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HolobiomicsLab

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1. ▌
   Frequency Threshold Adduct Selection · holobiomicslab

   Use when after feature clustering has grouped co-eluting features and assigned candidate KEGG metabolites with multiple potential adduct forms, use this skill when you need to reduce false positive annotations by filtering out low-frequency adducts.
   2 installs
2. ▌
   Hardware Specification Documentation · holobiomicslab

   Use when releasing or evaluating scientific software with claimed performance benefits, particularly when the software processes large datasets (e.g., multi-gigabyte files) or when execution speed is marketed as a key feature.
   0 installs
3. ▌
   Hdf5 File Format Reading And Writing · holobiomicslab

   Use when you have isotope-corrected or raw ion-image intensity matrices from LipidQMap or similar MSI software and need to: (1) export them as persistent HDF5 containers for archival or sharing, (2) programmatically read an existing Cardinal::HDF5 export to extract intensity matrices and feature.
   2 installs
4. ▌
   Heatmap Clustering And Visualization · holobiomicslab

   Use when you have a gene expression matrix (samples × genes, with numeric values) and corresponding sample group/phenotype labels, and you need to identify co-expression patterns, sample clustering, or condition-specific expression trends.
   1 install
5. ▌
   In Silico Spectrum Metadata Curation · holobiomicslab

   Use when when processing collections of in-silico mass spectra from OMSLs (Open Mass Spectra Libraries) where the adduct field is absent, null, or not explicitly specified in the source file;
   0 installs
6. ▌
   Integrative Omics Pathway Enrichment · holobiomicslab

   Use when you have a preprocessed peak table with statistically significant or differentially abundant metabolites (e.g., from ANCOVA or PLS/PLS-DA), and you want to move beyond individual peak-level interpretation to understand which biological pathways or metabolic networks are perturbed.
   2 installs
7. ▌
   Isotope Corrected Image Quantitation · holobiomicslab

   Use when after isotopic correction has been performed on MSI ion images and you need to convert normalized intensities into absolute quantitative values.
   2 installs
8. ▌
   Isotopic Peak Intensity Distribution · holobiomicslab

   Use when when you have one or more peptide sequences (as strings) and need to predict their isotopic distribution pattern for MS instrument simulation, peak deconvolution, or validation of observed isotopic envelopes.
   1 install
9. ▌
   Isotopologue Ratio Quality Filtering · holobiomicslab

   Use when when extracting isotopologue patterns from centroided mzML files in non-targeted metabolomics workflows, apply this filter after detecting candidate isotopologue peaks but before finalizing the benchmark dataset.
   0 installs
10. ▌
    Java Library Dependency Provisioning · holobiomicslab

    Use when deploying a Java-based scientific application (such as CEU Mass Mediator) to an application server and the deployment documentation specifies required JAR libraries.
    0 installs
11. ▌
    JSON Schema Validation For Dashboard · holobiomicslab

    Use when after running the msfeast_pipeline notebook to generate dashboard_data.json from quantification tables, metadata, and spectral data. Use this skill to verify that the exported JSON contains all required fields and structure before attempting to load the file into msFeaST_Dashboard_bundle.
    0 installs
12. ▌
    Lipid Adduct Pairing By Neutral Mass · holobiomicslab

    Use when when processing mass spectrometry imaging data with multiple adduct forms of the same lipid species, and you need to correct one adduct form (e.g. [M+H]+) for isotopic interference from a co-occurring adduct (e.g. [M+Na]+).
    2 installs
13. ▌
    Lipid Feature Annotation And Sorting · holobiomicslab

    Use when after quantifying ion images in LipidQMap and before exporting to HDF5 format, when you need to organize per-feature metadata (lipid ID, class, adduct, m/z, internal standard flag) into aligned datasets that can be linked to intensity data via dimension scales and sorted for reproducible.
    1 install
14. ▌
    Lipid Species Classification Mapping · holobiomicslab

    Use when you have a table of lipid species names or identifiers output from LipidSearch or LIQUID (with associated quantification data) and need to annotate each lipid with its standardized LIPID MAPS classification (e.
    0 installs
15. ▌
    Mass Spectrometry Data Serialization · holobiomicslab

    Use when after RAMClustR clustering and molecular weight inference via do.findmain, when you need to export deconvoluted cluster spectra for import into external annotation tools (MSFinder or Sirius).
    0 installs
16. ▌
    Mass Spectrometry Feature Collapsing · holobiomicslab

    Use when after XCMS CentWave feature extraction when your feature table contains redundant entries — multiple features with highly similar m/z and retention time values that represent the same metabolite.
    2 installs
17. ▌
    Mass Spectrometry Feature Extraction · holobiomicslab

    Use when you have raw mzML mass spectrometry data and need to detect which predicted candidate metabolites are present in the sample.
    0 installs
18. ▌
    Mass Tolerance Parameter Calibration · holobiomicslab

    Use when when converting raw line-scan mass spectrometry imaging data (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .mzML formats) and must decide which m/z values from a reference mass list correspond to peaks in the raw spectra.
    0 installs
19. ▌
    Memory Efficient Pairwise Statistics · holobiomicslab

    Use when you have an MSI intensity matrix (msimat object) and an annotated mass-difference table (massdiff object with known or hypothesized parent–adduct ion pairs) where the number of peak pairs exceeds available RAM.
    2 installs
20. ▌
    Meta Analysis Effect Size Estimation · holobiomicslab

    Use when when you have tabulated results (p-value, fold-change, study size N) from two or more independent metabolomics studies addressing the same research question and need a single meta-analytic estimate of effect size and statistical significance without access to raw data or variance estimates.
    0 installs
21. ▌
    Metabolite Abundance Standardization · holobiomicslab

    Use when you have a metabolomics featuredata matrix with known batch effects, matrix effects, or unwanted technical variation, and you have identified a set of negative control metabolites (e.g., spiked internal standards or blank-derived features) that are expected to show no biological signal.
    0 installs
22. ▌
    Metabolite Cluster Export Formatting · holobiomicslab

    Use when after running do.findmain on a RAMClustR-clustered object to infer molecular weights and assign features to compound clusters, when you need to conduct structural elucidation in MSFinder or Sirius and require spectra in their native import formats rather than the intermediate MSP or.
    2 installs
23. ▌
    Metabolite Interaction Visualization · holobiomicslab

    Use when after computing a Jacobian matrix from covariance data in MInfer, when you need to render metabolite-to-metabolite interaction networks as publication-quality figures.
    0 installs
24. ▌
    Metabolite Overdispersion Correction · holobiomicslab

    Use when working with untransformed metabolomics count data (e.g., c57_nos2KO_mouse_countDF) that will be input to variance-sensitive methods such as random forest classification or univariate statistical tests.
    0 installs
25. ▌
    Metabolite Retention Time Comparison · holobiomicslab

    Use when after executing retention-order prediction on a test set of metabolites, you have both predicted retention orderings and experimentally measured ground-truth retention orderings for the same set of compounds, and you need to quantify prediction accuracy to validate the model's performance.
    0 installs
26. ▌
    Metabolomics Batch Effect Adjustment · holobiomicslab

    Use when you have a log-transformed metabolomics featuredata matrix with missing values handled (via knn or replacement) and you observe systematic variation across batches, quality control samples, or sample order that is NOT of biological interest.
    0 installs
27. ▌
    Metabolomics Batch Effect Correction · holobiomicslab

    Use when you have log-transformed, imputed metabolomics data from multiple experimental batches (rawImpute assay) that shows visible batch effects in PCA plots or signal drift across runs, and your study design includes intra-batch replicates (technical replicates within a run) and inter-batch.
    0 installs
28. ▌
    Metabolomics Data Import And Parsing · holobiomicslab

    Use when when you have metabolomics comparison results from one or more studies in tabular format (spreadsheet or text file) with columns for compound name/identifier, statistical p-value, relative fold-change (including negative values indicating down-regulation), study sample size (N), and.
    2 installs
29. ▌
    Metacyc Database Query And Retrieval · holobiomicslab

    Use when you need to (1) quantify how many MetaCyc reactions can be represented by different numbers of generalized rules, (2) select a subset of rules for reaction network expansion based on coverage targets (e.
    0 installs
30. ▌
    Missing Data Simulation And Recovery · holobiomicslab

    Use when you have metabolomics peak intensity data with pathway annotations and want to benchmark whether a pathway scoring method (PALS, ORA, GSEA) degrades gracefully under conditions of missing peaks and measurement noise.
    0 installs
31. ▌
    Molecular Coordinate Generation 2d3d · holobiomicslab

    Use when you have canonicalized SMILES strings from a chemical structure database and need both 2D (flat) and 3D (conformer) representations for molecular visualization, molecular docking, or structure archival.
    0 installs
32. ▌
    Molecular Fingerprint Generation Rdk · holobiomicslab

    Use when you have a set of chemical compounds represented as InChI or SMILES strings and need to extract molecular features for input into a neural network or traditional ML model.
    0 installs
33. ▌
    Molecular Model Benchmark Comparison · holobiomicslab

    Use when when you have (1) a candidate foundation model or pre-trained weights for natural products (e.g., NaFM), (2) one or more baseline models pre-trained on synthetic molecules (e.g., ChemBERTa, MolBERT), (3) a held-out test set from a downstream task (e.
    2 installs
34. ▌
    Molecular Structure Dataset Curation · holobiomicslab

    Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values, and you need to format and validate them as input to a machine learning CCS prediction model.
    0 installs
35. ▌
    Morphological Alignment Optimization · holobiomicslab

    Use when you have two or more spatial omics datasets (e.
    2 installs
36. ▌
    Ms1 Data Preprocessing Normalization · holobiomicslab

    Use when when you have loaded raw MS1 data from multiple instrument formats (Agilent, Thermo, Bruker, mzML) across a multi-sample cohort and need to prepare the ion intensity feature matrix for PCA analysis or cross-sample quality assessment.
    0 installs
37. ▌
    Multi Algorithm Comparative Analysis · holobiomicslab

    Use when when you have prepared metabolomics data (e.g., covid_data) with a binary outcome variable and need to select the most appropriate predictive algorithm for your classification task.
    2 installs
38. ▌
    Multimodal Input Tensor Construction · holobiomicslab

    Use when when you have completed multimodal dataset production via data_prep.py and need to prepare sample or production input batches that combine molecular graph features and SMILES embeddings for forward pass validation or model training on TransG-Net.
    0 installs
39. ▌
    Natural Product Database Preparation · holobiomicslab

    Use when you need to update your local LOTUS natural-product database file before running metadata enrichment or structure-query workflows, or when a pre-existing provided LOTUS file is unavailable or suspected to be stale. Trigger on project initialization or on a scheduled basis (e.
    2 installs
40. ▌
    Nearest Neighbor Candidate Retrieval · holobiomicslab

    Use when when you have a large spectral library (thousands to millions of spectra represented as high-dimensional vectors) and need to search unknown query spectra against it, particularly under open modification search scenarios where all possible mass shifts must be considered.
    0 installs
41. ▌
    Network Graph Filtering By Hierarchy · holobiomicslab

    Use when your network contains multiple edge types between the same pair of nodes and you need a deterministic, single-edge representation per node pair.
    2 installs
42. ▌
    Network Visualization Ranked Scoring · holobiomicslab

    Use when when you have computed betweenness centrality (or other igraph topology metrics) for metabolites in a pathway-metabolite bipartite network and wish to highlight which metabolites occupy central positions—i.e., have high regulatory potential through bridging multiple pathways.
    0 installs
43. ▌
    Numeric List Construction Validation · holobiomicslab

    Use when implementing a backendInitialize() method for a custom MsBackend class and you have raw m/z and intensity vectors (from files, data frames, or lists) that must be converted into the internal NumericList representation required by the Spectra package.
    0 installs
44. ▌
    Omics Data Integration Visualization · holobiomicslab

    Use when you have completed statistical analysis of omics data (proteomics, metabolomics, transcriptomics, or multi-omic) and possess both abundance/expression measurements and computed statistical metrics (p-values, effect sizes, fold-changes).
    0 installs
45. ▌
    Organism Taxonomy Identifier Mapping · holobiomicslab

    Use when integrating organism records from 31 or more initial open databases with inconsistent taxonomy nomenclature, or when you need to count unique organisms in a validated structure-organism pair collection and verify the count against a known aggregate (e.
    0 installs
46. ▌
    Pairwise Mass Comparison Computation · holobiomicslab

    Use when after peak m/z values and molecular formulas have been extracted and pre-processed from FT-ICR MS data, and you need to reconstruct biochemical transformation networks ab initio.
    0 installs
47. ▌
    Pairwise Mass Difference Computation · holobiomicslab

    Use when after loading preprocessed MSI intensity data (via msimat from CSV export) or a simple numeric vector of mass peak values, when you need to discover which masses in your dataset co-vary as parent–adduct pairs.
    0 installs
48. ▌
    Pareto Scaling Multivariate Analysis · holobiomicslab

    Use when apply Pareto scaling when preparing normalized metabolomics data for unsupervised multivariate analysis (PCA or hierarchical clustering heatmaps) where features span multiple orders of magnitude in intensity and you want to reduce the influence of high-abundance metabolites without.
    0 installs
49. ▌
    Pathway Annotation Database Matching · holobiomicslab

    Use when after marker identification or metabolite annotation has produced a curated list of compound IDs (e.g., KEGG IDs or CAS numbers) and you need to determine which metabolic pathways are statistically overrepresented in your dataset.
    1 install
50. ▌
    Pca Score Interpretation In Networks · holobiomicslab

    Use when you have both (1) a sparse network graph from GLASSO showing conditional dependencies among variables, and (2) PCA scores representing variance or loadings in a lower-dimensional space.
    0 installs
51. ▌
    Peak Detection Targeted Metabolomics · holobiomicslab

    Use when you have mass spectrometry data in .raw, .d, or mzXML format and a predefined list of target compounds (m/z and retention time ranges) you wish to quantify.
    0 installs
52. ▌
    Peak Mass Intensity Feature Encoding · holobiomicslab

    Use when you have raw mass spectra (e.g., from NIST 2017 or MassBank) and need to prepare them for Word2vec embedding or other token-based neural models. Use it as a preprocessing step before training spectral embedding models, especially when scale and accuracy of spectrum matching are priorities.
    0 installs
53. ▌
    Permanova Effect Size Interpretation · holobiomicslab

    Use when after running PERMANOVA on distance matrices derived from FT-ICR MS metabolite peak intensities or other high-dimensional compositional data, when p-values indicate statistical significance but ordination plots (NMDS, PCA) fail to discriminate among treatment groups.
    0 installs
54. ▌
    Principal Component Analysis Scaling · holobiomicslab

    Use when you have a log2-transformed metabolite abundance matrix and need to visualize sample clustering patterns, batch structure, or the effect of batch correction. Scaling is essential because metabolites often have widely different absolute concentrations;
    0 installs
55. ▌
    Protein Interaction Score Prediction · holobiomicslab

    Use when you have co-fractionation/mass-spectrometry (CF-MS) elution profiles (raw intensity vectors across fractions) paired with a gold standard of known positive and negative protein–protein interactions, and your goal is to predict interaction scores for all protein pairs without hand-crafted.
    0 installs
56. ▌
    Query Latency Throughput Measurement · holobiomicslab

    Use when when you have implemented or obtained a spectral library search algorithm (such as Flash Entropy Search) and need to empirically verify its performance against reported benchmark metrics, or when comparing query performance across different library sizes, mass spectral file formats (.mgf, .
    0 installs
57. ▌
    Raw Mass Spectrometry Data Ingestion · holobiomicslab

    Use when you have raw mass spectrometry data in mzML, abf (Reifycs), or cdf (NetCDF) format and need to load it into MS-DIAL or a similar open-source metabolomics platform.
    2 installs
58. ▌
    Reactomics Annotation And Clustering · holobiomicslab

    Use when you have a formula-assigned dataset from FT-ICR MS or other mass spectrometry with molecular formulas assigned to each mass feature, and you want to identify and quantify the molecular transformations (e.
    0 installs
59. ▌
    Reference Database Tolerance Mapping · holobiomicslab

    Use when you have calculated pairwise mass differences from MS peaks (via massdiff()) and binned them into a histogram, and now need to identify which observed mass differences correspond to known molecular adducts (e.g., [M+Na]+, [M+H]+, matrix-related species) rather than random noise.
    0 installs
60. ▌
    Regression Model Training Comparison · holobiomicslab

    Use when you have a labeled dataset of molecular structures with experimental continuous outcomes (e.
    0 installs
61. ▌
    Retention Time Mz Alignment Matching · holobiomicslab

    Use when you have extracted feature tables (m/z, intensity, retention time) from multiple breath samples (mzML or mzXML files) via feature extraction, and need to identify which features represent the same volatile organic compound (VOC) across samples to enable cross-sample intensity comparisons.
    0 installs
62. ▌
    Retention Time Mz Coordinate Mapping · holobiomicslab

    Use when when you have mass-spectrometry data in tabular form (Pandas DataFrame) with columns for m/z, retention time or ion mobility, and intensity, and you need to visualize the 2D distribution of peaks to assess peak separation, detect co-elution, or examine chromatographic and mass resolution.
    2 installs
63. ▌
    Retention Time Mz Feature Extraction · holobiomicslab

    Use when you have LC-HRMS profile-mode data (e.g., netCDF or mzML format) and need to convert detected or reference chromatographic peaks into fixed-size 2D arrays (rt × mz regions) to train or apply a convolutional neural network for peak classification and bounding-box prediction.
    0 installs
64. ▌
    Rust Library Compilation And Testing · holobiomicslab

    Use when when you have access to Rust source code in a repository with a Cargo manifest (Cargo.toml) and need to verify that a library's read and write APIs produce byte-equivalent or structurally equivalent output.
    0 installs
65. ▌
    Self Contained Pipeline Construction · holobiomicslab

    Use when when you have metabolomics datasets (loaded as SummarizedExperiment objects) and need to apply a sequence of data-processing and analytical steps (e.
    0 installs
66. ▌
    Smiles String Parsing And Validation · holobiomicslab

    Use when when you have SMILES strings as input to a molecular machine learning pipeline (e.g., retention time prediction, spectral prediction) and need to convert them into structured molecular representations before calculating descriptors or constructing molecular graphs.
    0 installs
67. ▌
    Sparse Inverse Covariance Estimation · holobiomicslab

    Use when when you have a feature matrix (samples × features) and need to infer sparse conditional dependencies among features—particularly when the number of features is comparable to or exceeds sample size, and you want to identify which features are directly related after accounting for all.
    5 installs
68. ▌
    Spatial Spot Coordinate Registration · holobiomicslab

    Use when when you have paired spatial transcriptome and metabolome datasets with spot-based coordinates that need to be aligned for multi-modal integration.
    2 installs
69. ▌
    Spectral Database Search And Scoring · holobiomicslab

    Use when you have preprocessed mass spectrometry data (peak-picked, baseline-corrected) from DI-MS, ASAP-MS, or LDI-MS instruments and need to identify unknown samples by comparing their spectral fingerprints against a validated reference database of known species or compounds.
    0 installs
70. ▌
    Spectral Ion Matching Across Vendors · holobiomicslab

    Use when you have raw line-scan MSI data from any supported vendor (Agilent .d, Bruker .tsf/.baf/.tdf, Thermo .raw, or .
    0 installs
71. ▌
    Spectral Peak Parent Product Pairing · holobiomicslab

    Use when you have mass spectrometry imaging data with a histogram of pairwise mass differences that have already been matched to known adducts (via adductMatch), and you need to retrieve the actual mass peak pairs corresponding to a specific adduct of interest—particularly when you want to test.
    1 install
72. ▌
    Spectral Smoothing Method Comparison · holobiomicslab

    Use when when you have raw mass spectra in an MSImagingArrays object and need to decide between Savitzky-Golay and Gaussian smoothing methods based on their effects on peak shape fidelity and baseline noise. Apply this skill when peak preservation is a priority (e.
    0 installs
73. ▌
    Spike Artifact Detection And Removal · holobiomicslab

    Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that exhibits isolated high-intensity noise artifacts or instrumental artifacts that appear as discrete, non-continuous signals in the retention time, ion mobility, or m/z dimensions.
    0 installs
74. ▌
    Stochastic Weight Averaging Ensemble · holobiomicslab

    Use when training a heavily regularized deep neural network on molecular property prediction tasks (e.g., retention time prediction) where you observe signs of overfitting despite L1/L2 penalties, or when you need to reduce variance in predictions on held-out test sets.
    2 installs
75. ▌
    Strain Correlation Score Computation · holobiomicslab

    Use when when you have paired genomics and metabolomics data from multiple strains (e.g., from Paired Omics Data Platform), have clustered BGCs into GCFs and detected molecular features, and need to score all potential GCF–MF links to prioritise true biosynthetic relationships.
    0 installs
76. ▌
    Structure Standardization Validation · holobiomicslab

    Use when you have raw or heterogeneous molecular structure inputs (SMILES strings or SDF files) that will be used for fingerprint calculation, descriptor extraction, or retention time prediction modeling.
    0 installs
77. ▌
    Tensorflow Model Metadata Inspection · holobiomicslab

    Use when deploying a TensorFlow model through TensorFlow Serving and you need to verify that the exposed model's input layer names ('input_2048' and 'input_4096') and output layer name ('output') match the specifications required by downstream code.
    2 installs
78. ▌
    Training Convergence Loss Monitoring · holobiomicslab

    Use when executing a multi-stage deep learning pipeline (pretraining → fine-tuning → alignment) where each stage loads a checkpoint from the previous stage and you need to confirm that loss is decreasing monotonically within each stage, that checkpoints are being saved, and that no training.
    0 installs
79. ▌
    Variance Stabilization Normalization · holobiomicslab

    Use when after k-nearest neighbor imputation (cutoff ≥0.6 data retention) and outlier sample removal have been completed on your MultiAssayExperiment object.
    0 installs
80. ▌
    Web Application Server Logic Mapping · holobiomicslab

    Use when you are wrapping an existing R package or analytical library in a web interface and need to connect UI form inputs (file uploads, parameter selections, configuration checkboxes) to the backend computation functions and render their outputs reactively.
    0 installs
81. ▌
    XML Spectrum Element Deserialization · holobiomicslab

    Use when when you have retrieved a decompressed XML data block from an indexed gzip file (via GSGR bracket notation) and need to convert that raw XML string into a usable Python spectrum or chromatogram object for downstream analysis, filtering, or comparison.
    0 installs
82. ▌
    Graph Builder Subclassing Squidpy · holobiomicslab

    Use when you have spatial molecular data (e.g., coordinates from microscopy or sequencing assays stored in an AnnData object), you need to compute a k-nearest-neighbor graph for spatial statistics (e.
    0 installs
83. ▌
    Moderated T Statistic Computation · holobiomicslab

    Use when you have a fitted linear model (lmFit object) from microarray, RNA-seq, qPCR, or proteomics data and need to test for differential expression across genes while maintaining statistical stability despite having few biological replicates or arrays.
    0 installs
84. ▌
    Rna Seq Abundance Matrix Handling · holobiomicslab

    Use when you have transcript-level quantification output files (quant.sf, quant.gz) from salmon, kallisto, sailfish, or oarfish and need to produce gene-level count matrices, abundance matrices, and length-based offsets for differential expression analysis in DESeq2, edgeR, or limma-voom.
    0 installs
85. ▌
    Rna Seq Quantification Validation · holobiomicslab

    Use when you have quantification output from two versions or implementations of the same tool (e.g., C++ vs. Rust rewrites, pre- and post-bugfix releases) and need to verify that they produce equivalent results before deploying the new version.
    0 installs
86. ▌
    Sam Bam Mapping Record Inspection · holobiomicslab

    Use when after quantifying the same read set with two versions of a mapping/quantification tool (e.g., C++ salmon 1.11.
    0 installs
87. ▌
    Sam Record Parsing And Validation · holobiomicslab

    Use when salmon quant is run with the --writeMappings/-z flag and you need to verify that all mapped reads appear in the SAM output file.
    0 installs
88. ▌
    Single Cell Rna Seq Normalization · holobiomicslab

    Use when immediately after loading raw single-cell gene expression count matrices (AnnData objects) and before identifying highly variable genes or performing dimensionality reduction.
    2 installs
89. ▌
    Sparse Matrix Csr Format Assembly · holobiomicslab

    Use when when you have computed k-nearest neighbor indices and distances (e.
    0 installs
90. ▌
    Spatial Statistics Interpretation · holobiomicslab

    Use when when you have a spatial molecular dataset (e.g., Visium, MERFISH) with categorical cell-type or feature annotations and want to test whether specific categories are preferentially located near or away from each other in tissue space, beyond what random spatial distribution would predict.
    0 installs
91. ▌
    Statistical Ranking Wilcoxon Test · holobiomicslab

    Use when when you have leiden or louvain cluster assignments in single-cell data (stored in adata.obs) and need to identify cluster-specific marker genes.
    0 installs
92. ▌
    Temporal Gene Expression Dynamics · holobiomicslab

    Use when you have time-ordered gene expression data (e.
    1 install
93. ▌
    Transcript Level Abundance Import · holobiomicslab

    Use when you have transcript-level quantification files (quant.sf.gz or quant.gz) from salmon, sailfish, kallisto, or oarfish and need to aggregate them into gene-level or transcript-level count, abundance, and length matrices for input to DESeq2, edgeR, or limma-voom.
    0 installs
94. ▌
    Chemical Annotation Matrix Construction · holobiomicslab

    Use when you have selected a subset of public tandem MS files from ReDU/MassIVE that have been processed through GNPS spectral library matching, and you need to organize their chemical annotations into a matrix (rows = files, columns = annotated features) before performing PCA or other multivariate.
    0 installs
95. ▌
    Electron Ionization Spectral Comparison · holobiomicslab

    Use when you have a query electron ionization (EI) mass spectrum in msp format and wish to identify it by matching against a reference spectral library. Apply this skill when you need ranked similarity scores between the query and each library entry to prioritize candidate identifications.
    2 installs
96. ▌
    Ms Spectra Extraction And Preprocessing · holobiomicslab

    Use when you have raw LC-MS/MS data in mzML or mzXML format and need to: (1) identify the top-abundance MS1 signals in an LC run, (2) compute a single scalar metric (separation efficiency) that summarizes how well compounds are resolved across the chromatogram, and (3) feed that metric into a.
    0 installs
97. ▌
    Parameter Driven Preprocessing Pipeline · holobiomicslab

    Use when you have converted mass spectrometry data in mzXML or mzML format and need to extract metabolic features via region-of-interest (ROI) search followed by preprocessing and augmentation.
    0 installs
98. ▌
    Reconstruction Algorithm Implementation · holobiomicslab

    Use when when you have raw or preprocessed mass spectrometry data (feature matrices or transient files) acquired at lower mass resolution or with signal degradation, and you possess high-resolution reference MSI data or simulated ground truth to train a reconstruction model.
    1 install
99. ▌
    Analyte Discrimination Machine Learning · holobiomicslab

    Use when you have raw chromatography–mass spectrometry data (GC-MS or LC-MS) in 2D m/z–retention time format and need to identify and discriminate multiple analytes while avoiding false peak detections inherent in conventional peak picking.
    0 installs
100. ▌
     Baseline Correction Algorithm Selection · holobiomicslab

     Use when when you have imported a raw GCxGC-MS chromatogram as a 2D-TIC (2D Total Intensity Chromatogram) object from a NetCDF file and observe steady or increasing baseline intensity caused by instrumental contamination, column bleeding, or thermal drift.
     0 installs