Use when immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality…
Use when you observe sawtooth or discontinuous peak profiles in EICs after running tardisPeaks() on LC-MS data acquired with multiple overlapping or sequential m/z scan windows…
Use when you have a feature-by-sample matrix (rows = annotated chemical features such as m/z, retention time, GNPS spectral library matches;
Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS)…
Use when you have R Spectra objects and need to apply Python-only MS algorithms (e.
Use when when annotating large-scale untargeted metabolomics datasets where reference library coverage is incomplete and you need to infer metabolite identities for unannotated…
Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs,…
Use when when you have multiple batches of metabolomics data in SummarizedExperiment
Use when when you have validated SMILES strings or RDKit molecule objects representing chemical structures and need to feed them into a pre-trained deep learning model (such as…
Use when you have downloaded raw LC-MS spectral peak data from a public repository (e.g., DOI 10.25345/C5FD2F) and need to ingest it into memory and prepare it in the format…
Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before…
Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a…
Use when when you have pre-computed Word2vec spectrum embeddings and need to perform fast approximate nearest-neighbor retrieval from a library of millions of spectra (e.g., NIST…
Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
Use when after running DESeq() and extracting base results with results(), apply shrinkage when you have differential expression estimates and want to reduce the variance of log…
Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for…
Use when you have a count matrix (genes × samples) from HTSeq, featureCounts, or transcript abundance quantification (Salmon, kallisto), a sample metadata table with experimental…
Use when after completing outlier detection, batch correction, and quality metric calculation on a SummarizedExperiment object using mzQuality's doAnalysis function, and after…
Use when you have transcript-level quantification (salmon, Sailfish, or kallisto output) summarized to gene level by tximport, and you observe or suspect differential isoform…
Use when after loading and preprocessing a Cardinal MSImagingExperiment object (with normalized peaks and optional spatial segmentation results), and before conducting spatial…
Use when after executing a Nextflow-based LC-HRMS metabolomics workflow with Docker or Singularity containerization on .mzML LC-MS data, before proceeding to downstream…
Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by…
Use when you have one or more small-molecule chemical structures (as SMILES, MOL, or SDF) and need to systematically explore their fate across mammalian biotransformation, human…
Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and you need to quantify whether measured C — from…
Use when when you have raw or preprocessed 1H NMR spectral tensors from flavor or chemical mixtures and need to generate high-level feature representations that capture both…
Use when you have a 1D ¹H NMR spectrum (as chemical shift vs. intensity) and a corresponding peak list (chemical shift values), and you need to identify which metabolites are…
Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an…
Use when you have a tandem MS/MS spectrum of a structurally modified compound and a known reference structure (SMILES), and you need to annotate which fragment ions correspond to…
Use when when you have an mzML file that you want to store persistently in a queryable format for repeated access, or when memory constraints prevent loading entire mzML files…
Use when you have Spectra objects in an R environment and need to apply Python MS algorithms (e.g., matchms similarity scoring, spectrum normalization, or filtering) that operate…
Use when you have generated a lipid spectral library (with lipid identities, adducts, m/z values, and fragmentation patterns) and need to export it for downstream mass…
Use when after defining a transformer encoder architecture with multi-head self-attention and positional encoding, and before training or inference on mass spectrometry data.
Use when you have raw INADEQUATE NMR spectra files and need to transition from continuous spectral data to discrete peak coordinates.
Use when you have executed a spectrum search against one or more domain-specific
Use when when you need to verify a Python package installs successfully from a cloned or local repository, validate that all tests pass after installation, or prepare a…
Use when after peak detection and before any comparative analysis (e.g., diversity indices, ordination, or statistical testing) when working with direct injection FT-ICR MS data…
Use when when starting a fresh ENPKG installation, you have a GitHub URL (e.g., https://github.com/enpkg/enpkg_full or https://github.
Use when when two mapping implementations (or versions of the same mapper) show disagreement on per-read mapping status—e.g., one mapper leaves reads fully unmapped that the other…
Use when after XCMS feature detection and retention time correction, when you have a feature table (CSV or XCMS object) with m/z and retention time values aligned across samples.
Use when you have a feature table from LC-MS analysis (containing m/z, retention time, and intensity values) and need to identify which detected features represent the same…
Use when apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection…
Use when when you have seed metabolite structures (SMILES or MOL format) from metabolomics data and a curated biotransformation rule database (each rule specifying reactant…
Use when you have an untargeted metabolomics dataset with partial metabolite annotations (from database matching or prior curation) and need to extend annotation coverage to…
Use when when you have raw mzML or mzXML mass spectrometry files with uncompressed numeric arrays (not pre-compressed with zlib or msnumpress) and need to reduce file size for…
Use when when designing a targeted lipidomics experiment and you have lipid species definitions (including chain composition and adducts) but need to configure precursor–fragment…
Use when you have acquired complementary spectroscopic measurements (NMR, HSQC, COSY, IR) for the same molecular sample and need to combine them for structure elucidation.
Use when when you have a web-based visualization of aligned mass spectrometry peaks (m/z, intensity, retention time, alignment quality metrics) and need users to interactively…
Use when you have mzPeak files (Parquet-based archives containing mass spectrometry spectra and chromatogram data) that you want to analyze in R, and you need to convert the Arrow…
Use when training embeddings from MS/MS spectra and you need to simultaneously enforce: (1) discrimination between spectra with different structural properties via contrastive…
Use when after NPFimg's automated detection algorithm has identified marker features from a two-dimensional MS map (m/z vs retention time), especially when you need to validate…
Use when when you have loaded a raw mass spectrum (e.g., ESI_NEG_SRFA.d in Bruker or .raw format) and need to apply one of several noise-threshold strategies based on user…
Use when you have spatial metabolomics data with semi-colon-delimited multi-isomer annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you want to quantify…
Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its — from…
Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and…
Use when after executing feature detection and quantification on raw LC-MS data (mzML or NetCDF format) using an automated pipeline such as MetaboAnalystR 4.0, and before…
Use when when you have access to a set of gallery or benchmark scripts executed across multiple plotting backends and need to quantify which backend delivers the fastest median…
Use when you have mass spectrometry spectral data from multiple instrument types (e.g., direct infusion MS, ambient ionization MS, laser desorption/ionization MS) and need to…
Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity…
Use when you have an experimental or public MS/MS spectrum (e.g., from MassBank in msp format, or a raw centroid-mode chromatogram) and need to create a reusable library entry for…
Use when you have ion-mobility mass spectrometry metabolomics data with putative metabolite identifications (e.g., from database matching) and want to reduce false positives by…