Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with…
Use when you have acquired LC-MS peak tables from both unlabeled (12C) and isotope-labeled (13C) samples from a stable isotope tracing experiment, paired with sample metadata…
Use when when you have a set of molecules with known chemical structures and need to prepare them for classification or prediction tasks.
Use when you have independently generated or received both scATAC-seq peak count matrices and scRNA-seq gene expression matrices from the same set of cells (multiome experiment),…
Use when when you have raw tandem mass spectra in mz/intensity format with precursor m/z values, and need to extract all fragmentation features (observed peaks and neutral losses)…
Use when you receive a JSON response from a REST API endpoint (e.g., TensorFlow Serving /model/metadata) and need to extract and validate specific fields such as model input…
Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API.
Use when your research proposes a new spectral embedding, matching algorithm, or retrieval method and you need to quantify its improvement over known baselines.
Use when you have a feature table from LC-MS data alongside blank (solvent-only) sample runs, and you want to remove features whose intensity in study samples is not substantially…
Use when when tabulating chemical annotation enrichment (e.g., GNPS spectral library matches) across sample groups stratified by metadata category (e.g., sample type, extraction…
Use when you have trained multiple machine learning classifiers (e.g., AdaBoost, SVM, Random Forest) on the same metabolomics peak-quality training set using k-fold…
Use when you have GNPS-style MGF spectral files from MS/MS experiments and need to predict the molecular structure (as SMILES) of unknown compounds.
Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular…
Use when after executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix…
Use when raw Agilent MassHunter (.d) or UIMF mass spectrometry files exhibit jagged or noisy peaks, particularly for low-abundance ions where signal-to-noise ratio is poor.
Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with…
Use when after calling buildExperiment on metabolomics data to construct a SummarizedExperiment object, before performing batch correction, outlier detection, or other QC…
Use when when you have a small set of matched reference features (isolated, high-quality chromatographic peaks from reference chromatograms that have been aligned to a…
Use when you have raw spectroscopic datasets from heterogeneous sources (multiple Zenodo repositories with different file formats and scales) that must be jointly normalized,…
Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral…
Use when you have CE-MS test files archived in the msdata Bioconductor package and need to load them into an in-memory or on-disk R representation to extract ion…
Use when after constructing baseline-corrected mass tracks (either composite across samples or per-sample) when you need to identify individual chromatographic peaks for feature…
Use when when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform untargeted feature detection with chromatographic alignment across multiple…
Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association…
Use when when importing a tab-delimited or Sciex OS text export metabolomics dataset into mzQuality, before building the SummarizedExperiment object.
Use when when you are developing or contributing to a Python package (like cooltools) and need to test changes to utility functions, library integrations, or API implementations…
Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon…
Use when when you have Thermo Orbitrap .raw files containing known reference peptides (e.
Use when you need to set up a cloned or downloaded scientific Python package for local development, testing, or execution.
Use when you have statistically significant LC-MS features (e.g., filtered by p-value < 0.01) from multi-assay metabolomics datasets and need to group features that represent the…
Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for…
Use when after chromatographic peak detection on preprocessed LC-MS data when you have an xcms result object (XcmsExperiment or xcmsSet) with detected peaks and need to collapse…
Use when after mass tracks have been aligned across samples into a MassGrid structure (m/z-aligned, same mass-to-charge ratio) and retention time calibration dictionaries — from…
Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before…
Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert…
Use when after feature extraction and quality control filtering (blank masking, sample dropping, normalization) have been applied, but before statistical analysis or machine…
Use when when fitting a nonlinear retention time (RT) mapping spline to anchor feature pairs (m/z and RT values) from two LC-MS datasets acquired under different conditions, you…
Use when after applying frequency domain calibration (Ledford, linear, or quadratic equation) to a raw FT-ICR mass spectrum, validate the calibration quality by measuring residual…
Use when after LDA topic inference has assigned dominant topic labels to mass spectra, and before those labels are passed to MLP or GNN multi-task training.
Use when when you have an existing real mzML file from a metabolomics LC-MS/MS acquisition (e.g., beer or urine samples) and need to populate a virtual mass spectrometer with the…
Use when when you have raw feature tables exported from a tandem LC-MS/MS preprocessing tool (e.g., Progenesis QI, MS-DIAL, Bruker Metaboscape) and need to combine them with…
Use when after obtaining 512-dimensional representation vectors from the Encoder module, when you need to compress these vectors for visualization, clustering, or downstream…
Use when after instantiating a specXplore dashboard session layer with a loaded session data object from disk, before conducting visual exploration of LC-MS/MS spectral data.
Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate…
Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and…
Use when you have raw ChIP-Seq and control BED files with potential PCR duplicates or unequal sequencing depths.
Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate…
Use when gNPS has ceased supplying ClassyFire ontology information for spectral library matches, causing downstream ConCISE consensus classification to fail or produce incomplete…
Use when when processing in-silico or experimental MS spectra records from databases with incomplete metadata, specifically when the adduct field is null or absent but the ionmode…
Use when after computing a pairwise sample distance matrix from aligned MS2 fingerprint vectors and you need to visualize sample relationships, clustering, or separation by group…
Use when when processing multiple LC-MS samples in a cohort study and MassGrid construction reveals that anchor mass tracks (13C/12C isotope or Na/H adduct pairs) in non-reference…
Use when you have extracted metadata or spectral information from a Thermo Fisher Scientific .
Use when after successfully resolving a USI string to a specific mass spectrum scan, and before performing spectral matching, library search, or comparative analysis.
Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to…
Use when when you have access to a curated dataset (such as LOTUS) with published headline statistics in a peer-reviewed article or enriched index, and you need to validate data…
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 after anchor selection and retention-time spline mapping have produced a candidate list of feature pair alignments, but before final scoring and reduction of the combined…
Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to…
Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
Use when you have a validated or curated dataset (e.g., a TSV or gzip-compressed