← all publishers

HolobiomicsLab

@holobiomicslab source repo

Report this profile Claim this profile

• 11k skills
• 0 followers
• last month last updated

1. ▌
   Retention Time Feature Distribution Analysis · holobiomicslab

   Use when you have extracted retention times from top MS1 features in an LC-MS/MS experiment and need to assess whether the gradient configuration (start and end time in minutes) achieves adequate compound separation across the full chemical space.
   0 installs
2. ▌
   Sample Metadata Stratification And Filtering · holobiomicslab

   Use when when you have retrieved a large, heterogeneous collection of tandem MS files from ReDU or MassIVE and need to isolate a subset sharing specific sample characteristics (e.
   0 installs
3. ▌
   Sample To Reference Retention Time Remapping · holobiomicslab

   Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for each sample during prior alignment steps.
   0 installs
4. ▌
   Sequential Tool Integration And Data Routing · holobiomicslab

   Use when when you have raw LC-HRMS metabolomics data in .mzML or .
   0 installs
5. ▌
   Spectral Match Scoring Algorithm Development · holobiomicslab

   Use when when building or extending MS/MS library search tools that must re-rank top candidate spectra (e.g., top 2000 from MS2Deepscore) to identify the analogue or exact match.
   2 installs
6. ▌
   Spectral Noise Filtering And Quality Control · holobiomicslab

   Use when you have raw MS/MS spectra in multiple formats (.mgf, .msp, .mzML) that contain background noise, instrument artifacts, or low-abundance fragments that would degrade downstream LDA motif discovery.
   0 installs
7. ▌
   Spectral Peak Filtering By Quality Threshold · holobiomicslab

   Use when you have raw or annotated MS/MS spectra (in MGF, mzML, or mzXML format) destined for de novo peptide sequencing with Casanovo. Use it specifically when your dataset contains variable spectral quality (e.
   0 installs
8. ▌
   Spectral Scoring And Significance Assessment · holobiomicslab

   Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) against a chemical structure database of known natural products, and you need to: (1) identify which pipeline(s).
   2 installs
9. ▌
   Spectral Similarity Prediction Deep Learning · holobiomicslab

   Use when when you have paired MS/MS spectra (unknown and known metabolites) with annotated structural similarity labels, and you need to rank candidate structures for metabolite identification.
   0 installs
10. ▌
    Spectrum Preprocessing Binning Normalization · holobiomicslab

    Use when when preparing raw MS/MS spectra for input to a Siamese neural network trained to predict structural similarity scores (Tanimoto).
    0 installs
11. ▌
    SQL Query Optimization For Similarity Search · holobiomicslab

    Use when when migrating spectral library data from file-based formats (JSON, CSV, binary) into a persistent store and need to support fast filtered queries on metadata and similarity computations against query spectra.
    2 installs
12. ▌
    Sterol Structure Representation And Curation · holobiomicslab

    Use when when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or collision cross section (CCS) prediction workflows.
    0 installs
13. ▌
    Tandem Mass Spectrometry Data Interpretation · holobiomicslab

    Use when you have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation and identification at systems scale.
    0 installs
14. ▌
    Unit Test Coverage For Conditional Workflows · holobiomicslab

    Use when when refactoring or adding workflow branching logic that routes spectral results into separate processing paths (e.
    0 installs
15. ▌
    Vimms Controller Configuration And Execution · holobiomicslab

    Use when you have a set of chemical compounds (with known retention times and intensities) loaded into a ViMMS IndependentMassSpectrometer and need to simulate a specific MS/MS fragmentation strategy (e.
    0 installs
16. ▌
    Confounder Adjustment Epidemiological Analysis · holobiomicslab

    Use when when testing associations between metabolic features (from NMR or MS) and a phenotype of interest (e.g., BMI, disease status) in a cohort where age, gender, or clinical confounders are known to correlate with both the metabolite and phenotype.
    0 installs
17. ▌
    Fid To Frequency Domain Fourier Transformation · holobiomicslab

    Use when after simulating and convolving individual metabolite multiplets with realistic lineshapes (Lorentzian or Gaussian) and combining them into a single time-domain FID array.
    0 installs
18. ▌
    Metabolite Stability Assessment Across Cohorts · holobiomicslab

    Use when you have uploaded a pre-analytical data table containing sample metadata, processing timestamps (pre- and post-centrifugation), and NMR metabolomic measurements for a cohort of peripheral blood samples (plasma/serum), and you need to quantify the magnitude and direction of metabolite.
    0 installs
19. ▌
    Transformer Attention Mechanism Implementation · holobiomicslab

    Use when you have a sequence-to-structure prediction task where: (1) inputs are token sequences or embeddings representing molecular fragments or spectral data; (2) outputs are structured molecular representations (adjacency matrices for connectivity, formula vectors);
    0 installs
20. ▌
    Chromatin Accessibility Variability Ranking · holobiomicslab

    Use when you have sparse, single-cell or bulk ATAC/DNAse-seq data from multiple cell types or conditions (e.g., GM vs H1 cell lines), pre-filtered and GC-bias-corrected, with motif-to-peak matches already computed.
    0 installs
21. ▌
    Cpg Base Filtering By Statistical Threshold · holobiomicslab

    Use when after calculateDiffMeth() has been run on a methylBase object and you have a methylDiff object with q-values and methylation difference estimates.
    0 installs
22. ▌
    Juicer Pipeline Configuration And Execution · holobiomicslab

    Use when you have raw Hi-C FASTQ files from a high-throughput chromatin conformation capture experiment and need to generate a normalized contact matrix (.hic file) for downstream genomic analysis.
    0 installs
23. ▌
    Local Background Estimation Multiple Scales · holobiomicslab

    Use when when performing ChIP-Seq peak calling with MACS3, after duplicate filtering and fragment length prediction (d), to construct the background model that will be compared against ChIP signal.
    0 installs
24. ▌
    Method Comparison Statistical Summarization · holobiomicslab

    Use when you have extracted clustering or classification accuracy metrics (NMI, ARI, purity scores) for two or more competing methods evaluated on multiple datasets, and need to determine which method performs overall rather than on individual datasets alone.
    0 installs
25. ▌
    Single Cell Atac Fragment Import Processing · holobiomicslab

    Use when you have aligned single-cell ATAC-seq data as BAM files or fragment files (TSV format with genomic coordinates) and need to prepare it for spectral embedding, clustering, and peak calling. This is the entry point after alignment but before any dimension reduction or statistical analysis.
    0 installs
26. ▌
    Singular Value Decomposition Interpretation · holobiomicslab

    Use when after loading and normalizing a beta-valued methylation matrix (450K or EPIC array), apply SVD interpretation when you need to assess whether observed variation is driven by batch effects rather than biological signal, or when you want to determine the true dimensionality of latent.
    0 installs
27. ▌
    Software Environment Containerization Setup · holobiomicslab

    Use when you have a bioinformatics pipeline (like HiC-Pro) with mixed Python, R, and compiled tool dependencies, and you need to ensure consistent reproducibility across machines and team members without manual per-tool installation. Use this when dependencies include version-pinned libraries (e.
    0 installs
28. ▌
    Spectral Embedding Scalability Benchmarking · holobiomicslab

    Use when you have a large single-cell count matrix (≥10 million cells) in CSR format and need to verify whether the matrix-free spectral embedding in SnapATAC2 achieves its documented linear scaling behavior on your hardware and dataset characteristics.
    2 installs
29. ▌
    Annotation Coverage Statistics Computation · holobiomicslab

    Use when you have run MSMetaEnhancer's annotate_spectra() method on a .
    0 installs
30. ▌
    Binary Format Specification Implementation · holobiomicslab

    Use when you have a compressed file format (e.g., igzip) with a custom binary header structure that encodes metadata (index-to-offset mappings) in a fixed layout, and you need to parse or generate compliant files.
    0 installs
31. ▌
    Compute Converter Interface Implementation · holobiomicslab

    Use when you need to add a new local chemical structure conversion capability to MSMetaEnhancer when existing web-service converters (CTS, CIR, PubChem) are unavailable, too slow, or unsuitable for your workflow, and you have a chemical transformation (e.
    0 installs
32. ▌
    Cross Platform Software Capability Mapping · holobiomicslab

    Use when you are designing a new tool for FT-ICR MS analysis (or similar high-resolution mass spectrometry domain) and need to understand which analytical and visualization features are already implemented in competing or complementary tools (e.
    0 installs
33. ▌
    Data Serialization Format Interoperability · holobiomicslab

    Use when you have a new or draft file format specification (e.g., mzPeak) with multiple independent language implementations, and you need to verify that all readers agree on the structured data they extract before recommending the format for production use.
    0 installs
34. ▌
    Descriptor Fingerprint Feature Engineering · holobiomicslab

    Use when use when the workflow requires descriptor-fingerprint-feature-engineering.
    2 installs
35. ▌
    Git Repository Cloning And Version Control · holobiomicslab

    Use when when you need to reproduce a computational workflow described in a GitHub repository, validate CI/CD pipeline definitions (e.g., GitHub Actions workflows), inspect source code structure, or execute local versions of automated tests.
    0 installs
36. ▌
    Igzip Compression And Indexed Block Format · holobiomicslab

    Use when you have mzML mass spectrometry files that need both compression and rapid random access by spectrum ID (e.g., direct retrieval of spectrum 2540 without sequential scanning).
    0 installs
37. ▌
    Mass Spectrometry Data Parsing Mzml Bruker · holobiomicslab

    Use when you have raw mass spectrometry data in mzML or Bruker .d format and need to ingest it into a tabular format (pandas DataFrame) for visualization, statistical analysis, or integration with other Python-based mass spectrometry tools.
    0 installs
38. ▌
    Mass Spectrometry Plot Type Specialization · holobiomicslab

    Use when you have a Pandas DataFrame containing mass spectrometry data (e.
    0 installs
39. ▌
    Metabolic Regulation Classification Scheme · holobiomicslab

    Use when when you have computed Reaction Activity Scores (RAS) from transcriptomics and GPR rules, Reaction Presence Scores (RPS) from RAS normalized flux predictions, and Flux Fold-change Distributions (FFD) from metabolomic data and mass-action constraints across multiple sample pairs, and you.
    0 installs
40. ▌
    Metabolite Prediction Correlation Analysis · holobiomicslab

    Use when after training a neural network or regression model to predict metabolomic profiles from microbiome data.
    2 installs
41. ▌
    Metabolite Set File Parsing And Validation · holobiomicslab

    Use when when a user has prepared a custom collection of metabolite sets (e.g., from spectral fragmentation clustering, literature curation, or domain-specific grouping) in CSV or JSON format and wants to score their activity levels using PALS without modifying the core PALS codebase.
    0 installs
42. ▌
    Metabolomics Quality Metric Interpretation · holobiomicslab

    Use when after batch correction of metabolomics data using pooled study quality control (SQC) samples and calculation of compound/internal standard ratios, when you need to decide which compounds are reliable for reporting and which internal standard minimizes technical variation (RSDQC) for each.
    0 installs
43. ▌
    Precursor Peptide Extraction From Clusters · holobiomicslab

    Use when you have assembled genome FASTA sequences (from SPAdes, metaSPAdes, or antiSMASH output) and need to systematically identify precursor peptides corresponding to a target RiPP class before constructing the structure database for dereplication.
    2 installs
44. ▌
    Python Package Installation And Management · holobiomicslab

    Use when when you need to validate that a Python package (or update to it) is accessible to end users through official distribution channels, or when you are preparing a release and need to confirm that installation from PyPI and/or Bioconda does not introduce import failures or missing.
    0 installs
45. ▌
    R Object Size Measurement And Benchmarking · holobiomicslab

    Use when evaluating alternative implementations of data storage or retrieval strategies in R objects—specifically when deciding whether to eagerly populate all columns in a data frame slot (e.
    0 installs
46. ▌
    Reference Peak Matching And Fallback Logic · holobiomicslab

    Use when when performing m/z domain calibration on FT-ICR or high-resolution MS data and the initial calibration attempt finds fewer than 5 reference m/z matches within the standard PPM window (typically ±1–5 ppm).
    0 installs
47. ▌
    Regression Model Validation Quantification · holobiomicslab

    Use when when you have fitted one or more regression models (linear or polynomial) to external calibration standards in MS data and need to verify model adequacy before applying it to unknown samples.
    0 installs
48. ▌
    Spectra Variable Initialization Strategies · holobiomicslab

    Use when when designing or configuring an MsBackend subclass (e.
    0 installs
49. ▌
    Stochastic Weight Averaging Implementation · holobiomicslab

    Use when training a deeply regularized deep neural network on a large molecular feature dataset (e.
    0 installs
50. ▌
    Wine Environment Initialization Validation · holobiomicslab

    Use when use this skill after building a Docker image that installs Wine and .NET Framework 4.8 on a Ubuntu 22.04 base, but before running production conversion tasks or batch jobs with AirdPro.
    0 installs
51. ▌
    API Query Routing Conditional Per Database · holobiomicslab

    Use when when you have a chemical structure query (as a SMILES string or molecular identifier) and need to search across multiple external chemical repositories simultaneously, but only some repositories are relevant for your specific compound class (e.
    0 installs
52. ▌
    CI CD Pipeline Configuration And Execution · holobiomicslab

    Use when when you have a multi-platform Qt5 C++ project (Windows, macOS, Linux) that requires automated compilation and executable packaging across different operating systems.
    0 installs
53. ▌
    Classification Workflow Parameter Toggling · holobiomicslab

    Use when gNPS has stopped supplying ClassyFire ontology information for your spectral library matches, or when ClassyFire data is missing for in silico structural annotations.
    0 installs
54. ▌
    Cluster Assignment Extraction And Labeling · holobiomicslab

    Use when after executing hierarchical clustering via Sample_Separation() with method='HCA' on a feature-by-sample metabolomic matrix, when you need to assign each sample to a discrete cluster group (typically k=2 clusters) for use in marker identification, batch effect assessment, or sample.
    0 installs
55. ▌
    Cluster Validation Cdf Threshold Selection · holobiomicslab

    Use when when you have generated multiple biclusters or clusterings from ensemble models (e.g., 100 trained neural network models via cross-validation) and need to select an objective cluster number k without manual inspection.
    0 installs
56. ▌
    Cnn Architecture Design For Chromatography · holobiomicslab

    Use when you have LC-HRMS profile-mode chromatograms with ground-truth peak annotations (reference features) and need to detect peaks in new samples with high sensitivity and specificity, especially when peaks exhibit variable morphology (left/right isomers), overlapping background signals.
    0 installs
57. ▌
    Compound Library Construction And Curation · holobiomicslab

    Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate, octanal, undecane) and need to evaluate them against reference compound categories, or when you want to restrict structural matching to specific compound type sets (e.
    2 installs
58. ▌
    Computational Reproducibility Verification · holobiomicslab

    Use when you have access to both raw data (deposited in a repository like Zenodo) and analysis scripts (in a GitHub repository), and you need to confirm that the published figures, tables, or quantitative findings are reproducible.
    2 installs
59. ▌
    Conditional Threshold Logic Implementation · holobiomicslab

    Use when when visualizing numeric columns with unknown or highly variable ranges, and the visualization quality depends on parameter selection tied to data statistics. Specifically: after loading a numeric column (e.
    0 installs
60. ▌
    Contrastive Learning Objective Formulation · holobiomicslab

    Use when when pre-training a graph neural network on a domain-specific molecular corpus (natural products vs. synthetic molecules) where you need to capture both evolutionary relationships encoded in molecular scaffolds and diverse structural variations in side-chains, and when supervised learning.
    0 installs
61. ▌
    Core Node Identification From Perturbation · holobiomicslab

    Use when you have a directed metabolic network (digraph) with node perturbation data (e.g., from metabolomics fold-changes or experimental treatment effects) and you need to identify which nodes are core drivers of the observed perturbation.
    2 installs
62. ▌
    Data Lineage Preservation In Etl Pipelines · holobiomicslab

    Use when when consolidating entries from multiple heterogeneous source databases into a unified table, and you need to maintain auditable connections between final curated records and their original source entries.
    0 installs
63. ▌
    Decoy Database Generation For Metabolomics · holobiomicslab

    Use when performing large-scale untargeted metabolomics annotation where you need to estimate the false discovery rate of metabolite identifications.
    2 installs
64. ▌
    Deep Learning Model Input Layer Adaptation · holobiomicslab

    Use when you have a trained deep-learning model (e.g., MSNovelist) that depends on a specific fingerprint format (e.g., SIRIUS 6 fingerprints) as input, but you want to substitute an alternative fingerprint prediction system (e.
    0 installs
65. ▌
    Differential Metabolite Abundance Analysis · holobiomicslab

    Use when you have raw metabolomics data structured as a matrix with metabolites as rows and samples as columns, samples are annotated with group labels (e.
    2 installs
66. ▌
    Dotnet Framework Compilation In Containers · holobiomicslab

    Use when you have a C# GUI application targeting .NET Framework 4.8 (Windows-only) and need to execute it on macOS or Linux hosts without modifying the source code. The application requires compilation from source and GUI display support via X11 forwarding or headless CLI execution.
    0 installs
67. ▌
    Environmental Degradation Pathway Analysis · holobiomicslab

    Use when you have a target compound (in SMILES or structure format) and need to predict what metabolites will form via environmental microbial biotransformation, including the reaction types and parent–product relationships.
    0 installs
68. ▌
    Evolutionary Pattern Encoding In Molecules · holobiomicslab

    Use when when building or fine-tuning a molecular representation model intended for natural product mining, taxonomy classification, or bioactivity prediction, and you have access to natural product SMILES data with scaffold and side-chain structural annotations.
    2 installs
69. ▌
    Experimental Predicted Fragment Comparison · holobiomicslab

    Use when when you have downloaded or retrieved fragment records from both experimental and predicted fragment databases as part of the DNA adductomics resource, and you need to verify that all fragments can be successfully mapped to their parent compound entries in the reference SDF-format compound.
    2 installs
70. ▌
    False Discovery Rate Estimation Untargeted · holobiomicslab

    Use when performing untargeted metabolomics annotation (i.e., matching observed spectra to a compound database without a pre-defined target list) and you need to assign statistical significance or confidence to candidate metabolite identifications.
    0 installs
71. ▌
    Fragment Record Cross Reference Validation · holobiomicslab

    Use when you have downloaded fragment records from separate experimental and predicted fragment databases and need to verify that every fragment can be traced back to a valid compound entry in the reference SDF-format compound database, particularly when integrating multiple database sources into a.
    0 installs
72. ▌
    Genome Scale Model Validation And Curation · holobiomicslab

    Use when you have multiple draft genome-scale metabolic reconstructions in standard formats (JSON, XML, SBML) representing individual community members or assembly variants, and you need to verify they are structurally sound and consistently annotated before merging them into a consensus model or.
    0 installs
73. ▌
    Ggplot2 Multivariate Scatter Visualization · holobiomicslab

    Use when after performing PCA (or other dimensionality reduction) on a metabolite matrix, when you need to visualize whether batch effects are present in uncorrected data, or whether a batch correction method (e.
    0 installs
74. ▌
    Hierarchical Clustering Dendrogram Cutting · holobiomicslab

    Use when after XCMS feature detection, grouping, retention time correction, and missing value filling have produced an aligned feature matrix, when you need to group features (m/z, retention time pairs) that likely originate from the same metabolite.
    2 installs
75. ▌
    Hierarchical Metabolite Annotation Mapping · holobiomicslab

    Use when you have a metabolomics count data frame with metabolite identifiers (e.g., compound IDs, KEGG IDs) and wish to organize them into functional or taxonomic hierarchies for class-based statistical testing, fold-change stratification, or visualization by metabolic pathway or organism type.
    0 installs
76. ▌
    Imputation Performance Metrics Calculation · holobiomicslab

    Use when when you have imputed a metabolomics dataset using multiple MNAR (missing not at random) imputation methods and possess the ground-truth values (from simulation or manual retrieval).
    0 installs
77. ▌
    Ion Image Augmentation Intensity Dependent · holobiomicslab

    Use when training a contrastive encoder on mass spectrometry imaging (MSI) data in ISO mode (isotope ions from the same molecule).
    0 installs
78. ▌
    Isoform Sequence Extraction And Formatting · holobiomicslab

    Use when after completing differential isoform expression analysis using IsoformSwitchAnalyzer or equivalent isoform quantification, when you have identified sets of differentially expressed isoforms and need to perform functional characterization through sequence-based homology and structural.
    0 installs
79. ▌
    Iterative Peak Selection From Latent Space · holobiomicslab

    Use when you have latent low-dimension peak features extracted by a Graph-attention autoencoder from imaging mass spectrometry (IMS) datasets, and you need to automatically identify a ranked subset of marker ions without manual inspection.
    0 installs
80. ▌
    M Z To Normalized Kendrick Mass Conversion · holobiomicslab

    Use when you have uploaded peak list data containing m/z values and wish to construct a Kendrick mass plot where alkane homolog series (or other homologous families) are expected to appear as horizontal lines.
    0 installs
81. ▌
    Machine Learning Cross Validation Training · holobiomicslab

    Use when you have a labeled dataset (e.g., mass spectra with molecular structures, SIRIUS 6 fingerprint annotations) that you wish to train a supervised deep learning model on, and you need to estimate generalization performance and reduce variance from a single train–test split.
    0 installs
82. ▌
    Machine Learning Hyperparameter Extraction · holobiomicslab

    Use when you have completed cross-validation tuning of one or more machine-learning models (e.g., AdaBoost, SVM, Random Forest) on a development dataset using the caret package and need to identify which specific hyperparameter values were selected as optimal.
    2 installs
83. ▌
    Mass Spectrometry Data Matrix Construction · holobiomicslab

    Use when you have raw spatial metabolomics imzML files (paired with .ibd binary data files) that need to be loaded into a unified AnnData format for integration with spatial transcriptomics data or for cross-modal spatial pattern identification in single or multiple sample datasets.
    0 installs
84. ▌
    Metabolic Model Merging Consensus Building · holobiomicslab

    Use when you have multiple draft metabolic reconstructions (in JSON, XML, or SBML format) representing individual members or assembly variants of a community and need a single, non-redundant consensus model that captures shared and community-supported metabolic capacity.
    0 installs
85. ▌
    Metabolic Network Reconstruction From Kegg · holobiomicslab

    Use when you have selected two organisms (by KEGG code, e.
    0 installs
86. ▌
    Metabolite Change Direction Categorization · holobiomicslab

    Use when when you have omu_summary output containing log2FoldChange values and adjusted p-values (padj) for metabolites, and you need to stratify them by direction of change within a specific compound class (e.g., organic acids, amino acids) at a defined significance threshold (typically padj ≤ 0.
    0 installs
87. ▌
    Metabolite Disease Correlation Computation · holobiomicslab

    Use when after training a DeepMSProfiler deep learning model and generating per-sample predictions and metabolite signal intensities, use this skill when you need to: (1) identify which metabolites are most strongly associated with each disease class, (2) generate publication-ready visualizations.
    0 installs
88. ▌
    Metabolite Feature Distribution Comparison · holobiomicslab

    Use when when metabolomics data contains both QC control samples and biological samples that will be normalized together using methods like tGAM, rGAM, rLOESS, QC-RLSC, or QC-RSC. Apply this skill to verify that QC and biological sample distributions remain consistent;
    1 install
89. ▌
    Metabolite Missingness Threshold Filtering · holobiomicslab

    Use when when you have a metabolite measurement matrix with missing values across samples and need to decide which metabolites to retain before applying k-nearest neighbor imputation.
    0 installs
90. ▌
    Metabolite Sample Clustering Visualization · holobiomicslab

    Use when when you have a feature-by-sample metabolomic matrix (finalData) and corresponding sample group labels (finalLabel) and need to visualize how samples cluster together and separate by group using hierarchical clustering;
    2 installs
91. ▌
    Metabolomic Workflow Ranking Visualization · holobiomicslab

    Use when after running NOREVA's multi-class or time-course assessment functions (normulticlassqcall, normulticlassnoall, normulticlassisall, nortimecourseqcall, or nortimecoursenoall) that produce an overall ranking CSV file of preprocessed workflows.
    0 installs
92. ▌
    Missing Value Detection And Quantification · holobiomicslab

    Use when you have a raw abundance matrix (e.g., metabolite or gene features × samples) and need to decide which features to retain before downstream analysis.
    0 installs
93. ▌
    Module Refactoring And Legacy Code Removal · holobiomicslab

    Use when when a major version release (e.g., v1.x → v2.0.0) deprecates a core neural module class, and new equivalent modules must be designed and integrated without breaking downstream prediction pipelines. Triggered by breaking changes in CHANGELOG or deprecation warnings in model initialization.
    0 installs
94. ▌
    Molecular Descriptor Calculation Via Rdkit · holobiomicslab

    Use when when you have a set of SMILES strings representing small molecules and need to generate a unified descriptor feature matrix for downstream machine learning (e.g., retention time prediction, property regression).
    0 installs
95. ▌
    Multi Class Performance Metric Computation · holobiomicslab

    Use when when evaluating a taxonomy classification model on held-out natural product data where multiple classes exist (e.
    1 install
96. ▌
    Multi Tool Spectral Compatibility Encoding · holobiomicslab

    Use when after RAMClustR clustering and do.findmain molecular weight inference are complete, when you need to submit the same inferred spectra to multiple third-party annotation tools (MSFinder and Sirius) that each require distinct file formats and cannot share a common intermediate representation.
    0 installs
97. ▌
    Multivariate Feature Importance Extraction · holobiomicslab

    Use when you have a preprocessed peak table (feature matrix: samples × peaks) with known class labels or phenotype groupings, and you want to identify which individual peaks contribute most to classification or discrimination between groups.
    0 installs
98. ▌
    Neural Network Hyperparameter Optimization · holobiomicslab

    Use when when you have preprocessed joint ST/SM AnnData objects (output from joint_adata_sm_st and normalize_total_joint_adata_sm_st) and need to fit a ConditionalVAESTSM model to unify spatial transcriptomics and spatial metabolomics data to a common resolution.
    1 install
99. ▌
    Parameter Flag Toggling For Software Modes · holobiomicslab

    Use when when integrating edited Modular.r scripts into the LipidMatch-4.2 distribution and you need to switch between Modular mode (standalone R execution with manual or CSV inputs) and Flow mode (integrated pipeline execution).
    0 installs
100. ▌
     Pathway Enrichment Analysis Tool Selection · holobiomicslab

     Use when you have completed differential expression analysis (DEA) on genes, miRNA, proteins, or lipids and need to identify significantly enriched biological pathways. The multiOmicsIntegrator pipeline requires explicit tool selection via the pea_genes parameter in params.
     0 installs