Skills tagged: metabolomics

• code-repository-analysis - Verify implementation details and compare tool features.

  code-analysisbioinformaticsfeature-verificationdependency-mapping

  ★ 15 · Updated 2026-09-22

  Extracts implementation details from software repositories and documentation to build comparative feature tables.

  ⚙ Clone source repositories⚙ Inspect pipeline code⚙ Cross-reference dependency declarations
• validated-link-enrichment-analysis - Assess GCF-MF link predictions with Fisher exact test

  metabolomicsgenomicsenrichment analysisFisher exact test

  ★ 15 · Updated 2026-09-21

  Quantifies whether high-scoring GCF-MF link predictions are enriched for experimentally validated pairs using Fisher exact test.

  ⚙ Apply score percentile thresholds⚙ Calculate validated link proportions⚙ Perform Fisher exact test
• validated-link-proportional-comparison - Compare validated GCF-MF link enrichment across scores.

  metabolomicsgenomicsFisher exact testlink scoring

  ★ 15 · Updated 2026-09-21

  Compares enrichment of validated GCF-MF links across scoring categories using proportional analysis and Fisher exact tests.

  ⚙ Partition links into scoring categories⚙ Calculate validated link proportions⚙ Compute Fisher exact test p-values
• metabolite-feature-clustering-by-retention-time - Metabolite Feature Clustering by Retention Time

  metabolomicsmass spectrometryfeature clusteringretention time

  ★ 15 · Updated 2026-09-21

  Groups mass spectrometry features derived from the same metabolite using retention time similarity and intensity correlation patterns across samples.

  ⚙ Cluster mass spectrometry features⚙ Calculate retention time similarity⚙ Compute sample intensity correlations
• metabolomics-msdial-preprocessing - Preprocess LC-MS metabolomics data using MS-DIAL

  ms-dialmetabolomicslc-mspreprocessing

  ★ 97 · Updated 2026-09-21

  Processes LC-MS metabolomics data via MS-DIAL, covering peak detection, alignment, annotation, filtering, and export for R and Python analysis.

  ⚙ Detect LC-MS chromatographic peaks⚙ Align peaks across samples⚙ Annotate metabolites using database
• spectral-peak-intensity-normalization - Normalize m/z peak intensities across LC-MS/MS samples.

  metabolomicslc-msnormalizationbatch-correction

  ★ 15 · Updated 2026-09-21

  Normalize m/z peak intensities across LC-MS/MS samples to account for batch effects, sample concentration differences, and technical variation.

  ⚙ Correct batch and concentration variation⚙ Filter low-intensity m/z features⚙ Normalize peak intensity data
• natural-product-classifier-substitution - Substitute NPClassifier for ClassyFire in ConCISE

  metabolomicsconcisenpclassifiergnps

  ★ 15 · Updated 2026-09-20

  Substitutes NPClassifier for ClassyFire ontology assignments in ConCISE consensus classification when GNPS ClassyFire data is unavailable.

  ⚙ Toggle NPClassifier mode in ConCISE CLI⚙ Derive NPClassifier ontologies from annotations⚙ Generate consensus classification outputs
• rippp-candidate-structure-generation - Generate PTM variants of RiPP precursor peptides

  metabolomicsRiPPsmass-spectrometrygenome-mining

  ★ 15 · Updated 2026-09-20

  Enumerates chemical space of PTM variants for RiPP precursor peptides to build a candidate structure database for downstream spectral matching.

  ⚙ Enumerate PTM variants of precursor peptides⚙ Build class-specific RiPP structure databases⚙ Map precursor metadata to candidates
• hmdb-database - Access human metabolome database for metabolite research

  metabolomicsdatabasemetabolitebioinformatics

  ★ 2 · Updated 2026-09-19

  Search, retrieve, and download human metabolite data including chemical properties, biomarker associations, spectra, and pathways.

  ⚙ Search metabolites by text query⚙ Search metabolites by chemical structure⚙ Search metabolites by spectral data
• metabolic-module-significance-calculation - Calculate metabolic module significance for sample traits

  metabolomicswgcnametabodiffmodule-significance

  ★ 15 · Updated 2026-09-19

  Calculates module significance statistics to assess if metabolic correlation modules associate with categorical sample traits.

  ⚙ Calculate module significance statistics⚙ Generate module-trait association plots⚙ Extract significant metabolic correlation modules
• cnn-inference-on-spectral-data - Generate molecular embeddings from MS/MS spectra with CNN

  mass-spectrometrymetabolomicscnninference

  ★ 15 · Updated 2026-09-19

  Passes preprocessed MS/MS spectra through a trained CNN model to extract multidimensional molecular embedding vectors for downstream metabolite matching.

  ⚙ Load preprocessed MS/MS spectral data⚙ Initialize trained CNN model checkpoint⚙ Extract molecular embedding vectors
• ion-to-molecule-relationship-mapping - Map LC-MS ions to predicted molecular networks

  metabolomicslc-msbipartite networkcytoscape

  ★ 15 · Updated 2026-09-18

  Constructs a bipartite network graph linking predicted molecules to parent ions for visualization in Cytoscape.

  ⚙ Construct bipartite network graph⚙ Assign molecular and ion attributes⚙ Export GraphML and CSV files
• feature-metadata-extraction-from-clustering-objects - Extract spectral metadata from RAMClustR clustering objects.

  metabolomicsmass-spectrometryramclustrxcms

  ★ 15 · Updated 2026-09-18

  Extracts m/z, intensity pairs, retention time, and molecular weight annotations from RAMClustR objects for downstream spectral format conversion.

  ⚙ Extract spectral metadata from RAMClustR objects⚙ Verify retention time cluster consistency⚙ Map metadata to target software schemas
• ms1-feature-extraction - Prioritize LC-HRMS features using MS1 chemical predictors

  LC-MSmetabolomicssuspect-screeningfeature-extraction

  ★ 15 · Updated 2026-09-18

  Extracts and integrates MS1 chemical predictors to compute proximity scores and prioritize candidate compounds in LC-HRMS suspect screening workflows.

  ⚙ Compute mass error distance scores⚙ Calculate retention time proximity⚙ Match theoretical isotopic patterns
• precursor-mz-window-filtering - Filter MS spectra by precursor m/z to generate negatives.

  mass spectrometrymetabolomicsdata augmentationprecursor m/z

  ★ 15 · Updated 2026-09-18

  Filters mass spectrometry spectra by precursor m/z proximity to generate negative training examples within a defined mass window.

  ⚙ Filter spectra by precursor m/z⚙ Generate cross-spectrum negative examples⚙ Downsample dataset to target ratio
• spectral-metadata-integration - Integrate MS2 spectra with feature groups in DDA LC-MS

  metabolomicslc-msddaspectral-consolidation

  ★ 15 · Updated 2026-09-18

  Extract, consolidate, and annotate MS2 spectra with isotopic relationships and adduct information across grouped feature ions in DDA LC-MS workflows.

  ⚙ Retrieve MS2 scans from raw data⚙ Select representative MS2 spectra⚙ Annotate spectral metadata
• mass-spectrometry-target-list-preparation - Prepare TARDIS-compatible target lists for LC-MS analysis.

  mass-spectrometrylc-msmetabolomicstardis

  ★ 15 · Updated 2026-09-17

  Loads compound spreadsheets, filters by ionization polarity, and extracts target metadata into standardized data frames for LC-MS analysis.

  ⚙ Load tabular compound files⚙ Filter targets by ionization polarity⚙ Extract compound metadata columns
• positional-encoding-for-spectral-sequences - Positional encoding for mass spectrum tensors in IDSL_MINT

  metabolomicsmass-spectrometrypositional-encodingtransformer

  ★ 15 · Updated 2026-09-17

  Embeds ordinal and sequential information into mass spectrum m/z-intensity pairs for transformer encoder layers in IDSL_MINT.

  ⚙ Compute sinusoidal positional encodings⚙ Add positional encodings to embeddings⚙ Prepare spectrum input tensors
• pyopenms - Python Platform for Mass Spectrometry Data Processing

  mass-spectrometryproteomicsmetabolomicspyopenms

  ★ 602 · Updated 2026-09-16

  Provides Python bindings to OpenMS for proteomics and metabolomics data processing, feature detection, and identification.

  ⚙ Load mass spectrometry data files⚙ Filter and smooth spectral signals⚙ Detect and link spectral features
• pyopenms - Python Interface for Mass Spectrometry Data Analysis

  mass-spectrometryproteomicsmetabolomicspyopenms

  ★ 2 · Updated 2026-09-16

  PyOpenMS provides Python bindings to OpenMS for proteomics and metabolomics mass spectrometry data processing, feature detection, and identification.

  ⚙ Load mass spectrometry file formats⚙ Process raw spectral data⚙ Detect and link spectral features

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