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HolobiomicsLab

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1. ▌
   Flux Variability Analysis Interpretation · holobiomicslab

   Use when when you have sampled the feasible flux solution space of constraint-based metabolic models (via optGpSampler or equivalent uniform sampling) and need to normalize flux predictions across reactions and cell lines for concordance analysis with transcriptomics and metabolomics data.
   0 installs
2. ▌
   Hierarchical JSON Structure Construction · holobiomicslab

   Use when your input is a tabular file (CSV or Excel) with column headers annotated using MESSES tagging syntax (#<table_name>.id for record identifiers and #.
   2 installs
3. ▌
   Internal Standard Selection Optimization · holobiomicslab

   Use when after batch correction of metabolomics QC samples using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to determine which one stabilizes the compound/internal standard ratio for each compound.
   0 installs
4. ▌
   Mass Calibration Coefficient Computation · holobiomicslab

   Use when after successfully matching at least 5 reference m/z points (from a .ref file) to spectrum peaks within a PPM error window (starting at ±1.0 ppm and widened iteratively to ±1.5, ±3, ±5, ±7, or ±10 ppm if needed).
   0 installs
5. ▌
   Mass Spectrometry Ion Formula Assignment · holobiomicslab

   Use when when you have a metabolite structure (SMILES or molecular graph) and need to predict its ionization behavior in a mass spectrometry experiment using a specific derivatizing matrix or ionization mode. Use this skill when the expected ions are non-standard (i.
   2 installs
6. ▌
   Metabolomics Study Design Interpretation · holobiomicslab

   Use when when you have received Sciex Multiquant TXT export files from a completed metabolomics or lipidomics analytical run and need to verify that QC pool samples were injected at the designed regular intervals throughout the sequence(s).
   3 installs
7. ▌
   Model Hyperparameter Transfer And Tuning · holobiomicslab

   Use when you have a trained baseline GNN model with established hyperparameters (dropout rate, learning rate, epochs, optimizer settings) and want to evaluate whether alternative message-passing GNN architectures (Graph Attention Networks, Message-Passing Neural Networks) achieve comparable or.
   0 installs
8. ▌
   Molecular Graph Construction From Smiles · holobiomicslab

   Use when you have raw SMILES strings from a chemical database (e.g., CCSBase, METLIN, or custom sources) and need to feed them into a graph neural network model.
   2 installs
9. ▌
   Pandas Dataframe Manipulation Ms Columns · holobiomicslab

   Use when when you have raw mass spectrometry data (from mzML, Bruker .d, or CSV format) loaded into a Pandas DataFrame and need to ensure it has the correct column structure (m/z, retention time, intensity) before invoking pyOpenMS-Viz plotting functions like .plot(kind='spectrum'), .
   2 installs
10. ▌
    Parallel Factor Generation From Metadata · holobiomicslab

    Use when when you have a Spectra object backed by an on-disk MS data source (e.g., MsBackendMzR reading mzML, mzXML, or CDF files) and need to process large numbers of spectra in parallel or serial chunks.
    0 installs
11. ▌
    Python Dependency Resolution And Pinning · holobiomicslab

    Use when when setting up a multi-stage bioinformatics workflow (e.g., ENPKG) that calls external tools (MZmine, Sirius, SPARQL engines) and depends on specific Python libraries; when reproducibility across team members or cloud infrastructure is required;
    0 installs
12. ▌
    Python Package Migration And Refactoring · holobiomicslab

    Use when you have a mature Python package (e.g., Mummichog 2.x) that needs to be relocated to a new GitHub organization (e.
    0 installs
13. ▌
    Quality Control Sample Outlier Detection · holobiomicslab

    Use when you have a SummarizedExperiment object containing pooled quality control samples with measured compound and internal standard peak areas.
    2 installs
14. ▌
    Strain Correlation Score Standardisation · holobiomicslab

    Use when you have computed raw strain correlation scores (based on shared strain membership) between genomic and metabolomic objects of heterogeneous sizes, and you need to compare link quality fairly across pairs with different numbers of strains.
    0 installs
15. ▌
    Structured Logging And Metric Extraction · holobiomicslab

    Use when when executing a multi-converter annotation workflow on mass spectra metadata (.
    0 installs
16. ▌
    Tanimoto Similarity Pairwise Calculation · holobiomicslab

    Use when you have a collection of molecular fingerprint vectors (such as biosynfoni count fingerprints) and need to measure structural similarity between all pairs of molecules.
    0 installs
17. ▌
    Uncertainty Quantification Rt Prediction · holobiomicslab

    Use when you have trained a DNN retention time predictor and need to rank candidate metabolites for an unknown compound: the DNN outputs both point estimates and uncertainty bounds for each candidate's RT, and you need to convert these into probabilistic scores that reflect confidence in each.
    0 installs
18. ▌
    Asynchronous Converter Job Orchestration · holobiomicslab

    Use when you have mass spectrum records in .msp format lacking computed chemical metadata (SMILES, InChI, CAS numbers, formulas, IUPAC names) and want to fetch these properties from multiple heterogeneous web services without blocking on individual API calls.
    0 installs
19. ▌
    Batch File Processing Across Directories · holobiomicslab

    Use when when you need to systematically extract a specific field or set of fields from multiple files scattered across nested directories—for example, to reconstruct an index of entry statuses from thousands of JSON annotation records, or to audit a repository's content without manually visiting.
    0 installs
20. ▌
    Benchmark Table Generation And Reporting · holobiomicslab

    Use when when you need to quantify and document the computational cost of a multi-stage analysis pipeline (such as MetaboDirect) across varying input sizes (e.
    0 installs
21. ▌
    Binary Mask Generation From Thresholding · holobiomicslab

    Use when you have imported a laser ablation ICP-MS image into pew² and need to distinguish tissue-bearing pixels from background noise or non-ablated regions.
    0 installs
22. ▌
    Ceramide Name Standardization With Regex · holobiomicslab

    Use when when downloading a lipidomics dataset from Metabolomics Workbench (e.
    2 installs
23. ▌
    Chemical Structure Annotation And Export · holobiomicslab

    Use when after executing BioTransformer's environmental microbial degradation module on a small-molecule input, when you need to capture predicted metabolites alongside the specific transformation rules applied and degradation pathway information in a format suitable for subsequent analysis.
    0 installs
24. ▌
    Chemical Structure Identifier Conversion · holobiomicslab

    Use when when you have a metabolomic dataset with heterogeneous chemical identifiers (names, InChI strings, InChIKeys, or SMILES) and need a single canonical identifier per metabolite to enable comparison across studies, detect redundant entries, or link to external chemical databases for.
    0 installs
25. ▌
    Classification Performance Visualization · holobiomicslab

    Use when you have a CSV file with predicted probabilities and true binary labels from a classification model, and you need to evaluate classification performance across decision thresholds and communicate it via a standard diagnostic plot suitable for publication or presentation.
    0 installs
26. ▌
    Cmake Build Configuration For Extensions · holobiomicslab

    Use when when you have C++ source code that needs to be wrapped as a Python extension module (e.g., pyOpenMS nanobind bindings), and you need to automate the build process via CMake to handle compilation, linking, and module artifact generation across multiple platforms (Windows, macOS, Linux).
    2 installs
27. ▌
    Comparative Abundance Heatmap Generation · holobiomicslab

    Use when when you have parsed lipid expression data (quantitative abundance measurements) organized as rows (lipid identities) and columns (experimental conditions or samples), and need to simultaneously display relative abundance levels across many lipids and conditions to identify clustering.
    2 installs
28. ▌
    Consensus Clustering Module Construction · holobiomicslab

    Use when after training a neural network model on paired microbiome-metabolome data and extracting microbe-metabolite feature attribution scores for significant interactions (e.g., at the 97.5th percentile threshold).
    1 install
29. ▌
    Deep Learning Signal Inference With Onnx · holobiomicslab

    Use when when you have a TransitionGroup structure containing normalized intensity traces (1D signal data from chromatograms or mobilograms) and you want to automatically detect peak regions with high precision by leveraging a conformer-based deep learning model.
    0 installs
30. ▌
    Deletion Reason Logging And Traceability · holobiomicslab

    Use when when processing OMSLs (Open Mass Spectra Libraries) with heterogeneous data quality, inconsistent annotations, or mixed ionmode/chromatographic modes (LC/GC), and you need to track which spectra were discarded, why, and potentially recover or reprocess them in future iterations.
    0 installs
31. ▌
    Descriptor Deduplication Across Toolkits · holobiomicslab

    Use when when computing molecular descriptors from SMILES strings using both RDKit and mordred libraries simultaneously, and you need to combine their outputs into a single feature matrix without redundant features.
    0 installs
32. ▌
    Developer Extension Point Identification · holobiomicslab

    Use when when you need to onboard developers into a modular, object-oriented codebase (such as CloMet) and want to pinpoint specific classes, abstract interfaces, or factory patterns that serve as official extension points rather than requiring developers to read through entire source trees.
    0 installs
33. ▌
    Disease Stratified Network Visualization · holobiomicslab

    Use when you have metabolite-disease correlation scores and protein association predictions from a deep learning model (such as DeepMSProfiler) and need to visualize which metabolites and proteins co-associate within specific disease groups.
    0 installs
34. ▌
    Docker Container Deployment Verification · holobiomicslab

    Use when after building and starting a Dockerized TensorFlow Serving instance (via `make server-compose` or equivalent) to validate that the model has the expected input layer names ('input_2048' and 'input_4096') and output layer name ('output') before routing live inference traffic through the.
    0 installs
35. ▌
    Enzyme Family Classification And Mapping · holobiomicslab

    Use when you have biotransformation reaction data from a curated source like EAWAG's Biodegradation and Biocatalysis Database and need to map enzyme families, reaction types, and substrate specificities into machine-readable rule formats (SMARTS patterns, condition thresholds) for automated.
    0 installs
36. ▌
    File Format Dispatch And Handler Routing · holobiomicslab

    Use when you have a parser library that must support multiple file formats (e.g., mzML, SQLite, compressed gzip) and want to avoid conditional logic scattered throughout the parsing code.
    0 installs
37. ▌
    File Interface Integration And Extension · holobiomicslab

    Use when when you need to parse mzML data stored in a format beyond the built-in mzML, mzML.
    2 installs
38. ▌
    Filter Subclass Implementation In Python · holobiomicslab

    Use when when you need to apply domain-specific or novel filtering logic to compounds during Pickaxe reaction network expansion—for example, filtering by Tanimoto similarity to targets, mass tolerance to metabolomics peaks, or custom molecular descriptors—and the built-in filters do not meet your.
    0 installs
39. ▌
    Fingerprint Similarity Computation Rdkit · holobiomicslab

    Use when when implementing a similarity-based filter for Pickaxe compound expansion that must retain or remove candidates based on their structural resemblance to a target compound set.
    2 installs
40. ▌
    Ft Icr Spectrum Recalibration Validation · holobiomicslab

    Use when after applying mass calibration functions (LedFord, linear, or quadratic equations) to an FT-ICR transient or magnitude-mode dataset, before running SearchMolecularFormulas. Specifically, validate recalibration when: (1) comparing recalibrated spectra against reference calibration files (e.
    0 installs
41. ▌
    Gradient Flow Backpropagation Validation · holobiomicslab

    Use when after implementing a multi-task fusion module (such as FuseBlock) that combines feature tensors from multiple prediction branches (e.g., isotope, charge, retention-time) and must verify that backpropagation signals flow from the fused representation to each upstream branch.
    0 installs
42. ▌
    Graph Neural Network Architecture Design · holobiomicslab

    Use when you have molecular structures that need to be represented as both fingerprint vectors (fixed-length chemical descriptors) and graph-structured data, and you need a model that can learn from both representations simultaneously to predict a continuous molecular property (e.
    0 installs
43. ▌
    Hierarchical Dataset Metadata Extraction · holobiomicslab

    Use when when you have received an MZA-format HDF5 file (or other hierarchical HDF5-based scientific data) and need to understand its internal structure before downstream processing, share it across programming languages (Python, R), or document its schema for reproducibility.
    0 installs
44. ▌
    High Resolution Spot To Spot Integration · holobiomicslab

    Use when you have two spatial omics datasets (e.g., spatial transcriptome and metabolome spot matrices) collected from the same or adjacent tissue sections, with both feature matrices (X: np.ndarray) and spatial coordinates (D: np.ndarray containing location information in .
    2 installs
45. ▌
    Hnsw Graph Construction And Optimization · holobiomicslab

    Use when when you have pre-computed Word2vec spectrum embeddings and need to perform fast approximate nearest-neighbor retrieval from a library of millions of spectra (e.g., NIST 2017, MassBank, or in-silico predicted spectra).
    0 installs
46. ▌
    Infrared Spectral Prediction Task Design · holobiomicslab

    Use when when you have a dataset of molecules with experimentally measured or simulated infrared spectra and want to train a graph neural network to predict spectral features (e.g., absorption peaks, intensities) from molecular structure.
    0 installs
47. ▌
    Internal Standard Optimization Selection · holobiomicslab

    Use when you have preprocessed metabolomics data with multiple candidate internal standards and QC (Quality Control) sample replicates, and you need to assign a single internal standard per compound that will minimize measurement variability across batches.
    0 installs
48. ▌
    K Nearest Neighbor Algorithm Application · holobiomicslab

    Use when your raw metabolomics dataset contains missing values scattered across metabolite columns, and you intend to perform statistical analysis (e.g., linear mixed models, ANOVA, or dimensionality reduction) that requires complete observations.
    0 installs
49. ▌
    Lc Gradient Vector Encoding And Decoding · holobiomicslab

    Use when when preparing LC gradient configurations for Bayesian optimization, or when converting predicted optimal vectors back into actionable LC instrument parameters. Specifically, use this skill when you have a set of gradient parameters to optimize (e.
    0 installs
50. ▌
    Linear Model Design Matrix Specification · holobiomicslab

    Use when when preparing to perform differential abundance analysis on batch-corrected lipid abundance matrices in designs with multiple factors (e.g., treatment × time, multi-group comparisons), repeated measures, or blocking structures.
    2 installs
51. ▌
    Local Statistics Median Mean Computation · holobiomicslab

    Use when you have raw LA-ICP-MS image data containing potential spike outliers (e.g., instrumental noise, ablation irregularities) and need to establish a local reference statistic for each pixel.
    0 installs
52. ▌
    Logical Operator Precedence In Gpr Rules · holobiomicslab

    Use when when computing Reaction Activity Scores (RAS) from transcriptomics data linked to a metabolic model via GPR associations, and the model contains reactions governed by mixed AND/OR logical rules (e.g., '(gene_A AND gene_B) OR gene_C').
    2 installs
53. ▌
    M Z And Retention Time Window Validation · holobiomicslab

    Use when before committing to full-scale targeted peak integration across all LC–MS runs in a metabolomics or lipidomics study. Apply this skill when you have a curated list of 5–50+ target compounds with theoretical m/z values and expected retention times, centroided .
    0 installs
54. ▌
    Mass Spectrometry Spectral Preprocessing · holobiomicslab

    Use when you have raw mass spectrometry spectra from an unknown analyte or a synthetic compound library and need to feed them into PS2MS or similar deep learning classifiers for NPS detection.
    2 installs
55. ▌
    Mass Spectrometry Spectrum Preprocessing · holobiomicslab

    Use when when you have raw LC–QTOF wastewater spectra (or other real experimental mass spectrometry data) and need to feed them into a pretrained MSGO model for molecular structure prediction.
    0 installs
56. ▌
    Metabolism Prediction Result Aggregation · holobiomicslab

    Use when when you have run CypReact predictions on a molecular dataset against multiple CYP isoforms (e.g., 1A2, 2A6, 2B6) and need to consolidate the per-isoform output files into a single combined result file for cross-isoform comparison, visualization, or downstream metabolite identification.
    1 install
57. ▌
    Metabolite Network Diffusion Propagation · holobiomicslab

    Use when after cluster-based filtering of KEGG candidates has produced a set of candidate metabolites with assigned scores, but before final annotation ranking.
    2 installs
58. ▌
    Metabolite Ranking By Network Centrality · holobiomicslab

    Use when when you have a directed metabolic network (digraph) and want to identify which metabolites are most central to observed perturbations; specifically when you have (1) a global network as an edge list, (2) seed nodes with known or hypothesized perturbation (e.
    0 installs
59. ▌
    Metabolomic Data Subsetting By Phenotype · holobiomicslab

    Use when you have a preprocessed MultiAssayExperiment with metabolite measurements across multiple phenotypic or disease subgroups, and you want to isolate one or more groups for comparison—for example, to compare AKT1-high versus MYC-high prostate tumor samples before applying diff_test for.
    0 installs
60. ▌
    Metabolomics Batch Correction Evaluation · holobiomicslab

    Use when when you have log2-transformed metabolomics data with known batch assignments and biological groupings, and you need to validate that a batch correction method (such as CordBat) has successfully removed batch-driven variation without collapsing true group differences in metabolite.
    0 installs
61. ▌
    Metabolomics Group Comparison Statistics · holobiomicslab

    Use when you have a metabolomics matrix with metabolites as rows and samples as columns, each sample labeled with one of two experimental group identifiers (e.
    0 installs
62. ▌
    Metabolomics Library Generation Pipeline · holobiomicslab

    Use when when you have cloned or accessed the Reverse_metabolomics_library_generation repository and need to verify that the Nextflow workflow is properly configured, executable, and produces expected spectral library outputs.
    0 installs
63. ▌
    Metabolomics Preprocessing Normalization · holobiomicslab

    Use when you have acquired raw SIMS (secondary ion mass spectrometry) metabolite images aligned with tissue regions and segmented single-cell masks, and you need to extract normalized metabolite intensity values per cell before performing cell-type assignment, VAE embedding, or protein–metabolite.
    0 installs
64. ▌
    Missing Value Imputation Method Dispatch · holobiomicslab

    Use when you have a metabolomics data matrix with missing-not-at-random (MNAR) left-censored values and need to apply multiple imputation methods to the same data in a standardized way, compare their outputs, or integrate the imputation step into a larger pre-processing pipeline.
    2 installs
65. ▌
    Molecular Formula Parsing And Validation · holobiomicslab

    Use when you have received a formula-assigned FT-ICR MS dataset (CSV or tab-delimited table containing molecular formulas and mass values) and need to convert those formula strings into quantified elemental compositions before computing molecular descriptors, diversity indices, or transformation.
    2 installs
66. ▌
    Molecular Structure File Format Handling · holobiomicslab

    Use when when you have molecular structures in one format (e.g., SMILES strings in a spreadsheet or text file) but need to feed them to a tool that accepts a different format (e.g., CypReact requires .sdf or .csv with SMILES).
    1 install
67. ▌
    Multiassayexperiment Object Manipulation · holobiomicslab

    Use when when you have parsed metabolite measurements into a table (rows = metabolites, columns = samples) and have corresponding sample-level covariates (e.g., disease status, treatment group) and/or feature-level annotations (e.
    0 installs
68. ▌
    Parametric Nonparametric Model Selection · holobiomicslab

    Use when you have preprocessed, log₂-scaled metabolomics data in CSV format (samples × features) with batch assignment labels and need to decide which batch effect correction model to apply.
    2 installs
69. ▌
    Pixel Intensity Scaling And Thresholding · holobiomicslab

    Use when after normalizing an MSI pixel array to TIC or an internal standard, when the raw pixel intensity distribution spans multiple orders of magnitude and produces images with poor contrast or where extreme outlier intensities would wash out spatial detail.
    0 installs
70. ▌
    Polymorphic Method Dispatch On Plot Kind · holobiomicslab

    Use when when building a plotting library that must support multiple visualization types (1D spectra, chromatograms, mobilograms, 2D peak maps) across heterogeneous rendering backends, and you want users to specify plot type via a single kind parameter rather than importing backend-specific classes.
    2 installs
71. ▌
    Psm Spectrum Identifier Regex Extraction · holobiomicslab

    Use when when you have PSM identifications from a search engine (e.
    2 installs
72. ▌
    Publication Figure Formatting And Export · holobiomicslab

    Use when after generating initial visualizations (volcano plots, heatmaps, box plots, or bar plots) of lipid expression data, apply this skill when figures must be submitted to journals, supplementary materials, or presentations and must meet publication-quality standards for axes labels, legends.
    2 installs
73. ▌
    Python Environment Dependency Resolution · holobiomicslab

    Use when when you have cloned a Python project repository and need to set up a working environment with all required packages, or when requirements.txt exists but dependencies are not yet installed in your current Python environment.
    0 installs
74. ▌
    Qt Application Compilation And Packaging · holobiomicslab

    Use when you have a Qt5-based C++ GUI application source tree (e.g., Maven GUI) that must be compiled and packaged for end-user distribution across macOS and Windows platforms, especially when automated builds are managed by CI/CD services (AppVeyor, Travis).
    0 installs
75. ▌
    Quality Control Sample Ratio Calculation · holobiomicslab

    Use when you have preprocessed metabolomics data stored in a SummarizedExperiment object containing QC sample measurements, assigned internal standards for compounds, and evidence of batch effects.
    0 installs
76. ▌
    R Data Frame Construction And Validation · holobiomicslab

    Use when when you have instrument-exported text files (e.g., Sciex MultiQuant txt format) containing QCpool sample measurements, metadata, and timestamps that need to be converted into a reproducible, schema-validated R object for metabolomics or lipidomics quality overview analysis.
    0 installs
77. ▌
    Retention Time Normalization And Scoring · holobiomicslab

    Use when you have XCMS-aligned feature tables with retention time values and need to compute pairwise feature similarity.
    0 installs
78. ▌
    Sampletype Phenotype Stratified Plotting · holobiomicslab

    Use when after loading and normalizing a LipidomicsExperiment object with logged Area measurements, when you need to assess whether clinical sample groups (e.
    0 installs
79. ▌
    Screening Performance Metric Computation · holobiomicslab

    Use when after running inference with a pre-trained or fine-tuned NaFM model on a virtual screening dataset (compounds with known bioactivity labels or ground truth), compute screening-specific performance metrics to evaluate retrieval and ranking capability.
    2 installs
80. ▌
    Sequence To Sequence Architecture Design · holobiomicslab

    Use when when you have encoder-produced fixed-size embeddings and need to generate variable-length discrete sequences (e.g., SMILES tokens, protein sequences, chemical formulas) as outputs.
    2 installs
81. ▌
    Similarity Score Computation For Spectra · holobiomicslab

    Use when you have a preprocessed unknown sample spectrum (m/z peaks and intensities) and need to identify the most likely species or reference entries by scoring it against a database of known spectra.
    2 installs
82. ▌
    Singular Value Decomposition Application · holobiomicslab

    Use when you have a metabolite intensity matrix (samples × metabolites, log₂-transformed and standardized) and pathway definitions (pathway IDs mapped to metabolite sets), and you need to score pathway activity across samples in a way that tolerates noise and missing peaks.
    0 installs
83. ▌
    Spans Centering Procedure Implementation · holobiomicslab

    Use when normalizing peptide or protein-level quantification matrices in proteomics workflows and you need to center the data but lack domain knowledge to manually select among mean, median, geometric mean, or robust centering methods.
    0 installs
84. ▌
    Spectral Library Annotation Augmentation · holobiomicslab

    Use when you have a GNPS DBResult file containing spectral library matches with InChIKey identifiers but lacking ClassyFire ontology columns (superclass, class, subclass), and you need to restore this taxonomic context for consensus classification or chemical ontology annotation workflows.
    0 installs
85. ▌
    Spectral Peak Filtering By Mass Accuracy · holobiomicslab

    Use when after molecular formula assignment has been performed on FT-ICR MS peaks (e.g., by Formularity or CoreMS), and before calculating thermodynamic indices, compound class assignments, or statistical analysis.
    0 installs
86. ▌
    Spectrum Filtering With Deletion Logging · holobiomicslab

    Use when processing heterogeneous mass spectrometry libraries (e.g., from OMSLs) where chemical identifiers are unevenly populated across records.
    0 installs
87. ▌
    Sub Network Detection From Scored Graphs · holobiomicslab

    Use when you have a GLASSO-inferred sparse network graph and associated PCA scores (e.g., from prior dimension reduction of omics or imaging data), and you need to identify which nodes cluster together based on both their PCA score patterns and their connectivity in the graph.
    0 installs
88. ▌
    Tomcat Application Server Initialization · holobiomicslab

    Use when when you need to deploy a Java web application packaged in a Tomcat Docker container to a specified HTTP endpoint, and must verify that the container starts successfully, the Tomcat server initializes, and the application becomes accessible at the mapped host port before proceeding with.
    2 installs
89. ▌
    Transformation Network Topology Analysis · holobiomicslab

    Use when when you have pre-processed FT-ICR MS peak lists with assigned molecular formulas and wish to move beyond univariate chemical composition analysis to understand metabolic transformation pathways and hub metabolites.
    0 installs
90. ▌
    U13c Labeled Standard Reference Matching · holobiomicslab

    Use when you have IM-MS measurements of samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract) and need to assess whether measured CCS values systematically deviate from their true reference values.
    0 installs
91. ▌
    Unit Test Design For Biochemical Filters · holobiomicslab

    Use when after implementing a custom Filter subclass (e.g., MetabolomicsFilter, TanimotoFilter) in minedatabase/filters.py, you must write unit tests to validate that _choose_cpds_to_filter correctly identifies compounds to retain/remove.
    0 installs
92. ▌
    Validated Dataset Integrity Verification · holobiomicslab

    Use when you have received a validated dataset (e.g., interim/tables/4_analysed/platinum.tsv.
    0 installs
93. ▌
    Gcms Deconvolution Identification Workflow · holobiomicslab bundle

    Use when you have GC-MS data (mzML / CDF, typically EI) and want deconvolved, retention-index-validated compound identifications — spectral deconvolution of co-eluting peaks, EI library matching, RI calibration, and differential analysis.
    0 installs
94. ▌
    Adaptive Prior Distribution Selection · holobiomicslab

    Use when after running DESeq() and extracting raw results with results(), when you have log fold change estimates with high variance and wish to improve their precision.
    0 installs
95. ▌
    Buffer Management And Flush Protocols · holobiomicslab

    Use when when quantifying or mapping RNA-seq reads with salmon quant using the --writeMappings (-z) flag, or in any streaming output scenario where record count discrepancies appear between reported totals (e.g., NumReads in quant.sf) and file contents (SAM record count).
    1 install
96. ▌
    Differential Gene Expression Analysis · holobiomicslab

    Use when when you have RNA-seq count matrices (from HTSeq, featureCounts, Salmon, kallisto, or RSEM quantification) and need to test for differential expression between two or more treatment groups.
    2 installs
97. ▌
    Gene Length Offset Matrix Computation · holobiomicslab

    Use when you have transcript-level quantification (salmon, Sailfish, or kallisto output) summarized to gene level by tximport, and you observe or suspect differential isoform usage across your experimental conditions.
    0 installs
98. ▌
    K Nearest Neighbor Graph Construction · holobiomicslab

    Use when after PCA dimensionality reduction and scaling of normalized, log-transformed gene expression data, when you need to identify local cell neighborhoods (typically with k=15 neighbors) before applying clustering algorithms like Leiden or computing UMAP embeddings.
    0 installs
99. ▌
    Pathway Activity Correlation Analysis · holobiomicslab

    Use when when you have run gene set enrichment analysis (e.
    0 installs
100. ▌
     Pearson Correlation Analysis Genomics · holobiomicslab

     Use when when comparing transcript quantification outputs (NumReads counts, abundance estimates) from two mapper implementations (e.
     0 installs