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HolobiomicsLab

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1. ▌
   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
2. ▌
   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.
   2 installs
3. ▌
   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
4. ▌
   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
5. ▌
   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
6. ▌
   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
7. ▌
   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
8. ▌
   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).
   2 installs
9. ▌
   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.
   2 installs
10. ▌
    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
11. ▌
    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
12. ▌
    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
13. ▌
    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.
    2 installs
14. ▌
    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
15. ▌
    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
16. ▌
    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.
    2 installs
17. ▌
    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.
    1 install
18. ▌
    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
19. ▌
    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.
    3 installs
20. ▌
    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.
    2 installs
21. ▌
    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
22. ▌
    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
23. ▌
    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.
    2 installs
24. ▌
    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.
    2 installs
25. ▌
    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
26. ▌
    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
27. ▌
    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
28. ▌
    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
29. ▌
    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
30. ▌
    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
31. ▌
    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
32. ▌
    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
33. ▌
    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
34. ▌
    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
35. ▌
    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
36. ▌
    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.
    2 installs
37. ▌
    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
38. ▌
    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
39. ▌
    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.
    1 install
40. ▌
    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
41. ▌
    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.
    2 installs
42. ▌
    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
43. ▌
    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.
    2 installs
44. ▌
    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
45. ▌
    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
46. ▌
    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
47. ▌
    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.
    2 installs
48. ▌
    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.
    2 installs
49. ▌
    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
50. ▌
    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.
    0 installs
51. ▌
    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
52. ▌
    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
53. ▌
    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.
    0 installs
54. ▌
    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.
    2 installs
55. ▌
    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.
    2 installs
56. ▌
    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
57. ▌
    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
58. ▌
    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.
    2 installs
59. ▌
    Fragmentation Pattern Classification · holobiomicslab

    Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
    2 installs
60. ▌
    Graph Based Knowledge Representation · holobiomicslab

    Use when annotating metabolites in untargeted metabolomics experiments where both established biochemical pathways and experimental MS2 similarity patterns must be simultaneously leveraged.
    0 installs
61. ▌
    Graph Node Edge Attribute Assignment · holobiomicslab

    Use when you have statistically significant LC-MS features grouped into structural clusters (isotopologue groups, adduct groups, cross-assay links) and correlation cluster assignments from upstream MamsiStructSearch, and you need to create an interactive graph representation suitable for Cytoscape.
    1 install
62. ▌
    Heterogeneous Graph Embedding Design · holobiomicslab

    Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time prediction across different chromatographic columns, methods, or conditions).
    0 installs
63. ▌
    Hit Metric Evaluation Fold Averaging · holobiomicslab

    Use when when you have a trained MS/MS spectral embedding model and need to measure compound identification accuracy on a held-out test set, but want to mitigate sensitivity to a single random train/test split. Use this skill if the original training set split is fixed (e.
    0 installs
64. ▌
    Hydrogen Rearrangement Rules Scoring · holobiomicslab

    Use when after MS-CleanR has filtered and clustered LC-MS features and formatted them for MS-FINDER input (m/z, retention time, MS/MS spectra).
    0 installs
65. ▌
    Interactive Plot Customization Bokeh · holobiomicslab

    Use when when you have loaded extracted ion chromatogram traces (via SqMassLoader from sqMass files) and need to render them as interactive web-based visualizations where users can pan, zoom, hover for metadata, mute individual traces, and optionally visualize peak boundaries from OpenSwath results.
    2 installs
66. ▌
    Interactive Visualization Inspection · holobiomicslab

    Use when after msFeaST pipeline execution has produced a dashboard_data.json file containing quantification, metadata, and spectral matrices, or when you need to validate that preprocessing steps correctly loaded and rendered ms/ms feature data before downstream statistical or network analysis.
    0 installs
67. ▌
    Internal Standard Feature Extraction · holobiomicslab

    Use when you have processed LC-MS run data (feature table or peak detection output) containing internal standard identifications and need to monitor internal standard retention time, m/z, and intensity variation across samples as part of automated or user-defined QC checks during instrument runs.
    0 installs
68. ▌
    Ion Mobility Dimension Interpolation · holobiomicslab

    Use when when processing raw IM-MS data (Agilent MassHunter .
    0 installs
69. ▌
    Ion To Molecule Relationship Mapping · holobiomicslab

    Use when after dereplication and cosine similarity clustering have been completed and you have merged molecular predictions with ion metadata (m/z, adduct type, intensity).
    0 installs
70. ▌
    Isotope Adduct Anchor Identification · holobiomicslab

    Use when when you have extracted mass tracks (EICs) from individual LC-MS samples and need to establish reliable landmarks for subsequent pairwise or global alignment across a cohort.
    0 installs
71. ▌
    Isotope Labeling Data Interpretation · holobiomicslab

    Use when you have LC-MS FAM measurements from an isotope-labeling experiment and need to correct them to obtain true MDV values.
    2 installs
72. ▌
    Jupyter Notebook Workflow Automation · holobiomicslab

    Use when when you have raw LC-MS/MS spectral data in .
    2 installs
73. ▌
    Kegg Pathway Prediction From Spectra · holobiomicslab

    Use when you have untargeted MS2 spectral data (in MS2MP-compatible format) and need to assign KEGG pathway annotations to unknown metabolites.
    0 installs
74. ▌
    Lc Hrms Metabolomics Data Processing · holobiomicslab

    Use when you have LC-HRMS raw data files (.mzML or .abf format) from metabolomics experiments and need to extract, align, and annotate features in a reproducible manner across multiple computational environments.
    1 install
75. ▌
    Lc Ms Scan Acquisition Orchestration · holobiomicslab

    Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that strategy will acquire MS1 and MS2 scans over a defined retention-time window.
    0 installs
76. ▌
    M Z Alignment And Mass Grid Assembly · holobiomicslab

    Use when when processing multiple centroided mzML LC-MS files from the same study and you need to identify which mass tracks represent the same metabolite across samples.
    2 installs
77. ▌
    Mass Distribution Vector Calculation · holobiomicslab

    Use when you have raw LC-MS fractional abundances (FAM) data from isotope labeling experiments and need to obtain true mass distribution vectors (MDV) that represent only the isotopic labeling contribution.
    2 installs
78. ▌
    Mass Spectra Encoding Neural Network · holobiomicslab

    Use when you have a collection of MS/MS spectra (in mzML or MGF format) from a proteomics experiment and need to group or retrieve spectra derived from the same peptide without prior peptide identification.
    1 install
79. ▌
    Mass Spectral Fingerprint Generation · holobiomicslab

    Use when you have unaligned MS2 spectra from one or more samples (in formats like .mgf, .mzML, or .mzXML) and need to compare them in a retention-time-agnostic manner.
    0 installs
80. ▌
    Mass Spectrometry Benchmark Analysis · holobiomicslab

    Use when you have implemented or modified a tandem mass spectrometry formula inference model and need to measure whether a specific architectural change (e.
    0 installs
81. ▌
    Mass Spectrometry Data Format Import · holobiomicslab

    Use when you have raw mass spectrometry data in one of the supported spectral formats (mzML, mzXML, msp, MGF, JSON, or metabolomics-USI) and need to load it into a Python environment for cleaning, processing, or similarity comparison.
    0 installs
82. ▌
    Mass Spectrometry Data Normalization · holobiomicslab

    Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed peak information into a transformer-based spectral embedding model that expects normalized, fixed-length tensor inputs.
    0 installs
83. ▌
    Mass Spectrometry Data Preprocessing · holobiomicslab

    Use when you have raw LCMS data in mzML or mzXML format from DDA, DIA, or fullscan analyses and need to extract metabolite features with unified m/z, retention time, and intensity values across multiple samples before performing MS2 annotation or in-source fragment analysis.
    1 install
84. ▌
    Correlation Matrix Construction · holobiomicslab

    Use when after obtaining per-sample model predictions and metabolite signal intensities from a trained deep learning model (e.g., DeepMSProfiler) on LC-MS data from multiple disease groups, and you need to identify and visualize metabolite–disease associations as correlation strengths.
    0 installs
85. ▌
    Cross Software Feature Matching · holobiomicslab

    Use when you have collected feature lists in CSV format from two or more MS acquisition methods (e.g., LC-MS vs. LC-IMS-MS), processing software packages (e.g., vendor-specific vs. open-source), or instrument platforms (e.
    0 installs
86. ▌
    Document Structure Verification · holobiomicslab

    Use when when uploading or ingesting paired omics project documents into the Pairing Omics Data Platform, or when you need to verify that a JSON project file conforms to the expected schema structure before processing MS/MS mass spectra linkages, genome associations, or submission to external.
    0 installs
87. ▌
    Evaluation Data Object Handling · holobiomicslab

    Use when after completing an Environment simulation run with save_eval flag enabled, when you need to preserve the EvaluationData object containing scan provenance, chemical source definitions, and fragmentation events for later inspection, validation, or reanalysis without re-running the full.
    0 installs
88. ▌
    Exact Mass Accuracy Calculation · holobiomicslab

    Use when you have feature pairs identified by temporal correlation in direct-injection MS data and need to confirm their relationship is consistent with known adduct/fragment mass shifts.
    0 installs
89. ▌
    Feature Abundance Normalization · holobiomicslab

    Use when after peak picking (e.g., via MS-DIAL) and quality control filtering, when you have a raw feature abundance matrix with intensity values across multiple samples and need to make intensities comparable before statistical testing or multivariate analysis.
    0 installs
90. ▌
    Feature Annotation Augmentation · holobiomicslab

    Use when when a traditional peak extraction pipeline (e.g., XCMS) has generated a feature table from LC-MS data but fails to detect known or suspected compounds present in your sample. Specifically, when you have a suspect database (e.
    0 installs
91. ▌
    Feature Grouping By Mass Defect · holobiomicslab

    Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.
    0 installs
92. ▌
    Feature Quantification Analysis · holobiomicslab

    Use when when you have loaded search result files from one or more DIA-MS analysis tools and need to assess the quantitative performance of identified features.
    0 installs
93. ▌
    Feature Specificity Calculation · holobiomicslab

    Use when when you have a quantitative feature table from MZmine2/MZmine3 with peak area and m/z data aligned across multiple extract samples, and you need to identify which features are characteristic of individual samples (high specificity) versus ubiquitous across the extract set.
    0 installs
94. ▌
    Fragment Match Rate Computation · holobiomicslab

    Use when after denoising MS/MS spectra at multiple frequency thresholds and matching each thresholded spectrum against a -matching reference spectrum.
    0 installs
95. ▌
    Gap Filling Algorithm Selection · holobiomicslab

    Use when when processing untargeted LC-MS data with SLAW and observing incomplete feature detection across the sample cohort—i.e., features present in some samples but with missing values (zeros or NAs) in others due to signal dropout, retention time drift, or mass calibration drift.
    0 installs
96. ▌
    Gcf Mf Hierarchical Aggregation · holobiomicslab

    Use when when you have predicted BGC-spectrum IOKR scores or other pairwise linking scores, and need to rank genomic clusters (GCFs from BiG-SCAPE) against metabolomic clusters (MFs from MS/MS spectra grouping), particularly in NPLinker workflows where one GCF may contain multiple BGCs and one MF.
    0 installs
97. ▌
    Gcf Mf Link Scoring Computation · holobiomicslab

    Use when you have paired GCF and MF datasets with strain membership information and need to rank candidate GCF–MF links to identify which biosynthetic gene clusters likely produce detected metabolites.
    1 install
98. ▌
    Gcf Spectra Association Ranking · holobiomicslab

    Use when when you have integrated genomic data (GCFs from AntiSMASH via BigScape clustering) and metabolomic data (spectra and molecular families from GNPS molecular networking) and need to identify and rank which secondary metabolites detected in spectra are likely produced by which biosynthetic.
    0 installs
99. ▌
    Gnps Workflow Result Processing · holobiomicslab

    Use when when you have run a spectral networking job on GNPS (e.g. ProteoSAFe-METABOLOMICS-SNETS-V2) and need to reuse the network output files locally with MetaMiner or another tool that accepts spectral network input directories.
    0 installs
100. ▌
     Inchikey Smiles Standardization · holobiomicslab

     Use when when you have raw MS/MS spectra from repositories like GNPS that lack or have inconsistent chemical structure annotations (InChI/SMILES), and you need to produce a curated dataset with uniform 14-character InChIKey and SMILES/InChI annotations for downstream machine learning or similarity.
     0 installs