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HolobiomicsLab

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1. ▌
   Msi Array Data Structure Handling · holobiomicslab

   Use when you have imported raw imzML or Analyze 7.5 imaging data and need to represent it as a preprocessed spectral array before applying statistical methods (PCA, clustering, classification).
   0 installs
2. ▌
   Msi Metadata Curation And Storage · holobiomicslab

   Use when after generating a 3D pixel array (shape n+1, y, x) from raw line-scan MSI data via MSIGen's get_image_data() call, curate and validate the accompanying JSON metadata file before visualization or downstream analysis.
   0 installs
3. ▌
   Multi Omics Latent Space Learning · holobiomicslab

   Use when you have preprocessed and jointly normalized ST and SM data from the same sample(s) aligned to a common spatial resolution (via joint_adata_sm_st and normalize_total_joint_adata_sm_st), and you need to discover shared latent structure across modalities to identify co-localized spatial.
   0 installs
4. ▌
   Natural Product Model Application · holobiomicslab

   Use when you have (1) a collection of natural product or drug candidate molecules in SMILES format, (2) a downstream task (classification at Class/Superclass/Pathway levels, bioactivity regression, or virtual screening ranking), (3) access to pre-trained NaFM weights, and (4) a need to leverage.
   0 installs
5. ▌
   Noise Estimation Snr Thresholding · holobiomicslab

   Use when after normalizing, smoothing, and baseline-reducing mass spectra via normalize(), smooth(), and reduceBaseline(), when you need to distinguish true peaks from noise-induced artifacts.
   0 installs
6. ▌
   Online Mode Environment Detection · holobiomicslab

   Use when when deploying an OpenMS streamlit application that must support both local development (offline mode with multiprocessing) and production cloud/HPC environments (online mode with Redis + RQ task queue), and you need to transparently route workflow job submissions to the correct backend.
   0 installs
7. ▌
   Outlier Sample Identification Pca · holobiomicslab

   Use when after normalizing and log-transforming a LipidomicsExperiment object, when you need to detect samples with aberrant lipid profiles before differential expression or multivariate analysis.
   0 installs
8. ▌
   P Value Combination Fisher Method · holobiomicslab

   Use when when you have tabulated p-values and study sample sizes (N) from multiple independent metabolomics studies measuring the same compounds or metabolites, and you need to compute a single meta-analytic p-value that reflects both statistical significance and study weight.
   0 installs
9. ▌
   Package Installation Verification · holobiomicslab

   Use when after installing ChemDistiller or similar Python-based command-line analysis packages, to confirm the package is properly installed in the Python environment and the primary entry point script is accessible and executable.
   0 installs
10. ▌
    Peak Area Intensity Normalization · holobiomicslab

    Use when you have a targeted metabolomics peak area intensity table (samples in rows, compounds in columns) with assigned internal standards and you need to prepare data for quantification via regression models or statistical testing.
    0 installs
11. ▌
    Polarity Based Compound Filtering · holobiomicslab

    Use when you have a multi-polarity compound target list (e.g., a .xlsx file with a polarity or ionization mode column indicating positive or negative ESI mode) and you are about to perform targeted peak detection in a single LC–MS acquisition mode (e.g., positive-ion mode only).
    0 installs
12. ▌
    Pre Post Normalisation Comparison · holobiomicslab

    Use when after completing a hierarchical batch normalisation workflow (e.g., hRUV with intra-batch loess smoothing and inter-batch RUV-III correction) to verify that normalisation has eliminated run-order signal drift and batch-specific effects visible in raw or imputed assays.
    0 installs
13. ▌
    Python Data Structure Engineering · holobiomicslab

    Use when you have raw mass spectrometry quantification tables (feature abundance matrices), sample metadata tables, and spectral data files (e.g., from the omsw_pleurotus dataset) that must be ingested into the msFeaST pipeline;
    0 installs
14. ▌
    Python Job Metadata Serialization · holobiomicslab

    Use when implementing online task queue deployments (RQ + Redis) where job execution may outlive the originating web session, or where workers may restart unexpectedly.
    0 installs
15. ▌
    Qm Output Parsing And Aggregation · holobiomicslab

    Use when you have completed parallel QUICK quantum calculations on multiple conformers filtered by ASE-ANI and need to extract electronic properties from the output logs and consolidate them into a single structured table for use in CCS calculations or metabolite annotation workflows.
    0 installs
16. ▌
    R Package Parameter Configuration · holobiomicslab

    Use when when preparing to preprocess Salmon-derived count matrices or other omics abundance data, and you need to specify multiple configurable options (e.
    0 installs
17. ▌
    R Package Workflow Implementation · holobiomicslab

    Use when you have raw unnormalized metabolomics intensity data organized by batch and sample type (QC vs. biological), and you need to remove systematic variation (drift, batch effects) while preserving biological signal.
    0 installs
18. ▌
    R Wrapper Function Implementation · holobiomicslab

    Use when when you have multiple imputation methods with different function signatures and parameter conventions that need to be applied to the same input data matrix, and you want to allow users or downstream code to switch between methods via a single method argument without rewriting calling code.
    0 installs
19. ▌
    Ranked Statistic List Preparation · holobiomicslab

    Use when after completing differential analysis (e.g., via run_de()) to generate p-values and log2 fold changes, and before executing fgsea-based MetSEA enrichment.
    0 installs
20. ▌
    Rare Variant Integration Analysis · holobiomicslab

    Use when when analyzing rare-variant associations where sample sizes are modest, individual-variant tests lack power, or you need to aggregate signal across multiple rare variants within a biological pathway.
    0 installs
21. ▌
    Record Sorting By Multiple Fields · holobiomicslab

    Use when when applying str or matrix directives to JSON table data, and you need deterministic ordering of records before building output values—e.
    0 installs
22. ▌
    Regression Performance Evaluation · holobiomicslab

    Use when after training or fine-tuning a retention time prediction model on a source chromatographic method (e.g., SMRT dataset) and you need to verify prediction accuracy on a held-out test set or on a target chromatographic method from a different dataset (e.g., PredRet).
    0 installs
23. ▌
    Regulatory Relationship Inference · holobiomicslab

    Use when you have matched multiomics measurements (CNV, mutations, DNA methylation, histone PTMs, coding/noncoding transcripts, miRNA, lncRNA, proteomics, phosphoproteomics) across a cohort of cell lines or samples and want to identify which upstream omics features predict metabolite abundance.
    0 installs
24. ▌
    Retention Time Direction Matching · holobiomicslab

    Use when after componentization of parent and TP features with generateComponents(algorithm='tp'), when structural formula or compound annotations are available and you wish to prioritize TP candidates whose retention time behavior aligns with expected electronegativity, polarity, or hydrophobicity.
    0 installs
25. ▌
    Run Order Batch Effect Correction · holobiomicslab

    Use when metabolomics featuredata exhibits run-order-dependent signal drift, matrix effects, or batch effects that correlate with the order in which samples were analyzed.
    0 installs
26. ▌
    Sample Group Metadata Association · holobiomicslab

    Use when you have a preprocessed count matrix (genes, miRNAs, isoforms, proteins, or lipids) and need to prepare it for differential expression analysis by linking sample identifiers to their experimental group assignments.
    0 installs
27. ▌
    Savitzky Golay Filter Application · holobiomicslab

    Use when apply Savitzky-Golay smoothing when your mass spectra contain significant noise but you need to preserve sharp peaks and spectral fine structure (e.g., isotope patterns, peak asymmetry).
    0 installs
28. ▌
    Shiny UI Component Implementation · holobiomicslab

    Use when you have an existing R package with statistical or data-processing functions and need to expose its functionality through an interactive web interface where end users (non-R programmers) can upload datasets, configure analysis parameters (e.
    0 installs
29. ▌
    Spatial Spectral Array Processing · holobiomicslab

    Use when you have preprocessed MSImagingArrays data (after normalization, smoothing, and baseline reduction) and need to detect peaks consistently across all spectra in an imaging experiment, create reference peak positions from a representative subset, and filter by signal-to-noise ratio and.
    0 installs
30. ▌
    Spectral Library Match Assignment · holobiomicslab

    Use when you have a set of candidate molecular structures from in silico fragmentation (e.
    0 installs
31. ▌
    Spectrum Grouping And Aggregation · holobiomicslab

    Use when you have loaded raw PSM search results from a proteomics search engine (e.g., MaxQuant, MSGFPlus, Sage) and need to prepare them for multi-rank rescoring in MS²Rescore.
    0 installs
32. ▌
    Statistical Sub Cluster Detection · holobiomicslab

    Use when you have a collection of Biosynthetic Gene Clusters that have been tokenised into Pfam domain and subPfam sequences and filtered for redundancy, and you seek to identify statistically significant groupings of genes that co-occur across multiple BGCs—particularly when downstream linking to.
    0 installs
33. ▌
    Statistical Test Dispatch Routing · holobiomicslab

    Use when after data preprocessing, quality control, and batch effect correction have produced a validated peak intensity matrix (feature table: samples × peaks) with associated sample metadata (phenotype, grouping, or class labels).
    0 installs
34. ▌
    Sub Cluster Assignment Extraction · holobiomicslab

    Use when after PRESTO-TOP topic modelling has been run on redundancy-filtered tokenised BGCs and raw topic assignments have been generated.
    0 installs
35. ▌
    Test Suite Execution Verification · holobiomicslab

    Use when when you have cloned or obtained a Python package repository and need to confirm that the codebase's tests pass before integration, contribution, or deployment. Particularly relevant when the repository advertises a Tests badge linked to a CI/CD workflow (e.
    0 installs
36. ▌
    Third Party Processor Integration · holobiomicslab

    Use when when you have raw MS files (e.g., .raw, vendor-specific formats) stored in a centralized repository and need to invoke a third-party proteomics analysis tool—such as a mass spectrometry feature detector or quantification engine—without manually managing file transfers or output.
    0 installs
37. ▌
    Treatment Group Comparison Design · holobiomicslab

    Use when you have paired metabolomics count data and metadata with at least two treatment groups (e.g., Strep vs Mock), a clear Factor column identifying group membership, and a research question about which metabolites differ significantly in abundance between treatments.
    0 installs
38. ▌
    Twim Instrument Offset Correction · holobiomicslab

    Use when you have raw TWIM-MS data with arrival times (detector timestamps) rather than drift times, and you need to calibrate collision cross section values. TWIM platforms inherently record arrival time, not drift time, so this correction must precede CCS calibration workflows.
    0 installs
39. ▌
    Ubuntu Package Inventory Analysis · holobiomicslab

    Use when when you have a Ubuntu-based software package (e.g., MetumpX) that advertises bundling a specific number of tools (~89) but the individual tool names, versions, installation sources, and installation methods are not enumerated in the README or primary documentation.
    0 installs
40. ▌
    Unit Test Design For File Parsing · holobiomicslab

    Use when when implementing or extending file format parsers in a spectral data pipeline, you need unit tests to ensure that format-specific parsers correctly instantiate spectrum objects with expected m/z arrays, intensity arrays, and metadata attributes before releasing to users or integrating.
    0 installs
41. ▌
    Bioconductor Package Operation · holobiomicslab

    Use when you have transcript-level quantification files (quant.gz, h5, or similar) from a known upstream quantifier (salmon, kallisto, sailfish, oarfish) and need to import them into R as matrices for differential expression analysis with edgeR, DESeq2, or limma-voom.
    0 installs
42. ▌
    Count Matrix Format Validation · holobiomicslab

    Use when after constructing a count matrix from transcript quantification files (via tximport, HTSeq, featureCounts, or direct alignment) and before running DESeq() differential expression analysis.
    0 installs
43. ▌
    Highly Variable Gene Selection · holobiomicslab

    Use when after normalization (normalize_total, log1p transformation) and before PCA or other dimensionality reduction on raw or near-raw single-cell gene expression matrices.
    0 installs
44. ▌
    Index Construction Determinism · holobiomicslab

    Use when when comparing quantification results between two versions of a tool (e.g., salmon 2.0 Rust rewrite vs. C++ salmon 1.12.0), or when validating a new tool implementation against a reference version.
    0 installs
45. ▌
    Inferential Replicate Handling · holobiomicslab

    Use when when performing transcript- or gene-level differential expression analysis and your quantification tool (Salmon, Sailfish, or kallisto) has produced Gibbs sample or bootstrap sample replicates, and you want edgeR to account for inferential uncertainty rather than treating point estimates.
    0 installs
46. ▌
    Leiden Clustering Partitioning · holobiomicslab

    Use when apply Leiden clustering after constructing a k-nearest neighbor (kNN) graph from single-cell expression data when you need to partition cells into discrete, biologically meaningful clusters for downstream trajectory inference, differential expression testing, or graph abstraction.
    0 installs
47. ▌
    Local Splicing Event Detection · holobiomicslab

    Use when you have a GTF annotation file and need to systematically extract all local alternative splicing event coordinates (not transcript isoforms) for downstream PSI calculation or when you require a searchable index mapping events to contributing transcripts for inclusion and skipping forms.
    0 installs
48. ▌
    P Value Adjustment Methodology · holobiomicslab

    Use when after running DESeq() to fit negative binomial GLMs and obtaining raw p-values from results(dds), when you need to reduce false positives from multiple testing across thousands of genes while maximizing statistical power.
    0 installs
49. ▌
    Paired End Read Quantification · holobiomicslab

    Use when you have paired-end RNA-seq reads (FASTQ) and a reference transcriptome (FASTA), and you need to estimate transcript-level expression (NumReads and TPM).
    0 installs
50. ▌
    Transcript To Gene Aggregation · holobiomicslab

    Use when when you have transcript-level quantification files (e.g., Salmon quant.sf.gz, kallisto abundance.h5, or RSEM .results) and need to construct a gene-level count matrix for DESeq2 differential expression testing.
    0 installs
51. ▌
    Conditional Routing Logic Extraction · holobiomicslab

    Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing pipelines.
    0 installs
52. ▌
    Cosine Similarity Matrix Computation · holobiomicslab

    Use when after generating normalized dense embeddings for both query and reference MS/MS spectra using a pre-trained model like SpecEmbedding.
    0 installs
53. ▌
    Metabolic Network Graph Construction · holobiomicslab

    Use when when you have an untargeted metabolomics feature table (m/z values, retention times, intensities) and aim to predict functional pathway activity without explicit metabolite identification.
    0 installs
54. ▌
    Peak Picking Parameter Configuration · holobiomicslab

    Use when when reconstructing a metabolite fragment library entry from raw MS/MS spectral data (e.g., from MassBank or local acquisition), you need to define peak-picking thresholds to separate true fragment ions from baseline noise and assign occurrence scores.
    0 installs
55. ▌
    Retention Time Based Ion Association · holobiomicslab

    Use when when processing Data Dependent Acquisition (DDA) raw mass spectrometry data (mzML or mzXML format) and you need to deconvolute fragmentation spectra by matching precursor ions to their corresponding fragment ions.
    0 installs
56. ▌
    Spectral Neutral Loss Transformation · holobiomicslab

    Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment ions) rather than absolute m/z values.
    0 installs
57. ▌
    Batch Effect Correction Qc Reference · holobiomicslab

    Use when your peak intensity matrix exhibits batch-to-batch variation (retention time drift, signal intensity fluctuation across injection sequences), you have QC samples injected at regular intervals throughout the analysis, and you want to preserve biological signal differences while removing.
    0 installs
58. ▌
    Compound Identification From Ms Data · holobiomicslab

    Use when you have raw GC-MS or LC-MS data in vendor format (NetCDF, .raw, .d) or generic mass lists, and you need to assign chemical identities to detected peaks.
    0 installs
59. ▌
    Compound Isotope And Adduct Grouping · holobiomicslab

    Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per compound. Use it when your data contains isotopic peaks (e.g., ¹³C variants) and multiple ionization products (e.
    0 installs
60. ▌
    Feature Pair Scoring In Metabolomics · holobiomicslab

    Use when use this skill after XCMS feature detection and alignment on non-targeted LC-MS or GC-MS metabolomics data, when you have aligned features with quantitative profiles across samples and need to group features that co-originate from the same compound (accounting for isotopic peaks, adducts.
    0 installs
61. ▌
    Gc Ms Spectral Similarity Clustering · holobiomicslab

    Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct a molecular network.
    0 installs
62. ▌
    Graph Clustering Community Detection · holobiomicslab

    Use when after constructing a spectral similarity network from pairwise cosine similarity scores between deconvolved GC-MS spectra.
    0 installs
63. ▌
    Left Censored Missingness Simulation · holobiomicslab

    Use when when you have a complete metabolomics abundance table (e.g., targeted LC/MS or untargeted GC/MS counts) and need to generate synthetic left-censored missingness for evaluating imputation algorithm performance.
    0 installs
64. ▌
    Mass Spectral Metadata Harmonization · holobiomicslab

    Use when you have multiple mass spectral libraries in different formats (NIST MSP + MOL folder, MoNA MSP, RIKEN MSP, SWGDRUG MSP) and need to merge them into a single, MS-DIAL-compatible MSP file with consistent SMILES assignments, Kovats retention indices (RI), and polarity annotations across all.
    0 installs
65. ▌
    Metabolomic Feature Table Processing · holobiomicslab

    Use when you have a metabolomics feature table (rows=features, columns=samples) generated from LC-MS or GC-MS preprocessing and need to identify which features contain systematic errors from peak integration or alignment.
    0 installs
66. ▌
    Missing Data Mechanism Specification · holobiomicslab

    Use when when you have a metabolomics abundance table with missing values and need to decide which imputation method to apply, or when designing a simulation to evaluate imputation performance.
    0 installs
67. ▌
    Ms1 Feature Detection And Annotation · holobiomicslab

    Use when you have FIA-MS, LC-MS, or GC-MS full-scan data in mzML format and need to identify unknown molecular features by accurate mass.
    0 installs
68. ▌
    Peak Intensity Vector Transformation · holobiomicslab

    Use when you have a peak intensity matrix from LC/GC-MS analysis with known QC sample indices and suspect batch-related systematic variation in feature intensities. Use it as a preprocessing step before downstream analysis (e.
    0 installs
69. ▌
    Plate Layout Parameter Configuration · holobiomicslab

    Use when after uploading a sample list to InjectionDesign and before performing inter-batch balancing and intra-batch randomization.
    0 installs
70. ▌
    Savitzky Golay Smoothing Application · holobiomicslab

    Use when after filtering retention time and drift time ranges on raw GCIMS samples but before decimation and alignment.
    0 installs
71. ▌
    Spectral Library Matching Validation · holobiomicslab

    Use when you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.
    0 installs
72. ▌
    Spectral Library Metadata Assignment · holobiomicslab

    Use when you have a compiled EI or MS2 library object (read from MSP format via read_lib) and access to NIST ri.dat and USER.DBU files; you need to populate RI values for capillary GC-MS workflows.
    0 installs
73. ▌
    Spectral Library Polarity Separation · holobiomicslab

    Use when you have loaded an MS2 library (from NIST, GNPS, or other sources via read_lib()) that contains both positive and negative ionization modes mixed in a single file, and you need to produce two separate, polarity-specific MSP files for use in MS-DIAL or similar tandem MS analysis software.
    0 installs
74. ▌
    Spectrum Peak Counting And Reporting · holobiomicslab

    Use when when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a selected noise-filtering strategy retains an expected number of peaks for downstream molecular formula assignment.
    0 installs
75. ▌
    Structure Ranking From Spectral Data · holobiomicslab

    Use when you have an experimental tandem mass spectrum (collision-induced dissociation or ESI-MS/MS) and a chemical formula, and you need to identify the correct structure among multiple isomeric candidates in a database like PubChem.
    0 installs
76. ▌
    Adduct Type Assignment Positive Mode · holobiomicslab

    Use when you have an unknown MS/MS spectrum with a measured precursor m/z and want to determine which positive-mode adduct type ([M+H]+, [M+Na]+, [M+K]+, etc.) is most likely responsible for ionization.
    0 installs
77. ▌
    Amino Acid Level Accuracy Evaluation · holobiomicslab

    Use when you have predicted peptide sequences from a de novo sequencing tool (e.g., Casanovo) and want to understand the fine-grained accuracy of the predictions beyond exact-match peptide-level scoring.
    0 installs
78. ▌
    Annotaterc Function Parameterization · holobiomicslab

    Use when you have LC–MS all-ion fragmentation chromatograms already processed by xcms and clustered by RamClustR, a feature table (targetTable.csv format) listing features to annotate, and you need rank-1 metabolite or lipid identifications with confidence metrics.
    0 installs
79. ▌
    Annotation Pipeline Data Preparation · holobiomicslab

    Use when when you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa.
    0 installs
80. ▌
    Anova Feature Significance Filtering · holobiomicslab

    Use when you have a normalized LC-MS/MS metabolite abundance matrix (e.g., from MS-DIAL preprocessing) with multiple samples across experimental groups (e.
    0 installs
81. ▌
    Assay Ratio Computation Verification · holobiomicslab

    Use when after calling buildExperiment on metabolomics data to construct a SummarizedExperiment object, before performing batch correction, outlier detection, or other QC calculations that depend on ratio assay values.
    0 installs
82. ▌
    Batch Wise Normalization Application · holobiomicslab

    Use when when processing a SummarizedExperiment containing metabolomics peak areas or intensities organized by batch (e.g., LC-MS/MS runs on different days or instruments), and you have pooled quality control samples injected repeatedly within or across batches to serve as batch anchors.
    0 installs
83. ▌
    Binary Classification Model Training · holobiomicslab

    Use when you have curated a labeled dataset of MS/MS spectra annotated as 'relevant' (compounds of interest obtained from reference standards) or 'other' (reference standards or non-target compounds), and you need to build a classifier to automatically distinguish these two classes on unknown.
    0 installs
84. ▌
    Bipartite Network Node Edge Assembly · holobiomicslab

    Use when after completing dereplication and cosine similarity clustering in the MolNotator workflow, when you have merged, dereplicated molecular and ion data (output from mode_merger and dereplicator steps) and need to assemble the final molecular network representation connecting predicted.
    0 installs
85. ▌
    Centroided Peak Extraction From Hrms · holobiomicslab

    Use when you have centroided data-dependent acquisition (DDA/ddMS2) mzML files from LC- or GC-HRMS measurements and need to systematically detect and characterize MS1 features across the mass-to-charge and retention-time dimensions prior to compound prioritization or suspect screening.
    0 installs
86. ▌
    Chemical Class Assignment Classyfire · holobiomicslab

    Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes molecules by chemical taxonomy.
    0 installs
87. ▌
    Chemical Database Query And Matching · holobiomicslab

    Use when when you have mass-to-charge (m/z) values from mass spectrometry imaging or other MS experiments and need to assign molecular formulae with high precision, especially in spatially-resolved metabolomics where traditional LC-MS annotation methods are insufficient.
    0 installs
88. ▌
    Chemical Noise Tagging And Filtering · holobiomicslab

    Use when you have MS/MS spectra contaminated with chemical noise (spurious fragment ions that do not correspond to real chemical bonds or rearrangements), a known or predicted molecular formula or SMILES structure for the precursor, the adduct type (e.
    0 installs
89. ▌
    Chemical Structure Smiles Assignment · holobiomicslab

    Use when you have a mass spectral library (EI or MS2 format) loaded into R via read_lib() and possess either MOL files (from Lib2NIST export) or an SDF file containing the corresponding chemical structures, but the library entries lack SMILES fields or have incomplete structure information.
    0 installs
90. ▌
    Chromatogram Peak Boundary Detection · holobiomicslab

    Use when when you have loaded a TransitionGroup (extracted ion chromatogram or mobilogram from DIA-MS data) and need to identify precise peak boundaries and apex positions for feature extraction.
    0 installs
91. ▌
    Compound Identifier Mapping Curation · holobiomicslab

    Use when when integrating MS/MS spectra from multiple source repositories or instruments into a unified library, and the compound identifiers, adduct annotations, collision energies, and instrument types differ in format, terminology, or completeness across sources.
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92. ▌
    Coverage Accuracy Metric Computation · holobiomicslab

    Use when you have two sets of lipid annotations—one from baseline spectral library matching and one from an enhanced method (e.
    0 installs
93. ▌
    Dda Spectrum Association To Features · holobiomicslab

    Use when you have centroided DDA mzML data and have already detected MS1 features (either via pyOpenMS or external feature finding), and need to extract MS2 fragment m/z values and diagnostic patterns (e.
    0 installs
94. ▌
    De Novo Mass Spectrum Interpretation · holobiomicslab

    Use when you have MS/MS spectra (centroided m/z and intensity pairs) and corresponding MS1 precursor masses but lack reference spectra or a priori formula information.
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95. ▌
    Detection Limit Threshold Definition · holobiomicslab

    Use when when preparing metabolomics abundance tables with left-censored missingness (values below instrument detection limit or quantification limit) for imputation.
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96. ▌
    Duplicate Spectrum Detection Removal · holobiomicslab

    Use when you have a large collection of MS/MS spectra with harmonized metadata and suspect that spectra for the same compound or adduct acquired under similar conditions may be duplicated or near-identical.
    0 installs
97. ▌
    Feature Consolidation Across Batches · holobiomicslab

    Use when you have two or more CSV feature tables from separate metabolomic experiments (each containing mass, retention time, intensity, isotope, and adduct columns), and you need to align and merge them into a single feature-by-sample matrix where features from different experiments are matched if.
    0 installs
98. ▌
    Few Shot Learning Calibration Design · holobiomicslab

    Use when you have experimental retention times measured on a source chromatographic method and want to predict RTs on a target chromatographic method, but possess only a small set (10–100) of molecules with ground-truth measurements on both methods.
    0 installs
99. ▌
    Fragment Peak Subformula Enumeration · holobiomicslab

    Use when you have a list of fragment peak m/z values and intensities from tandem MS/MS data and need to assign chemical subformulae to each peak for downstream formula ranking or structure inference.
    0 installs
100. ▌
     Fragmentation Pattern Classification · holobiomicslab

     Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
     0 installs