Use when when you have normalized peak intensity matrices from FT-ICR MS data or other high-resolution metabolomics experiments and need to visualize sample relationships and…
Use when you have an ArchR project object with dimensionality reduction results (LSI or combined dimensions from scATAC-seq ± scRNA-seq) and want to infer pseudotime trajectories…
Use when after filtering duplicate reads from ChIP-Seq data but before generating pileup coverage tracks.
Use when you have fitted a linear model to gene expression data (microarray, RNA-seq, qPCR, or proteomics) across multiple samples and need to compute gene-level test statistics.
Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment…
Use when when you have loaded mass spectrometry imaging data into a MSImagingArrays
Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
Use when you have an MS/MS spectrum and a ProForma 2.0 peptidoform specification,
Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or…
Use when when you have a pre-computed hierarchical dendrogram from structural clustering (e.g., of LC-MS features based on m/z and retention time) and want to compare or validate…
Use when when you need to support multiple plotting library backends (static or interactive) for the same data visualization domain (e.
Use when when you have preprocessed 1H NMR spectral data from flavor mixtures or similar compound identification tasks, and you need to identify which compounds are present.
Use when you have a table of detected chromatographic peaks (e.g., from CentWave peak detection in xcms) and need to isolate a single target m/z (e.g., m/z 304.1131 for a…
Use when when you have observed fragment peak m/z values from tandem mass spectra and need to assign chemical subformulae to them.
Use when after batch effect removal and data integration, when you have a feature-by-sample matrix (finalData) and wish to separate and visualize sample groups by their…
Use when you have SMILES strings or molecular structure files (e.g., from a synthetic drug database) and need to feed them into a deep learning model like PS2MS, NEIMS, or DeepEI…
Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test…
Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct infusion MS (DI-MS), ASAP-MS, or other high-throughput ambient ionization methods, an — from…
Use when after running tardisPeaks() with screening_mode=TRUE on centroided .mzML LC-MS data, when you need to visually inspect whether the 10 target compounds (internal standards…
Use when when you have paired MS/MS spectra with known structural similarity labels (Tanimoto scores from molecular fingerprints) and need to predict structural similarity for new…
Use when when you have raw mass spectrometry transition data from a triple-quadrupole
Use when when quantifying or mapping RNA-seq reads with salmon quant using the --writeMappings (-z) flag, or in any streaming output scenario where record count discrepancies…
Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public…
Use when when you have a multi-step computational chemistry or molecular modeling pipeline (3+ sequential or parallel stages) that must process many molecules, each requiring…
Use when you have deposited mass spectrometry imaging datasets in NetCDF (CDF) format with accompanying MATLAB workspace files (.
Use when when designing or optimizing S4-based data backends (such as MsBackend subclasses) and you need to decide whether to pre-populate all slots with complete data structures…
Use when when applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to AnnData objects where the expression matrix X is backed by a dask.array.Array, you need…
Use when after feature table normalization and imputation are complete, immediately before MS1 and MS2 annotation.
Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
Use when you need to verify that a QIIME 2 artifact (e.g., a Chemical Feature Tree from q2-qemistree, a FeatureTable[Frequency], or a Phylogeny[Rooted] object) has been correctly…
Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal…
Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
Use when when comparing the robustness of multiple pathway ranking methods (e.g., PLAGE, ORA, GSEA) on metabolomics or other omics data, and you need to establish which method is…
Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans,…
Use when you have a mass spectrum of an unknown metabolite with a known or inferred precursor m/z, you have run a deep-learning semantic similarity model (e.
Use when you have RNA-seq read count data (from alignment tools, transcript quantification, or feature counting) organized in a count matrix with samples as columns and genes as…
Use when you have raw mzML files and a feature table (CSV) from LCMS data processed by tools like mzMine, and you need to create train/test/validation batches with specific matrix…
Use when after mass-to-charge matching has produced a large table of candidate KEGG metabolites with multiple adduct assignments per feature.
Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural…
Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine…
Use when you are building a new data representation or storage strategy for MS spectra (e.g., on-disk HDF5, SQL database, remote file access) and need to integrate it seamlessly…
Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
Use when when you have TCN-predicted candidate formulas with ranked scores and need to train a Siamese rescore model to re-rank those candidates.
Use when when comparing mapped read counts between two RNA-seq quantification implementations (e.
Use when you have MS/MS spectra matched to a reference library via both identity search (exact or high-similarity matches) and fuzzy/analog search (structurally related compounds…
Use when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each…
Use when you have raw untargeted LC/MS data in open mzML or mzXML format and need to extract a quantified feature matrix (m/z and retention time coordinates with sample…
Use when you have a mass spectral library in MSP format (e.g., from NIST, SWGDRUG, or other sources) exported alongside a folder of MOL files, and you need to populate the SMILES…
Use when after you have processed raw LC-MS/MS spectral data through the specXplore importing pipeline in a Jupyter notebook and produced an in-memory specXplore session data…
Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
Use when when you have generated a set of candidate metabolites for a given experimental MS/MS spectrum and need to determine which candidate is most likely to be the true…
Use when when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries,…
Use when you have two or more complementary scoring functions (e.g., strain correlation and IOKR scores) that you wish to combine, and you need to determine which combination…
Use when you have a peak list extracted from MSI data that includes candidate peaks with potential m/z overlap or spatial co-localization patterns across tissue images.
Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
Use when you have preprocessed MS/MS spectra (noise-filtered, normalized) and need to compute pairwise similarity or distance scores for compound library matching, when your goal…
Use when you have computed or received a precomputed expected contact frequency table (e.
Use when you have SMILES strings for candidate novel psychoactive substance structures and need to convert them into a machine-readable molecular representation before computing…