslab

    Use when after parsing a centroid mzML file into (m/z, scan_number, intensity) tuples, when you need to organize sparse MS1 data for efficient peak detection and cross-sample alignment. Apply this skill when high mass resolution (e.
    0 installs
60. ▌
    Color Jitter Application Imaging · holobiomicslab

    Use when preparing ion image data for representation learning in mass spectrometry imaging, specifically when you need to augment raw ion images to generate pairs of diverse views for contrastive loss training.
    0 installs
61. ▌
    Community Constraint Propagation · holobiomicslab

    Use when you have consensus metabolic reconstructions for multiple community members (e.g., from a plant microbiome or synthetic consortium) and need to gap-fill incomplete models while preserving community-level feasibility.
    0 installs
62. ▌
    Converter Architecture Traversal · holobiomicslab

    Use when when you need to understand which chemical identifier conversions are available in MSMetaEnhancer (e.
    0 installs
63. ▌
    Cpu Gpu Performance Benchmarking · holobiomicslab

    Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate whether GPU acceleration is justified.
    2 installs
64. ▌
    Cyp Isoform Substrate Prediction · holobiomicslab

    Use when you have a set of molecular structures (in .sdf or .csv SMILES format) and need to predict which CYP isoforms will metabolize them.
    0 installs
65. ▌
    Cyp450 Enzyme List Specification · holobiomicslab

    Use when when you need to predict drug or xenobiotic metabolites across multiple CYP450 isoforms and must communicate which specific enzymes (e.g., 1A2, 2C9, 3A4) should be evaluated. Use this skill before invoking a metabolite prediction tool that accepts an enzyme list parameter.
    0 installs
66. ▌
    Cypreact Input Format Compliance · holobiomicslab

    Use when you have a collection of molecular structures intended for CypReact-based CYP isoform metabolism prediction and need to verify the input file conforms to CypReact's expected format (comma-separated SMILES in .csv or SDF molecular structure files) before submission to the tool.
    1 install
67. ▌
    Database Integration And Linkage · holobiomicslab

    Use when you have a list of metabolite identifiers sourced from one metabolome database (e.g., HMDB IDs, PubChem CIDs) and need to map them to equivalent identifiers in other databases for data integration, cross-referencing, or standardization in downstream metabolomics analysis.
    0 installs
68. ▌
    Dependency Version Specification · holobiomicslab

    Use when you encounter a scientific implementation (particularly deep learning or complex data processing pipelines) where the original authors have documented specific software versions, and you need to reproduce the exact computational environment.
    0 installs
69. ▌
    Docker Container Volume Mounting · holobiomicslab

    Use when when you have vendor raw mass spectrometry files on the host machine that need to be processed by a containerized tool (e.g., AirdPro), and the container must read input from and write output to specific host paths. Typical trigger: you have a .
    0 installs
70. ▌
    Dockerfile Dependency Management · holobiomicslab

    Use when when deploying a Shiny application with mixed R and Python dependencies (e.g., pmartR backend with Kaleido for plot export) to production or CI/CD pipelines, and when some dependencies are under active development alongside the application.
    0 installs
71. ▌
    Domain Specific Language Parsing · holobiomicslab

    Use when when you have SQL-inspired query strings that encode domain-specific assumptions and need to validate, transform, or execute them against data repositories. Specifically: input is human-readable DSL text containing mass spectrometry-specific clauses (e.
    0 installs
72. ▌
    Elemental Composition Extraction · holobiomicslab

    Use when you have formula-assigned FT-ICR MS data (CSV or tab-delimited table with molecular formulas and mass values) and need to quantify elemental stoichiometry, compute diversity indices, or assess molecular complexity across environmental organic mixtures.
    0 installs
73. ▌
    Expression Matrix Transformation · holobiomicslab

    Use when you have loaded raw expression data (linear-scale peptide or protein abundance quantification) into pmartR and need to prepare it for statistical analysis.
    0 installs
74. ▌
    Fdr Aware Psm Retention Strategy · holobiomicslab

    Use when rescoring PSMs with machine learning or statistical models where: (1) you want to consider multiple candidate PSMs per spectrum (e.
    0 installs
75. ▌
    Feature Vector Naming Convention · holobiomicslab

    Use when when applying sequential transformations to a metabolomics feature intensity table (samples × compounds) and you need to maintain a traceable record of original feature identities through each processing stage.
    2 installs
76. ▌
    Fixed Effect Regression Analysis · holobiomicslab

    Use when you have a long-format metabolomics dataset with one row per observation and need to estimate the independent association between one or more fixed effects (e.g., exposure dose, treatment group, demographic variable) and each dependent variable (e.
    0 installs
77. ▌
    Gene Network Seed Initialization · holobiomicslab

    Use when when you have metabolomic enrichment scores for genes (e.g., from MSEA analysis comparing a patient to controls) and need to prepare them as seed labels for label propagation over a gene/protein interaction network.
    0 installs
78. ▌
    Gene Tokenization Representation · holobiomicslab

    Use when when you have GenBank-format BGC sequences with Pfam domain annotations and need to prepare them for sub-cluster detection, redundancy filtering, or natural product structure association.
    0 installs
79. ▌
    Genomic Bgc Extraction Antismash · holobiomicslab

    Use when when you have genomic DNA sequences (from isolates or metagenomes) and need to identify and characterize biosynthetic gene clusters as input for downstream natural product linkage analysis.
    0 installs
80. ▌
    Graph Neural Network Fine Tuning · holobiomicslab

    Use when when you have a pre-trained GNN checkpoint and a smaller, task-specific dataset (e.g., Eawag_XBridgeC18_364.
    1 install
81. ▌
    HTML Bundle Rendering In Browser · holobiomicslab

    Use when you have a dashboard_data.json file (JSON export from the msFeaST pipeline) and need to interactively explore quantification tables, metadata, and spectral data on a desktop machine (macOS, Linux, or Windows).
    1 install
82. ▌
    Hyperdimensional Vector Encoding · holobiomicslab

    Use when you have preprocessed mass spectra (mz/intensity pairs in MGF format) and need to convert them into a compact, fixed-dimensional representation suitable for fast similarity computation and clustering.
    2 installs
83. ▌
    Image Threshold Method Selection · holobiomicslab

    Use when you have loaded a laser ablation ICP-MS image into pewpew and need to separate tissue pixels from background regions to enable region-based analysis or quantification.
    0 installs
84. ▌
    Interactive Plot Rendering Bokeh · holobiomicslab

    Use when when you have mass spectrometry data in a Pandas DataFrame with columns for m/z, retention time (or ion mobility), and intensity, and you want to generate interactive (rather than static) visualizations for exploratory analysis, interactive drill-down, or deployment in web applications or.
    0 installs
85. ▌
    Ion Mobility Feature Engineering · holobiomicslab

    Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction. Specifically, use it when you are preparing data to fit or apply a machine learning model (e.g., Sklearn v1.0.
    0 installs
86. ▌
    Jacobian Matrix Graph Conversion · holobiomicslab

    Use when after computing a Jacobian matrix from covariance data in MInfer, when you need to visualize and interpret the structure of metabolite-to-metabolite interactions as a network.
    0 installs
87. ▌
    Lipid Class Abundance Comparison · holobiomicslab

    Use when you have a LipidomicsExperiment object with logged and normalized Area measurements, sample-level phenotype annotations (e.g., SampleType: Cancer, Benign, Metastasis), and you want to identify which lipid classes show consistent directional change across all samples within a group.
    2 installs
88. ▌
    Loess Smoothing Parameter Tuning · holobiomicslab

    Use when your metabolomics SummarizedExperiment object shows signal drift across replicate measurements within individual batches (visible as systematic trends in PCA plots or replicate scatter), and you have intra-batch replicate samples available to estimate smooth drift corrections.
    0 installs
89. ▌
    M Z Intensity Feature Extraction · holobiomicslab

    Use when you have imported mass spectrometry data in .raw, .d, or mzXML format and need to inspect peak structure, verify instrument performance, or generate baseline visualizations before downstream peak annotation or statistical analysis.
    0 installs
90. ▌
    M Z Window Tolerance Application · holobiomicslab

    Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of specific isotopes, chemical species, or mass fragments.
    0 installs
91. ▌
    Marker Ion Ranking And Filtering · holobiomicslab

    Use when you have extracted latent low-dimensional peak features from imaging mass spectrometry (IMS) data using a graph-attention autoencoder and need to identify a ranked subset of marker ions that represent spatial metabolomic patterns.
    0 installs
92. ▌
    Mass Error Distribution Analysis · holobiomicslab

    Use when after applying polynomial m/z recalibration using a reference peak list (e.g., SRFA.ref) to an FT-ICR mass spectrum.
    0 installs
93. ▌
    Mass Error Threshold Calibration · holobiomicslab

    Use when you have isolated TIC peak regions and need to extract ion chromatograms (EICs) for XCMS parameter estimation via the EICparams function. Use it specifically when your mass analyzer's measurement accuracy is known (e.
    0 installs
94. ▌
    Mass Spectrometry Format Parsing · holobiomicslab

    Use when you have mzML or mzXML mass spectrometry data files and need to extract and validate spectral records (m/z and intensity arrays) for lossless compression, lossy transformation, or format conversion.
    0 installs
95. ▌
    Mass Spectrometry Quantification · holobiomicslab

    Use when you have measured MS intensity data from unknown samples and known-concentration standard compounds, and you need to convert sample intensities into predicted concentrations. Specifically applicable when intensity drift is observed across the measurement sequence (e.
    0 installs
96. ▌
    Metabolic Network Reconstruction · holobiomicslab

    Use when you have matched multiomics data (genomics, epigenomics, transcriptomics, proteomics, metabolomics) across a cohort of cell lines or samples and want to infer which molecular features (genes, transcripts, proteins, methylation sites) regulate metabolite abundance.
    0 installs
97. ▌
    Metabolite Annotation Validation · holobiomicslab

    Use when after running in silico annotation tools (SIRIUS, ISDB) or spectral library matching on your feature table, when you need to retain only annotations meeting a minimum confidence threshold.
    0 installs
98. ▌
    Metabolite Binary Classification · holobiomicslab

    Use when you have a preprocessed metabolomics dataset with a binary outcome variable (e.
    0 installs
99. ▌
    Metabolite Output Interpretation · holobiomicslab

    Use when after running CyProduct with a query molecule (SMILES or SDF) and a list of CYP450 enzymes, use this skill to collect, organize, and validate the predicted metabolite results stored in the output folder.
    2 installs
100. ▌
     Missing Value Imputation For Pca · holobiomicslab

     Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple standard deviation thresholds (e.g., 3 SD, 4 SD, 5 SD) on principal component scores.
     0 installs