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HolobiomicsLab

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1. ▌
   Pathway Feature Selection Information Gain · holobiomicslab

   Use when after computing a pathway dysregulation score matrix (PDSmatrix) from metabolite-to-pathway mappings, apply this skill when you need to reduce the dimensionality of pathway features and select only those pathways with sufficient information content to discriminate between phenotype classes.
   2 installs
2. ▌
   Performance Metric Aggregation And Display · holobiomicslab

   Use when after running NOREVA's assessment functions (normulticlassqcall, normulticlassnoall, normulticlassisall, nortimecourseqcall, nortimecoursenoall) on preprocessing workflows, use this skill to synthesize performance results across all five criteria into a single ranked output and create a.
   0 installs
3. ▌
   Preprocessing Workflow Comparative Ranking · holobiomicslab

   Use when you have multi-class or time-course metabolomic peak table data (raw or already peak-detected) with or without quality control samples and/or internal standards, and you need to evaluate which preprocessing workflow (normalization, imputation, scaling combination) will yield the most.
   0 installs
4. ▌
   Quality Control Sample Metadata Extraction · holobiomicslab

   Use when you have txt files exported from Sciex MultiQuant (>v3.0.
   0 installs
5. ▌
   Quality Control Visualization Metabolomics · holobiomicslab

   Use when after completing kNN imputation, outlier sample removal, and variance-stabilizing normalization (vsn) on a MultiAssayExperiment object containing metabolite measurements.
   0 installs
6. ▌
   Raw Spectral Data Import And Preprocessing · holobiomicslab

   Use when you have raw metabolomics data in mzML or mzXML format and need to convert it into a normalized feature table (CSV or mzTab) via automated batch processing.
   0 installs
7. ▌
   Regression Model Evaluation Absolute Error · holobiomicslab

   Use when after training a regression model on labeled continuous data (e.g., retention times, physicochemical properties) and generating predictions on held-out test data, compute MAE and MedAE to assess model generalization and compare against published reference performance.
   0 installs
8. ▌
   Retention Order Prediction Model Execution · holobiomicslab

   Use when you have access to the aalto-ics-kepaco/retention_order_prediction repository, have installed all Python (scipy, numpy, sklearn, joblib, pandas, networkx) and R dependencies, possess molecular feature data (MACCS fingerprints or equivalent), and need to execute a specific evaluation.
   2 installs
9. ▌
   Risk Stratification And Prognosis Indexing · holobiomicslab

   Use when when you have paired survival data (event indicator and follow-up time vectors), expression or metabolomic feature matrices, and need to generate individual prognosis indices and assign samples to risk groups for downstream prognostic classification or treatment planning.
   0 installs
10. ▌
    Robustness Metric Computation Metabolomics · holobiomicslab

    Use when when you have applied multiple normalization methods (e.g., tGAM, rGAM, rLOESS, QC-RLSC, QC-RSC) to metabolomics datasets and need to rank them by robustness and execution speed to determine which method is most suitable for your experimental design and computational constraints.
    0 installs
11. ▌
    Search Result Visualization Across Domains · holobiomicslab

    Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to synthesize results across domains (e.
    2 installs
12. ▌
    Sequence Motif Identification And Matching · holobiomicslab

    Use when you have differentially expressed isoform or exon FASTA sequences and need to identify conserved regulatory or structural motifs as part of comprehensive functional annotation.
    0 installs
13. ▌
    Siamese Neural Network Architecture Design · holobiomicslab

    Use when when you have pairs of mass spectrometry spectra and need to predict their molecular structural similarity as a scalar Tanimoto score in the range [0, 1].
    0 installs
14. ▌
    Signal Peptide Prediction And Localization · holobiomicslab

    Use when you have differentially expressed isoform or exon FASTA sequences from transcript assembly (e.g., IsoformSwitchAnalyzer output) and need to identify which predicted coding isoforms encode signal peptides for secretion or membrane targeting.
    0 installs
15. ▌
    Small Molecule Structure Input Preparation · holobiomicslab

    Use when you have a small-molecule chemical structure in an initial or non-standard format and need to predict its environmental microbial degradation, gut microbiota metabolism, or mammalian biotransformation using BioTransformer's prediction modules.
    2 installs
16. ▌
    Soil Aquatic Microbiota Pathway Simulation · holobiomicslab

    Use when when you have a small molecule (SMILES, MOL, or SDF format) and need to predict its degradation products in soil or aquatic microbial ecosystems; when environmental risk assessment, persistence prediction, or metabolite identification in these compartments is required;
    0 installs
17. ▌
    Spectrum Chromatogram Mobilogram Rendering · holobiomicslab

    Use when you have mass spectrometry data in a Pandas DataFrame with columns for m/z and intensity (spectrum), retention time and intensity (chromatogram), or drift time and intensity (mobilogram), and need to render 1D traces as static or interactive plots for exploratory analysis, quality control.
    0 installs
18. ▌
    Sqlite Database Design And Schema Creation · holobiomicslab

    Use when you have an mzML file and need to enable random-access spectrum retrieval by integer or string identifiers without holding the entire mzML in memory or decompressing indexed gzip files.
    0 installs
19. ▌
    Statistical Significance Filtering Q Value · holobiomicslab

    Use when after performing univariate statistical tests (e.g., ANOVA, t-tests) across sample classes in a normalized metabolomic feature table, you need to control false discovery rate and select a high-confidence subset of significantly differentiated metabolites for downstream analysis (e.
    0 installs
20. ▌
    String Value Concatenation With Delimiters · holobiomicslab

    Use when converting intermediate JSON to a target format (e.g., mwTab) and a single string field must be populated from multiple source records—for example, combining author names separated by semicolons, or concatenating a list of instrument names or experimental conditions.
    0 installs
21. ▌
    Structural Level Pathway Topology Modeling · holobiomicslab

    Use when when you need to compare metabolic network architecture between two organisms and want to analyze their topological properties (e.g., network connectivity, reaction ordering, pathway structure) separately from functional annotations.
    1 install
22. ▌
    Structural Representation Format Detection · holobiomicslab

    Use when when you have a mixed-format input query that may contain a compound identifier and a structural representation separated by a tab delimiter, and you need to determine which ClassyFire API endpoint (SMILES, InChI, IUPAC, or FASTA) to submit the query to for chemical classification.
    0 installs
23. ▌
    Subpfam Functional Resolution Augmentation · holobiomicslab

    Use when you have annotated genes with Pfam domains but require higher functional specificity to detect natural product sub-clusters.
    2 installs
24. ▌
    Tissue Spatial Analysis Pipeline Execution · holobiomicslab

    Use when you have raw IMC (protein imaging) and SIMS (metabolite imaging) data from tissue regions that require spatial co-registration, single-cell-level intensity quantification, and joint analysis of protein–metabolite relationships.
    0 installs
25. ▌
    Unit Test Development For Spectral Loaders · holobiomicslab

    Use when when you have implemented parser functions for one or more mass spectrometry file formats and need to verify that metadata and peak lists are correctly extracted and converted into matchms Spectrum objects before committing to a feature branch.
    0 installs
26. ▌
    Validity Constraint Enforcement For Msdata · holobiomicslab

    Use when when designing a custom MsBackend subclass (e.g., MsBackendTest) that stores spectral data in multiple slots (a data.frame for spectra variables, NumericList objects for m/z and intensity peaks). Use this skill to guard against slot desynchronization—e.
    0 installs
27. ▌
    Workflow Orchestration And Parallelization · holobiomicslab

    Use when when you have a multi-step computational chemistry or molecular modeling pipeline (3+ sequential or parallel stages) that must process many molecules, each requiring repeated tool invocations with different parameters, and you need reproducibility, fault tolerance, and the ability to.
    2 installs
28. ▌
    XML Parsing And Element Tree Serialization · holobiomicslab

    Use when when spectrum or chromatogram data is stored as serialized XML strings in a database or file system and must be converted into pymzML Spectrum or Chromatogram objects for programmatic access.
    0 installs
29. ▌
    Dask Array Lazy Evaluation Verification · holobiomicslab

    Use when when applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to AnnData objects where the expression matrix X is backed by a dask.array.Array, you need to verify that the operation completed without eagerly loading the full matrix.
    0 installs
30. ▌
    Dispersion Estimation Negative Binomial · holobiomicslab

    Use when you have raw RNA-seq count data (from HTSeq, featureCounts, Salmon, or similar quantification tools) organized in a count matrix with samples as columns and genes as rows, and you need to test for differential expression between conditions using a negative binomial model.
    0 installs
31. ▌
    Mapping Agreement Cross Tool Validation · holobiomicslab

    Use when when you have built a new tool implementation or major version and need to verify it produces equivalent results to a reference implementation on the same input data and index.
    0 installs
32. ▌
    Monte Carlo P Value Estimation Adaptive · holobiomicslab

    Use when when you have ranked gene statistics and gene set collections, and your analysis requires P-value discrimination below a fixed lower bound (e.g., distinguishing between pathways at p < 1e-10).
    0 installs
33. ▌
    Prior Distribution Fitting For Genomics · holobiomicslab

    Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the number of biological replicates is small (fewer than ~5–10 arrays/samples per group) and you want to avoid inflated variance.
    0 installs
34. ▌
    Results Table Extraction And Comparison · holobiomicslab

    Use when after running DESeq() on a DESeqDataSet and obtaining initial results via results(), use this skill when you need to (1) extract base results tables for specific contrasts (e.
    2 installs
35. ▌
    Scanpy Preprocessing Pipeline Execution · holobiomicslab

    Use when you have raw or minimally processed single-cell RNA-seq expression data loaded into an AnnData object (dense, sparse, or Dask-backed array as X), and you need to apply standardized preprocessing transformations (normalization, filtering, PCA) before downstream analysis such as clustering.
    0 installs
36. ▌
    R Workflow Scripting For Analytical Chemistry · holobiomicslab

    Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration times, m/z values, peak intensities) by orchestrating multiple R packages in a controlled, documented sequence.
    0 installs
37. ▌
    Large Scale All Pairs Similarity Benchmarking · holobiomicslab

    Use when you have multiple competing spectral similarity scoring methods (e.
    0 installs
38. ▌
    Metabolite Quantification Accuracy Assessment · holobiomicslab

    Use when you have executed mzExacto() on a preprocessed GC-MS dataset and need to verify that the returned dataframe correctly matches query chemicals to their m/z peaks, retention times, and quantitative measurements (area values).
    0 installs
39. ▌
    Multi Batch Experimental Design Understanding · holobiomicslab

    Use when your metabolomics experiment includes samples acquired across multiple instrument runs, different preparation dates, or distinct sample cohorts.
    0 installs
40. ▌
    Retention Index Extraction From Nist Database · holobiomicslab

    Use when you have a compiled EI or MS2 library object (from read_lib or c() combination of multiple sources) and a local NIST library installation with accessible ri.dat and USER.DBU files in the mssearch/nist_ri directory.
    0 installs
41. ▌
    Structural Similarity Ground Truth Validation · holobiomicslab

    Use when you have a spectral library with structural ground truth (InChIKey or SMILES annotations for ≥50% of spectra) and want to benchmark whether a new or existing spectral similarity scorer ranks structurally related compounds higher than unrelated ones.
    0 installs
42. ▌
    Untargeted Metabolomics Marker Identification · holobiomicslab

    Use when when you have untargeted GC–MS or LC–MS data in the form of a two-dimensional m/z vs retention time map and need to identify marker features without conventional peak picking.
    0 installs
43. ▌
    Word2vec Embedding Training Mass Spectrometry · holobiomicslab

    Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture fragmentation patterns and neutral loss relationships.
    0 installs
44. ▌
    Chromatographic Alignment Parameter Selection · holobiomicslab

    Use when after chromatographic peak detection (e.g. centWave) has been performed on LC-MS data and you need to group features that likely originate from the same compound.
    1 install
45. ▌
    Chromatographic Peak Annotation Visualization · holobiomicslab

    Use when after running tardisPeaks() with screening_mode=TRUE on centroided .mzML LC-MS data, when you need to visually inspect whether the 10 target compounds (internal standards and endogenous metabolites) were correctly detected within their expected m/z and retention time windows.
    0 installs
46. ▌
    Class Imbalance Downsampling Ratio Adjustment · holobiomicslab

    Use when after generating cross-spectrum negative examples via precursor m/z windowing and before training a rescore model (e.g., Siamese architecture in FIDDLE v2.0.0).
    0 installs
47. ▌
    Comparative Classifier Performance Assessment · holobiomicslab

    Use when you have a labeled peak quality dataset (development set with ground-truth pass/fail labels), a defined set of peak-quality metrics (e.
    0 installs
48. ▌
    Composite Spectra Assembly From Fragment Ions · holobiomicslab

    Use when you have DDA raw mass spectrometry data (mzML, mzXML, or netCDF format) and need to reconstruct composite fragmentation spectra by associating fragment ions with their parent precursor ions.
    2 installs
49. ▌
    Compound Specific Misalignment Identification · holobiomicslab

    Use when you have completed XCMS grouping on LC-MS data and suspect misaligned features due to long acquisition periods (>1 week) or large sample cohorts (hundreds of samples).
    2 installs
50. ▌
    Compound Specific Warping Function Generation · holobiomicslab

    Use when xCMS alignment produces suspected misaligned feature groups across hundreds of samples or long acquisition runs (>1 week), particularly when global XCMS warping functions fail to account for compound-specific or sample-neighborhood retention-time drift structures.
    2 installs
51. ▌
    Dashboard Session Initialization Verification · holobiomicslab

    Use when after loading a specXplore session data object (saved .
    2 installs
52. ▌
    Deep Learning Training Convergence Monitoring · holobiomicslab

    Use when training a CNN model from scratch on LCMS peak classification tasks (or similar image-like batched data) where you need to confirm the model reaches target performance (e.g., AUC ROC > 0.9) without overfitting.
    1 install
53. ▌
    Experiment Metadata Organization And Tracking · holobiomicslab

    Use when before initiating raw file conversion or feature extraction, when you have a heterogeneous collection of raw LC-MS files (.raw or .mzML) and sample information scattered across instrument logs, sequence files, or spreadsheets.
    0 installs
54. ▌
    Feature Network Construction And Partitioning · holobiomicslab

    Use when you have a preprocessed LC-MS feature table (m/z, retention time, intensity columns) and need to identify which features belong together as isotopes or adducts of the same neutral compound.
    2 installs
55. ▌
    Feature Pair Alignment Parameter Optimization · holobiomicslab

    Use when after anchor selection and retention-time spline mapping have produced a candidate list of feature pair alignments, but before final scoring and reduction of the combined table.
    0 installs
56. ▌
    Feature Table Annotation With Sample Metadata · holobiomicslab

    Use when your input is a feature intensity table (CSV or R data frame) with features as columns and samples as rows, and you have accompanying sample metadata (batch identifiers, QC/study sample labels, run order, sample phenotypes, collection dates).
    0 installs
57. ▌
    Feature Table Generation From Aligned Spectra · holobiomicslab

    Use when after retention-time and m/z-based peak alignment has been completed across a cohort of LC-MS samples, and you need to create a unified quantitative matrix for statistical testing, multivariate analysis, or annotation workflows.
    0 installs
58. ▌
    Fragment Ion Peak Detection And Normalization · holobiomicslab

    Use when immediately after loading raw MS/MS spectra from .mgf, .msp, or .mzML files, before generating the bag-of-fragments corpus or extracting neutral losses.
    2 installs
59. ▌
    Interactive Application Accessibility Testing · holobiomicslab

    Use when after instantiating a specXplore dashboard session layer with a loaded session data object from disk, before conducting visual exploration of LC-MS/MS spectral data.
    0 installs
60. ▌
    Internal Standard Area Mis Injection Flagging · holobiomicslab

    Use when after building a SummarizedExperiment object containing LC-MS peak areas and internal standard assignments, when you need to identify study samples with anomalous Internal Standard signal (indicating syringe failure, capillary clogging, or injection system malfunction) before applying.
    0 installs
61. ▌
    Isotopologue Adduct Cross Assay Link Encoding · holobiomicslab

    Use when after structural cluster assignment and correlation clustering are complete, and you need to represent the full set of structural relationships (isotopologues, adducts, cross-assay links, and correlation co-membership) in a single unified graph for interactive visualization, network.
    0 installs
62. ▌
    Isotopologue Distribution Matrix Construction · holobiomicslab

    Use when when you have measured fractional abundances of isotopologues (FAM) from LC-MS in an isotope labeling experiment and need to correct them to obtain true mass distribution vectors (MDV) that reflect only the labeling contribution, accounting for background from naturally occurring isotopes.
    4 installs
63. ▌
    Lc Ms Gradient Encoding Vector Representation · holobiomicslab

    Use when when you have a set of candidate LC gradients (parameter combinations) that you wish to evaluate with a Gaussian process model, or when you need to convert raw gradient specifications into a standardized numerical format for Bayesian optimization acquisition function computation.
    0 installs
64. ▌
    Masking Augmentation For Contrastive Learning · holobiomicslab

    Use when when training a transformer encoder on tandem mass spectra (MS/MS) and you need to generate positive sample pairs for contrastive learning without access to labeled chemical or spectral analogues.
    0 installs
65. ▌
    Mass Spectrometry Data Loading And Formatting · holobiomicslab

    Use when you have raw or curated mass spectrometry data (MS1, MS2, or MSMS) in mzML, mzXML, CDF, MGF, MSP formats, or from a MassBank/MetaboLights repository, and need to convert it into an in-memory or on-disk spectral object that supports filtering, comparison, and annotation workflows.
    0 installs
66. ▌
    Mass Spectrometry Feature Tree Interpretation · holobiomicslab

    Use when after running qiime qemistree make-hierarchy and obtaining a tree artifact (qemistree.
    1 install
67. ▌
    Mass Spectrometry Spectral Embedding Learning · holobiomicslab

    Use when when you have preprocessed MS/MS spectral pairs (peak intensities and m/z values) and need to predict molecular structural similarity scores, or when you want to project spectra into a learned chemical embedding space for visualization (e.g., via UMAP) or downstream similarity searches.
    0 installs
68. ▌
    Mass Spectrum Normalization And Preprocessing · holobiomicslab

    Use when you have raw tandem mass spectra data (mz/intensity pairs and precursor m/z values) and need to train interpretable machine learning models (regression or tree-based) where feature interpretability and direct chemical meaning are required.
    0 installs
69. ▌
    Mass To Charge Retention Time Feature Mapping · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA) mzML files from LC- or GC-HRMS measurements and need to convert continuous raw mass spectrometric signals into discrete, quantifiable chromatographic features (m/z, RT, intensity, charge, isotope) before PFAS-specific prioritization or.
    0 installs
70. ▌
    Memo Ms API Usage And Parameter Configuration · holobiomicslab

    Use when you have aligned feature tables (CSV format) with corresponding MS2 spectra data (MGF or mzML files), and need to construct a sample-level vectorization matrix where each row represents a sample and columns encode the occurrence counts of MS2 peaks and neutral losses observed in that.
    0 installs
71. ▌
    Metabolite Feature Grouping By Adduct Isotope · holobiomicslab

    Use when immediately after generating a feature table (m/z, retention time, intensity) from centroided mzML data when you need to collapse multiple feature detections of the same compound (arising from different ionization states, charge states, or isotope patterns) into unified empirical compound.
    0 installs
72. ▌
    Microbiome Metabolome Abundance Normalization · holobiomicslab

    Use when when you have raw count matrices from paired microbiome (16S rRNA or metagenomic) and metabolomic (LC-MS/MS) profiling data that will be used to train or apply a predictive model (e.g., MiMeNet, MelonnPan, Random Forest) to predict metabolite abundances from microbial composition.
    0 installs
73. ▌
    Molecular Fingerprint Generation And Encoding · holobiomicslab

    Use when when you have paired tandem MS spectra and corresponding molecular structures (as SMILES strings or InChI keys) and need to train a model that jointly embeds spectra and structures for structure annotation by database lookup.
    0 installs
74. ▌
    Multi Dimensional Data Loading And Formatting · holobiomicslab

    Use when you have raw or processed mass spectrometry data in HDF5 (.h5) or mzML format and need to ingest it into DEIMoS for multi-dimensional analysis.
    0 installs
75. ▌
    Neural Network Ensemble Inference Via Dropout · holobiomicslab

    Use when when you have a trained neural network and need to quantify prediction uncertainty or improve accuracy by filtering low-confidence predictions. Particularly useful when input spectra pairs have variable quality or when downstream tasks (e.
    0 installs
76. ▌
    Oracle Mode Structural Constraint Integration · holobiomicslab

    Use when when you have loaded both a known compound and its modified analog with MS/MS spectra, initially generated baseline modification probability scores, and then obtained or confirmed the structure of the modified compound.
    0 installs
77. ▌
    Pairwise Alignment With Anchor Prioritization · holobiomicslab

    Use when when processing LC-MS metabolomics datasets with 10 or fewer samples and requiring reproducible mass track alignment across the cohort.
    0 installs
78. ▌
    Peak Annotation Quantification And Comparison · holobiomicslab

    Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
    0 installs
79. ▌
    Peak Table Filtering By Mz And Retention Time · holobiomicslab

    Use when you have a table of detected chromatographic peaks (e.g., from CentWave peak detection in xcms) and need to isolate a single target m/z (e.g., m/z 304.1131 for a pesticide) or a narrow m/z range, or when you must restrict analysis to a known retention time window (e.
    0 installs
80. ▌
    Penalty Factor Application In Spectral Search · holobiomicslab

    Use when when performing reverse spectral search on MS/MS data suspected to contain chimeric spectra (multiple co-isolated precursors), and you need to increase the number of reliable spectral matches while filtering out false positives.
    0 installs
81. ▌
    Peptidoform Representation And Interpretation · holobiomicslab

    Use when when you have a tandem mass spectrometry spectrum with a known or inferred peptide sequence that may contain post-translational modifications (phosphorylation, glycosylation, cross-links), and you need to annotate which observed m/z peaks correspond to specific fragment ion types (b, y, a.
    0 installs
82. ▌
    Probabilistic Modeling Convergence Assessment · holobiomicslab

    Use when during the LDA training phase when you need to decide whether the model has learned a stable representation of Mass2Motifs.
    0 installs
83. ▌
    Retention Time Correlation Similarity Scoring · holobiomicslab

    Use when when you have detected multiple features from non-targeted mass spectrometry and need to group them by putative compound origin.
    0 installs
84. ▌
    Tab Delimited Export Formatting For Metabolomics · holobiomicslab

    Use when after completing batch normalization and quality control filtering on a Metaboprep object, when you need to share processed metabolomics data with collaborators, import into other statistical packages, or archive results in a platform-independent format.
    0 installs
85. ▌
    Targeted Metabolite Screening Mode Configuration · holobiomicslab

    Use when beginning a targeted LC–MS metabolomics or lipidomics study with a predefined list of compounds (e.g., 10+ targets) and you have centroided .
    0 installs
86. ▌
    Training Data Generation From Reference Features · holobiomicslab

    Use when you have isolated, manually curated reference chromatographic peaks (ground-truth features) matched to local maxima detected in LC-HRMS profile-mode data, and you need to train a CNN classifier to distinguish peaks from background signals across diverse sample compositions.
    0 installs
87. ▌
    Metabolomicshub Announcement Authoring · holobiomicslab

    Use when publishing a metabolomics dataset into the MetabolomicsHub index — building the common-model file, deriving and validating the announcement against the right profile, minting an identifier, and submitting a revision whose outcome only a polled task reports.
    0 installs
88. ▌
    Categorical Annotation Handling In Omics Data · holobiomicslab

    Use when you have (1) spatial omics data loaded in AnnData format with a pre-built spatial neighbor graph (from squidpy.gr.spatial_neighbors() or similar), (2) a categorical variable in the AnnData object (e.g., cell type, tissue compartment, annotation stored as .obs or .
    0 installs
89. ▌
    Coefficient And Standard Error Interpretation · holobiomicslab

    Use when after fitting a linear model to expression data using limma's lmFit function on a design matrix encoding experimental groups, inspect the resulting MArrayLM object to retrieve coefficient estimates (log-fold-changes) and standard errors needed to assess which genes show meaningful.
    0 installs
90. ▌
    Deseqdataset Construction From Quantification · holobiomicslab

    Use when you have transcript-level quantification files (quant.sf, kallisto abundance.h5, or RSEM output) from one or more RNA-seq samples and need to construct a count matrix for differential expression analysis.
    0 installs
91. ▌
    Differential Expression Result Interpretation · holobiomicslab

    Use when you have fitted a linear model to gene expression data (microarray, RNA-seq, qPCR, or proteomics) across multiple samples and need to compute gene-level test statistics.
    0 installs
92. ▌
    Image Feature Extraction From Tissue Sections · holobiomicslab

    Use when you have a spatial transcriptomics dataset (AnnData object) with cell/spot coordinates and an associated tissue microscopy image file, and you need to compute image-derived features (e.
    0 installs
93. ▌
    Transcript Expression Quantification Handling · holobiomicslab

    Use when you have transcript abundance estimates from RNA-seq quantification tools (e.
    0 installs
94. ▌
    Drift Time Retention Time Distance Metric Selection · holobiomicslab

    Use when after peak detection in GCIMS when you need to group detected peaks across multiple samples into reproducible clusters.
    0 installs
95. ▌
    Mz Retention Time Tolerance Parameter Configuration · holobiomicslab

    Use when when invoking Asari to process centroid mzML files for the first time in a PCPFM experiment, or when RT and m/z accuracy characteristics of your LC-MS instrument differ from the pipeline defaults (e.
    2 installs
96. ▌
    Scalability Extrapolation And Throughput Estimation · holobiomicslab

    Use when you have a new or modified LC-MS data processing tool and need to determine whether it can handle production-scale sample cohorts (50–100+ samples) on modest hardware (single-core CPU, ≤16 GB RAM).
    0 installs
97. ▌
    Benchmarking And Comparative Performance Evaluation · holobiomicslab

    Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains over established baselines. Use it specifically when you have access to ground-truth annotations (e.
    0 installs
98. ▌
    Command Line Interface Configuration And Automation · holobiomicslab

    Use when you have a batch of raw LC-IMS-MS/MS data in mzML or mzML.
    0 installs
99. ▌
    Constraint Based Model Sampling And Flux Prediction · holobiomicslab

    Use when you have constraint-based metabolic models with integrated multi-omics constraints (transcriptomics via Reaction Activity Scores, extracellular flux ratios via YSI bioanalyzer or LC-MS, nutrient availability bounds), and you need to determine whether differential enzyme expression.
    0 installs
100. ▌
     Cross Spectrum Negative Generation Within Mz Window · holobiomicslab

     Use when when preparing augmented training data for a Siamese rescore model that must learn to rank correct molecular formulas above incorrect ones;
     0 installs