Use when when benchmarking or validating the scalability of single-cell algorithms that claim linear or sublinear space complexity, particularly when processing datasets with ≥10…
Use when a user supplies a custom feature list from external feature-finding software (vendor tools, alternative open-source pipelines) instead of using pyOpenMS automatic…
Use when when you need to extract m/z and intensity peak values from a Spectra object backed by MsBackendMzR or similar on-disk backends; when analyzing subsets of spectra without…
Use when when you have an untargeted metabolomics dataset with MS2 fragmentation
Use when when you have a chromVARDeviations object with multiple annotation sets (e.
Use when when you have both an observed NMR mixture spectrum and a candidate reconstructed spectrum (each represented as intensity distributions across chemical shift bins), and…
Use when after an end-to-end neural model (CNN + transformer) has generated predicted molecular structures (formula and connectivity) from 1D NMR spectra.
Use when when you need to enable non-programmers or domain experts to formulate complex, unambiguous queries over specialized data (e.
Use when you have a GC-MS results table with a Match.Factor column (representing identification confidence) and you need to understand how many distinct compounds survive at…
Use when you need to validate that a published software tool (e.g., MassQL) executes correctly in your environment, reproduce published results, or contribute to development.
Use when you have processed the same set of untargeted LC/HRMS files (mzXML, mzML, or netCDF format) with two or more peak-picking tools and need to validate which tool produces…
Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or…
Use when when extending MSMetaEnhancer with a new local chemical transformation (e.g., SMILES to InChI) that should execute non-blockingly within an asynchronous annotation…
Use when you have a baseline GNN model trained on a molecular property prediction task (e.
Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
Use when you have raw mass spectrometry outputs (peak areas/heights across samples and fragmentation spectra) that need to be formatted and validated before running the tima…
Use when when you have ionized adduct structures (SMILES or MOL format) from an ionization-state determination step and need to create an ensemble of relaxed 3D geometries for…
Use when you have a feature table from untargeted metabolomics (with m/z, retention time, and p-values from differential abundance testing) but lack or wish to bypass metabolite…
Use when when you have multiple file format variants (compressed indexed gzip, standard gzip, SQLite database, uncompressed mzML) that all need to be read via a unified interface,…
Use when you have untargeted MS2 spectral data (from LC-MS/MS or similar instruments) and need to assign metabolic pathway context to detected compounds when standard spectral…
Use when after extracting and optionally combining MS2 spectra from a chromatographic peak (e.g., at a known m/z value like 304.1131), you need to determine which compound(s) in a…
Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single…
Use when you have a metabolomic SummarizedExperiment object with replicate QC (quality control) samples and need to remove non-reproducible metabolic features before phenotype…
Use when when you need to read proprietary or binary data formats (e.g., Thermo Fisher .raw files) from R but the native implementation is in .NET/C#, and direct language bindings…
Use when when you have a trained deep learning model (e.g., PS2MS) and an evaluation dataset of compounds, and you need to assess how prediction confidence varies across…
Use when you need to confirm that omitting an optional input parameter (such as secondaryAssay in buildExperiment) produces the expected mathematical result—specifically, when a…
Use when when you have 1D NMR spectra (1H and/or 13C) of an unknown compound with up to ~19 heavy atoms and need to predict both molecular formula and connectivity without manual…
Use when after acquiring a PRM experiment on a Thermo Fisher Orbitrap instrument when you need to verify that the mass spectrometer's data acquisition controller executed the…
Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment…
Use when you have paired spatial transcriptome and metabolome datasets (both as h5ad files with .obsm['spatial'] coordinate matrices and .
Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and…
Use when after peak detection when you have a table of detected peaks with m/z values and retention times from LC/HRMS data, and you observe systematic m/z drift across a — from…
Use when after loading and normalizing a beta-valued methylation matrix (450K or EPIC array), apply SVD interpretation when you need to assess whether observed variation is driven…
Use when you have received raw FT-ICR transient data from Bruker Solarix or ThermoFisher instruments and need to perform signal processing, apodization, calibration, or molecular…
Use when when designing or optimizing backends that handle large MS datasets (mzML, mzXML, CDF files via MsBackendMzR), to verify that claimed memory advantages of on-disk or…
Use when you have detected features in LC- or GC-HRMS data (via pyOpenMS or custom feature tables) and need to systematically rank them for likelihood of being PFAS compounds.
Use when when you have a set of query chemical compounds (by name or SMILES) and a reference library organized into named groups (e.
Use when when you need to verify that a wrapper package (e.g., rawrr) correctly bridges R and a managed .NET assembly (such as RawFileReader), specifically to confirm that…
Use when when you have generated a feature abundance matrix from mzrtsim() peak list simulation with known sample-level attributes (condition assignments, batch labels, sample…
Use when you have computed raw p-values from partial Spearman correlations (or other univariate tests) between each metabolite in a SummarizedExperiment object and a phenotype of…
Use when when you have imported raw mass spectrometry spectral data (in formats like mzML, mzXML, msp, MGF, or JSON) and need to clean peak lists before metadata validation,…
Use when after executing a Nextflow-based MS-DIAL workflow on .mzML LC-HRMS metabolomics data using Docker or Singularity container backends.
Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d) or UIMF format with jagged peaks and low-abundance ions that require signal enhancement, but you need to…
Use when you have a raw metabolite abundance matrix (e.g., from MSPrep or another LC-MS/MS pipeline) with many features and samples, and you observe that a substantial fraction of…
Use when you have multiple mzML or HDF5 feature tables from the same study acquired on the same or similar instruments and need to align feature coordinates across samples to…
Use when after rMSIcleanup has classified ions as matrix-related or non-matrix, and you need to audit, validate, or communicate the annotation decisions.
Use when when you have an unknown metabolite compound with mass spectral data, have retrieved candidate structures from a molecular structure database (PubChem, HMDB), and have…
Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) and need to convert them into normalized, queryable spectral objects for downstream anal — from…
Use when you have GC–MS data from human breath samples and need to identify marker metabolites for disease diagnosis, phenotyping, or biomarker discovery without a predefined…
Use when when you need to confirm that a Java project's GitHub Actions workflow (e.g., 'dev_build_release.yml') has completed successfully and generated usable build artifacts;
Use when after uploading a sample list to InjectionDesign and before performing inter-batch balancing and intra-batch randomization.
Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend.
Use when you have SWATH-MS data (mzML or vendor binary format) where precursor isolation windows intentionally capture multiple co-eluting compounds, resulting in multiplexed…
Use when when you have loaded centroided .mzML files into a Spectra object and plan to use TARDIS (tardisPeaks) with an MsExperiment object rather than file paths, and you need…
Use when you have mzML/mzXML chromatogram files from Thermo, Waters, or Bruker instruments and need to extract MS1 and MS2 scans matching both a target m/z value AND a known or…
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…
Use when you have raw mzML files and feature tables (CSV format from mzMine or XCMS) from untargeted LCMS experiments and need to distinguish true metabolite peaks from false…
Use when when you have detected multiple features from non-targeted mass spectrometry and need to group them by putative compound origin.
Use when you have untargeted metabolomics data with unknown metabolite structures and need to generate plausible candidate products by systematically applying known enzymatic or…
Use when after bias correction of ATAC-seq reads (via ATACorrect) when you have a bias-corrected bigWig file and need to measure transcription factor footprint strength within…