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HolobiomicsLab

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1. ▌
   Chromatogram Visualization Generation · holobiomicslab

   Use when after importing mass spectrometry data in .raw, .d, or mzXML format into R and before peak analysis or quality control steps.
   0 installs
2. ▌
   Class Conditional Calibration Mapping · holobiomicslab

   Use when you have TWIM-MS experimental data (arrival times and ion mobility parameters) paired with pre-assigned biomolecular class labels for an ion population, and you need to obtain class-conditioned CCS values without first performing feature-level identification.
   2 installs
3. ▌
   Classification Performance Evaluation · holobiomicslab

   Use when after running inference on test mass spectrometry spectra with a trained deep learning model (e.g., PS2MS) to verify that class label predictions and confidence scores match expected reference outputs.
   0 installs
4. ▌
   Compound Identifier Cross Referencing · holobiomicslab

   Use when when you have prepared raw mass spectrometry transition data (precursor m/z, product m/z, intensity, retention time, compound identifiers) and need to verify it conforms to EISA-EXPOSOME's required schema before database import. Specifically: you are building or validating a custom .xlsx/.
   0 installs
5. ▌
   Cross Database Nomenclature Alignment · holobiomicslab

   Use when when you have lipid abbreviations or names from different databases (HMDB, LIPID MAPS, LipidHome, RefMet, SwissLipids) or lipidomics software (LipidSearch, MS-DIAL, LipidBlast, etc.) that must be cross-referenced, compared, or integrated into a single annotation scheme.
   0 installs
6. ▌
   Cross Language Workflow Orchestration · holobiomicslab

   Use when you have multi-language code implementations (R and MATLAB scripts) for a single scientific workflow, documented example scripts for a reference sub-sample scenario, and need to verify that outputs from one language can serve as inputs to the next, or that both implementations produce.
   0 installs
7. ▌
   Dashboard Data Loading And Validation · holobiomicslab

   Use when after generating a dashboard_data.json file from the msFeaST Jupyter pipeline, use this skill to verify that the JSON file is correctly formatted and completely loaded into the interactive dashboard before conducting visual exploration or sharing the dashboard with collaborators.
   0 installs
8. ▌
   Differential Peak Abundance Detection · holobiomicslab

   Use when after raw mass spectrometry data has been converted to a peak feature table (CSV or tabular format) containing mass-to-charge ratios, retention times, and intensity values across samples, and you need to reduce noise and identify which peaks show meaningful differential patterns between.
   0 installs
9. ▌
   Domain Specific Masst API Integration · holobiomicslab

   Use when your research involves searching MS/MS spectra against multiple curated taxonomic or domain-specific databases (microbial, plant, tissue, microbiome, or food origin) and you need to aggregate, compare, and visualize matching results across all domains in a single interface.
   0 installs
10. ▌
    Expression Level Filtering With Edger · holobiomicslab

    Use when when you have a raw count matrix derived from Salmon or similar quantification tools and need to remove lowly-expressed features before normalization and batch correction.
    0 installs
11. ▌
    Expression Matrix Loading And Parsing · holobiomicslab

    Use when you have raw omics expression data in CSV format (rows=genes/features, columns=samples) and a separate group annotation file (sample IDs mapped to experimental groups or phenotypes), and you need to prepare them for heatmap or other omics visualizations in an R Shiny environment.
    0 installs
12. ▌
    Feature Attribution Score Calculation · holobiomicslab

    Use when after training a multi-layer perceptron neural network to predict metabolomic features from microbiome features using cross-validated evaluation, extract attribution scores to interpret which microbe-metabolite pairs have learned predictive relationships.
    2 installs
13. ▌
    Feature Filtering And Quality Control · holobiomicslab

    Use when after batch correction and concentration normalization have been applied to a merged m/z peak table and metadata file, but before statistical testing or machine learning.
    0 installs
14. ▌
    Fingerprint Feature Format Conversion · holobiomicslab

    Use when you have a pretrained deep learning model (e.
    0 installs
15. ▌
    Flux Variability Analysis For Scaling · holobiomicslab

    Use when you have a constraint-based metabolic model and need to establish per-reaction flux scaling factors derived from gene expression or other activity scores. Use FVA before integrating transcriptomics-derived constraints (e.
    0 installs
16. ▌
    Functional Level Metabolic Annotation · holobiomicslab

    Use when you have reconstructed the structural topology of two metabolic networks from KEGG and need to assign functional meaning (pathway annotations, metabolic functions) to each node or reaction so that you can compare the two organisms at the functional level rather than only at the topological.
    2 installs
17. ▌
    Galaxy Tool Registration Verification · holobiomicslab

    Use when after deploying Galaxy-M tool files and XML wrappers into a Galaxy installation's tool directories and restarting the Galaxy service, use this skill to confirm all metabolomics tools appear in the Galaxy admin interface and are ready for end-user access.
    0 installs
18. ▌
    Genbank Format Parsing And Processing · holobiomicslab

    Use when you have BGC sequences in GenBank format and need to extract gene-level features (coordinates, sequences, functional annotations) as input to domain annotation and tokenization pipelines. Use this skill when starting a BGC analysis from raw GenBank files rather than pre-parsed gene lists.
    0 installs
19. ▌
    Graph Embedding Coordinate Extraction · holobiomicslab

    Use when you have a network object (loaded as igraph or MetaNet format with edges and nodes defined) and need to assign two-dimensional spatial coordinates to nodes for downstream visualization on static platforms (ggplot2, base R graphics) or interactive viewers (Gephi, Cytoscape).
    0 installs
20. ▌
    Imaging Parameter Metadata Annotation · holobiomicslab

    Use when after mzML-to-imzML conversion has produced barebones imzML files with pixel alignment but no experimental metadata.
    1 install
21. ▌
    Interactive Filter Control Design Web · holobiomicslab

    Use when when you have a web-based visualization of aligned mass spectrometry peaks (m/z, intensity, retention time, alignment quality metrics) and need users to interactively explore subsets of those peaks by applying constraints on intensity thresholds, alignment score cutoffs, or peak.
    2 installs
22. ▌
    Isotopologue Ratio Quality Assessment · holobiomicslab

    Use when evaluating the reliability of non-targeted data pre-processing (NPP) tools (XCMS, MZmine 2, MS-DIAL, etc.) on known metabolite peaks.
    0 installs
23. ▌
    Jacobian Precision Matrix Computation · holobiomicslab

    Use when after generating a covariance matrix from normalized metabolite abundance data (e.
    0 installs
24. ▌
    JSON Conversion Directive Application · holobiomicslab

    Use when you have validated intermediate JSON data conforming to the Experiment Description Specification and need to convert it to a target format (e.g., mwTab for Metabolomics Workbench deposition).
    0 installs
25. ▌
    Latent Space Dimensionality Reduction · holobiomicslab

    Use when you have imaging mass spectrometry (IMS) datasets where peak intensities are high-dimensional and sparse, and you need to extract compressed latent features that preserve spatial adjacency relationships and enable iterative automatic peak picking to identify marker ions.
    1 install
26. ▌
    Lipid Abundance Differential Analysis · holobiomicslab

    Use when you have a preprocessed and normalized lipid abundance matrix with batch identifiers and experimental group assignments, and you need to compare lipid levels across treatment conditions (e.
    2 installs
27. ▌
    Lipid Sample Separation Visualization · holobiomicslab

    Use when after normalizing and log-transforming lipidomics intensity data in a LipidomicsExperiment object, use this skill when you need to assess whether your sample groups (e.
    0 installs
28. ▌
    Manifest Generation And Documentation · holobiomicslab

    Use when you need to audit a bioinformatics repository (such as MIBiG) to determine which sequence files are maintained locally but lack public accessions in NCBI GenBank/RefSeq. Use this to support curation workflows, data provenance tracking, or to identify candidate sequences for public release.
    2 installs
29. ▌
    Masked Modeling Pre Training Strategy · holobiomicslab

    Use when when you have unlabeled molecular structure data (SMILES or molecular graphs) from natural products and need to learn task-agnostic representations that capture both evolutionary (scaffold-level) and structural (side-chain) information before finetuning on downstream classification or.
    2 installs
30. ▌
    Mass Error Calculation And Assessment · holobiomicslab

    Use when after peak picking and before or after molecular formula assignment on FT-ICR data, especially when calibrating on a specific field strength (e.g., 12 T or 15 T).
    1 install
31. ▌
    Mass Spectrometry Image Normalization · holobiomicslab

    Use when after loading a pixel array (NumPy format) and its associated metadata JSON file from MSIGen, when you need to account for pixel-to-pixel variations in total ion signal or when comparing relative abundances of multiple ions within or across samples.
    0 installs
32. ▌
    Mass Spectrometry Imaging Data Import · holobiomicslab

    Use when you have raw MS imaging data in imzML (continuous or processed) or Analyze 7.5 format and need to load it into R for spectral processing, normalization, peak-picking, or statistical analysis.
    0 installs
33. ▌
    Matrix Numerical Stability Validation · holobiomicslab

    Use when after computing a Jacobian (precision) matrix from covariance matrix inversion in MInfer, or whenever precision matrices are derived via numerical linear algebra operations on covariance matrices.
    0 installs
34. ▌
    Metabolite Abundance Matrix Filtering · holobiomicslab

    Use when when you have multiple batches of metabolomics data in SummarizedExperiment format with log-transformed abundance assays and need to: (1) remove poorly-quantified metabolites with >50% missing values within each batch, (2) retain only metabolites present across all batches for cross-batch.
    0 installs
35. ▌
    Metabolite Feature Annotation Mapping · holobiomicslab

    Use when after importing raw metabolomics data (e.g., from Metabolon, Nightingale, SomaLogic, or Olink platforms) into a Metaboprep object, but before quality control or statistical analysis.
    0 installs
36. ▌
    Metabolomic Peak Matrix Preprocessing · holobiomicslab

    Use when you have a raw or minimally processed metabolomic peak matrix (in standardized or tool-generated format) from multi-class samples with optional quality control (QC) samples and/or internal standards (IS), and you need to generate a single normalized peak table suitable for statistical.
    0 installs
37. ▌
    Metabolomics Data Downstream Analysis · holobiomicslab

    Use when you have deposited spatio-molecular matrices (e.g., MORPHnMOL.csv from SpaceM analysis) and need to reproduce or extend the data transformations, feature extractions, and figure generation reported in a metabolomics manuscript.
    0 installs
38. ▌
    Metabolomics Missing Value Imputation · holobiomicslab

    Use when raw metabolomics data matrices contain zero values or NA entries representing undetected metabolic features. Imputation is required before batch effect correction models (ComBat, ber) can be reliably applied, as these models assume complete feature matrices.
    0 installs
39. ▌
    Missing Value Imputation Metabolomics · holobiomicslab

    Use when your raw metabolomics dataset contains missing values (NAs) in metabolite columns after loading and you have already identified and removed metabolite columns with >10% missing data prevalence.
    0 installs
40. ▌
    Molecular Formula Property Derivation · holobiomicslab

    Use when you have filtered FT-ICR MS peak data with valid molecular formula assignments (C, H, O, N, S, P elemental counts) and need to quantify molecular properties that predict metabolite reactivity, bioavailability, and biochemical role.
    2 installs
41. ▌
    Ms Data Format Parsing And Conversion · holobiomicslab

    Use when you have raw breath HRMS data in mzML or mzXML format and need to extract volatile organic compound (VOC) features as a standardized CSV table indexed by m/z value, with columns for scan time or sample identifiers and corresponding intensity measurements.
    0 installs
42. ▌
    Msi Data Processing Speed Measurement · holobiomicslab

    Use when when you need to validate that MSI software (e.g., LipidQMap) achieves documented processing speeds on your target hardware, or when you need to establish a performance baseline before deploying the software for high-throughput imaging studies.
    0 installs
43. ▌
    Msimagingexperiment Object Validation · holobiomicslab

    Use when after reading an imzML file (continuous or processed format) using readMSIData() and before proceeding to preprocessing or statistical analysis steps. Use this skill whenever you need to confirm that a parsed imaging dataset meets expected structural requirements—e.
    2 installs
44. ▌
    Msimagingexperiment Subset Operations · holobiomicslab

    Use when after peak alignment with peakAlign(), when you have an MSImagingExperiment with many detected peaks but want to retain only those present in a sufficient fraction of pixels.
    0 installs
45. ▌
    Multi Criteria Performance Evaluation · holobiomicslab

    Use when you have preprocessed multi-class or time-course metabolomic peak tables (with or without quality control samples and/or internal standards) and need to compare multiple preprocessing workflows to identify which performs for biomarker discovery or differential profiling.
    0 installs
46. ▌
    Multi Fold Split Validation Reporting · holobiomicslab

    Use when when evaluating a spectral embedding or compound identification model on a dataset where the training/test split has already been finalized (e.
    2 installs
47. ▌
    Multi Format Identifier Harmonization · holobiomicslab

    Use when you have metabolomics datasets from multiple studies that use different chemical identifier formats (names, InChI, InChIKey, SMILES), and you need to merge them for meta-analysis or cross-study comparison.
    0 installs
48. ▌
    Natural Isotope Abundance Calculation · holobiomicslab

    Use when when processing mass spectrometry imaging (MSI) data in positive ion mode where both [M+H]+ and [M+Na]+ adducts are present for the same lipid species, and you observe intensity overlap in [M+H]+ ion images caused by the isotopic fine structure of [M+Na]+ adducts.
    0 installs
49. ▌
    Neural Network Encoder Implementation · holobiomicslab

    Use when when you need to benchmark multiple encoder types (e.g., FFN vs. GNN) on the same predictive task and require evidence that performance differences reflect genuine architectural trade-offs rather than suboptimal tuning.
    0 installs
50. ▌
    Neural Network Model Layer Validation · holobiomicslab

    Use when after converting Keras models to HDF5 TensorFlow 2.0 format and before deploying them to a TensorFlow Serving endpoint.
    0 installs
51. ▌
    Neutral Mass Inference Via Regression · holobiomicslab

    Use when use this skill after khipu has assigned observed ions to grid positions (isotope and adduct combinations). Apply it when you have a connected subnetwork of feature ions that have been matched to known isotope and adduct patterns and need to estimate the neutral mass of the parent compound.
    0 installs
52. ▌
    Nonparametric Reproducibility Ranking · holobiomicslab

    Use when you have high-dimensional replicate experiment data (e.
    2 installs
53. ▌
    Over Representation Analysis Workflow · holobiomicslab

    Use when when you need to reproduce published ORA simulation results, validate pathway enrichment findings from a metabolomics study, or examine pitfalls and practices in Over-representation Analysis methodology.
    2 installs
54. ▌
    Pandas Dataframe Column Specification · holobiomicslab

    Use when when you have mass spectrometry data in a Pandas DataFrame with column names that do not match pyOpenMS-viz's default expectations (e.g., 'm/z' vs 'mz' or 'retention_time' vs 'rt'), or when your data uses domain-specific column labels (e.g., 'mass_to_charge', 'scan_time', 'peak_intensity').
    0 installs
55. ▌
    Parameter Sharing In Siamese Networks · holobiomicslab

    Use when when processing paired augmented versions of the same input (e.g., two augmented ion images in COL or ISO mode) and you need to learn meaningful low-dimensional representations via contrastive loss.
    0 installs
56. ▌
    Peak Background Binary Classification · holobiomicslab

    Use when you have LC-HRMS profile-mode chromatograms with extracted local maxima exported as standardized 2D rt×mz areas, and you need to disambiguate true chromatographic peaks from background signals (including wall artifacts and noise) at scale.
    0 installs
57. ▌
    Peak Detection Parameter Optimization · holobiomicslab

    Use when when loading and processing raw or recalibrated FT-ICR mass spectrum data (Bruker .d format) on a defined field-strength instrument (e.g., 12 T or 15 T), before executing molecular formula search.
    0 installs
58. ▌
    Phase I Phase Ii Transformation Rules · holobiomicslab

    Use when when you have a parent drug's raw chemical formula and need to predict its likely metabolite formulas for subsequent mass spectrometry matching, especially in high-resolution MS workflows where exact mass matching requires known candidate formulas.
    2 installs
59. ▌
    Phenotype Pathway Association Ranking · holobiomicslab

    Use when after computing a pathway dysregulation score matrix (PDSmatrix) from metabolite-pathway associations, apply this skill when you need to reduce the pathway feature space to those most predictive or explanatory of a phenotype label.
    0 installs
60. ▌
    Physicochemical Descriptor Extraction · holobiomicslab

    Use when when you have validated RDKit molecule objects derived from PubChem or HMDB molecule IDs and need to generate quantitative chemical property representations as one modality in a multimodal feature tensor for neural network training.
    2 installs
61. ▌
    Pytorch Installation And Verification · holobiomicslab

    Use when when setting up a computational environment to run pre-trained PyTorch models that were trained on GPU hardware (e.g., NVIDIA A100 with CUDA 11.8), and the released model weights are GPU-trained artifacts. Specifically, when you have a jestr_requirements.
    0 installs
62. ▌
    Quality Control Metric Interpretation · holobiomicslab

    Use when after normalizing a metabolomics featuredata matrix (samples × metabolites), use this skill to visually and quantitatively assess normalization quality. Specifically, apply it when you need to decide whether a chosen normalization method (e.
    0 installs
63. ▌
    Query String Parsing And Tokenization · holobiomicslab

    Use when when you have a user-provided or system-generated query string containing a chemical structure in unknown or mixed format, and you need to route it to a structure-specific API endpoint (such as ClassyFire) that requires knowing whether the input is SMILES, InChI, IUPAC nomenclature, or.
    0 installs
64. ▌
    Rapid Spectrum Retrieval Optimization · holobiomicslab

    Use when you have a large collection of mass spectrometry spectra (m/z and intensity pairs) and need to rapidly retrieve similar or candidate spectra from the archive in response to queries.
    0 installs
65. ▌
    Recursive Descent Parser Construction · holobiomicslab

    Use when you have a formal grammar specification for a domain-specific language (or can extract one from reference implementations) and need to convert user-written query strings into structured, machine-processable representations (ASTs or JSON) that preserve domain-specific semantics—such as mass.
    0 installs
66. ▌
    Reference Peak Matching And Alignment · holobiomicslab

    Use when when you have a processed mass spectrum object (e.g., from Bruker FT-ICR acquisition) and a reference peak list (e.g., SRFA.
    1 install
67. ▌
    Release Versioning Schema Enforcement · holobiomicslab

    Use when when preparing a release branch for a Maven-based project (like NMRFx) and you need to verify that all pom.xml files in the repository tree declare identical version strings before applying release branch naming conventions (e.g., 'release/X.Y.Z').
    2 installs
68. ▌
    S7 Object Construction And Validation · holobiomicslab

    Use when after successfully parsing vendor-specific metabolomic data files (Metabolon Excel, Nightingale, Olink, SomaLogic) into separate data, samples, and features tables, and before applying quality control or batch normalization pipelines.
    0 installs
69. ▌
    Smiles Inchi Fasta Format Recognition · holobiomicslab

    Use when when you have a mixed batch of chemical structure queries in unknown or variable formats (e.
    0 installs
70. ▌
    Soft Thresholding Adjacency Weighting · holobiomicslab

    Use when after computing a biweight midcorrelation similarity matrix across normalized metabolite abundance data, and before hierarchical clustering on dissimilarity.
    0 installs
71. ▌
    Spatial Distribution Pattern Analysis · holobiomicslab

    Use when when you have loaded MSI peak data with associated m/z values and need to disambiguate matrix ions from analyte ions. Apply this skill when chemical formula alone is insufficient (e.g., overlapping or isobaric peaks exist) and you have pixel-level spatial intensity maps for each ion.
    0 installs
72. ▌
    Spectral Fragment Identifier Matching · holobiomicslab

    Use when when you have downloaded fragment records from separate experimental and predicted online databases and need to verify that each fragment can be traced back to a valid compound entry in a reference compound database (e.g., SDF-format DNA adduct compound collection).
    2 installs
73. ▌
    Spectral Noise Filtering Dynamic Peak · holobiomicslab

    Use when use this skill after normalizing, smoothing, and baseline-reducing MSImagingArrays objects when you need to detect peaks across multiple spectra with consistent SNR-based thresholding.
    1 install
74. ▌
    Spectral Peak Alignment Across Pixels · holobiomicslab

    Use when after peak picking across individual spectra in an MSImagingExperiment, when you need to harmonize peak m/z positions across pixels to account for small shifts in peak location due to instrumental drift, calibration differences, or natural variation.
    1 install
75. ▌
    Spectral Peak Detection And Alignment · holobiomicslab

    Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or vendor formats).
    2 installs
76. ▌
    Spectral Reference Peak Summarization · holobiomicslab

    Use when after peak picking and alignment have been performed on preprocessed spectra (normalized, smoothed, and baseline-reduced), and you need to create a unified peak reference table that can be applied consistently across all spectra in an imaging dataset.
    1 install
77. ▌
    Statistical Result Mapping To Display · holobiomicslab

    Use when you have omics abundance or expression measurements paired with corresponding statistical results (p-values, effect sizes, fold-changes) and need to create an interactive, exploratory display where each omics feature (protein, metabolite, gene) occupies its own panel and can be filtered or.
    1 install
78. ▌
    Structure Organism Pair Deduplication · holobiomicslab

    Use when you have a curated natural products dataset (e.g., LOTUS platinum validation dataset in TSV format) and need to establish ground-truth counts of unique chemical structures, unique organisms, and unique referenced structure-organism associations.
    0 installs
79. ▌
    System Path Environment Configuration · holobiomicslab

    Use when when setting up imzML Writer for the first time on a new machine, or when raw vendor mass spectrometry file conversion fails with 'msconvert not found' or Docker image unavailable errors. Specifically: on Windows/PC systems before invoking RAW_to_mzML conversion;
    0 installs
80. ▌
    Systems Biology Model Standardization · holobiomicslab

    Use when you have multiple draft metabolic reconstructions of community members or assembly variants (e.g., from different annotation pipelines or genome assemblies) in diverse or non-standard formats, and you need to merge them into a single consensus model.
    0 installs
81. ▌
    Targeted Compound Metadata Formatting · holobiomicslab

    Use when you have a raw list of target compounds (in .xlsx, CSV, or database form) with heterogeneous column names and layouts, and you need to prepare it for targeted peak detection, EIC extraction, or quality metric calculation in TARDIS or similar LC–MS metabolomics tools.
    0 installs
82. ▌
    Theoretical To Observed Peak Matching · holobiomicslab

    Use when you have a mass spectrum scan containing observed precursor ions (m/z, intensity pairs) in a narrow isolation window, a known peptide sequence with specified charge state and stable isotope labeling parameters (atom type, incorporation probability), and you need to determine which observed.
    2 installs
83. ▌
    Time Temperature Degradation Modeling · holobiomicslab

    Use when you are planning a blood sampling campaign and need to know whether specific lipid or polar-metabolite analytes will degrade during storage or processing delays at known temperatures, or you are troubleshooting retrospective stability concerns for analytes already measured under documented.
    1 install
84. ▌
    Trend Classification From Fold Change · holobiomicslab

    Use when when you have harmonized metabolomics data with fold-change and p-value columns from multiple studies and need to assign trend categories prior to vote-counting meta-analysis.
    0 installs
85. ▌
    Statistics Biomarker Discovery Workflow · holobiomicslab bundle

    Use when you have a metabolomics feature/quant table and want a statistically rigorous comparison and candidate biomarkers — cleaning and normalization, multivariate analysis, differential features, enrichment/pathway analysis, and biomarker selection with ROC.
    0 installs
86. ▌
    Adjacency Matrix Sparsity Analysis · holobiomicslab

    Use when immediately after calling squidpy.gr.spatial_neighbors() or similar spatial graph construction methods on an AnnData object. It is essential when validating that the computed spatial graph has been correctly stored in adata.
    0 installs
87. ▌
    Alternative Splicing Event Parsing · holobiomicslab

    Use when when you have a GTF genome annotation and need to identify all local alternative splicing events (SE, RI, A5/A3, MX, AF/AL) or transcript-level isoform events for a given gene set, prior to quantifying PSI values across samples or performing differential splicing analysis.
    0 installs
88. ▌
    Gene Expression Log Transformation · holobiomicslab

    Use when after normalizing total UMI counts per cell using normalize_total, and before PCA or feature selection. Use this when working with raw or depth-normalized count matrices where gene expression values span multiple orders of magnitude and variance is not homogeneous across expression levels.
    0 installs
89. ▌
    Gene Filtering By Expression Level · holobiomicslab

    Use when you have a large gene expression matrix (e.g., thousands of genes) from normalized microarray or RNA-seq data and need to reduce computational burden before running pathway enrichment analysis (e.g., GSEA or GESECA).
    0 installs
90. ▌
    Independent Filtering Optimization · holobiomicslab

    Use when you have completed DESeq differential expression analysis on a DESeqDataSet and obtained raw results with p-values across all genes.
    0 installs
91. ▌
    Microarray Expression Data Loading · holobiomicslab

    Use when you have raw or normalized microarray expression matrices stored in public repositories (GEO accessions) along with sample metadata, and you need to load both into R as structured objects (expression matrix and phenotype data frame) to construct a design matrix and fit linear models for.
    0 installs
92. ▌
    Python Data Structure Verification · holobiomicslab

    Use when after executing a spatial analysis function (e.g., squidpy.gr.sepal) that modifies or augments a data object, verify that the expected output fields exist with correct names, data types, and array dimensions before proceeding to interpretation or visualization.
    0 installs
93. ▌
    Trajectory Inference Preprocessing · holobiomicslab

    Use when you have raw or normalized single-cell RNA-seq expression data stored in an AnnData object (`.h5ad` format) and your analysis goal is to infer developmental or differentiation trajectories.
    2 installs
94. ▌
    Transcript Level Count Aggregation · holobiomicslab

    Use when you have transcript-level abundance and count estimates from salmon, sailfish, kallisto, or oarfish and need gene-level matrices for downstream differential analysis with edgeR, DESeq2, or limma-voom.
    0 installs
95. ▌
    Candidate Spectrum Retrieval And Ranking · holobiomicslab

    Use when when you have a large reference MS/MS spectral library (>10k spectra) and need to perform open modification searches on query spectra without exhaustively comparing against every library entry.
    0 installs
96. ▌
    Mass Spectrometry File Format Conversion · holobiomicslab

    Use when you have raw MS data files in vendor-native format (.raw, .d, .ms) from CE-MS or LC-MS instruments and need to process them through AriumMS or other open-source metabolomics pipelines that require standardized XML-based interchange formats.
    0 installs
97. ▌
    Metabolite Detection Matrix Construction · holobiomicslab

    Use when after GNPS spectral library matching has been completed on a batch of MS2 spectra from public MassIVE datasets and you need to aggregate chemical annotations into a tabular format suitable for downstream comparative metabolomics, co-analysis, or chemical explorer visualizations across.
    2 installs
98. ▌
    Spectral Clustering And Feature Grouping · holobiomicslab

    Use when you have raw MS/MS feature data with m/z, retention time, and fragmentation spectra from an untargeted metabolomics experiment, and you need to annotate reaction-derived metabolites of xenobiotics without relying on a priori targeted methods.
    0 installs
99. ▌
    Compound Area Aggregation Across Samples · holobiomicslab

    Use when you have a GC-MS dataset with multiple sample files (e.g., Std_soln_00, Std_soln_07, Std_soln_00a) where the same chemical is detected in different runs with varying Match.Factor scores, and you need to consolidate area values by compound identity rather than by individual peak detection.
    0 installs
100. ▌
     Ei Mass Spectra Structure Representation · holobiomicslab

     Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing. Specifically, when you must extract precursor m/z values, peak intensity pairs, and spectrum metadata (e.
     0 installs