Use when after executing a Squidpy spatial analysis function (e.g., gr.spatial_neighbors, gr.nhood_enrichment, gr.sepal, im.
Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100…
Use when you have raw Illumina EPIC or 450k methylation array data (.idat files or beta-valued matrices) and need to perform comprehensive quality assessment, probe correction,…
Use when when preparing raw mass spectrometry imaging (MSI) ion images for deep learning–based representation learning, especially when you need to generate augmented image pairs…
Use when after executing MassQL queries against a MotifDB reference database and retrieving ranked motif matches, when you need to determine which database entries represent true…
Use when when you need to enable bracket notation (e.g., handler[5]) for random access to blocks within a large compressed or remote data source, or when you want to support both…
Use when when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
Use when you have computed low-dimensional embeddings (e.g., t-SNE coordinates) or clusterings of mass spectra and need to validate that the learned representation space organizes…
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 applying AbundanceSimilarityParam (with threshold ≥0.7 and log2 transform) to retention-time-based feature groups from SimilarRtimeParam, when you need to examine…
Use when you have two separate LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to establish feature-to-feature correspondence…
Use when when you have baseline MS/MS peak annotations from a known compound but need to refine them using newly available structural information (e.
Use when after autoQ has extracted isotopologue peak area measurements from mz(X)ML files and you need to prepare the integrations data frame for visualization with metBarPlot or…
Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate…
Use when you have a user-submitted spectrum with associated domain context metadata (e.g., selected as 'microbial origin', 'plant tissue', 'food sample') and need to route that…
Use when when you have MS/MS spectra from both query compounds and a reference library and need to decide which similarity metric will maximize identification accuracy (true…
Use when you have aligned ChIP-Seq reads (in BED or BEDPE format) and need to convert them into quantitative genome-wide signal tracks (coverage, p-value, or q-value scores) for…
Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which…
Use when after generating an ensemble of 3D conformers via RDKit conformation sampling, when you need to reduce the conformer set size before expensive quantum-chemical…
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…
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 loaded MSI data with an extracted peak list and need to annotate matrix-related signals, particularly when the dataset may contain isobaric ions or peaks with…
Use when after detecting local-maxima in LC-HRMS profile mode datasets and before training or inference with a CNN model for peak classification.
Use when when you need to generate 2D metabolomic NMR spectra (COSY for homonuclear or HSQC/HMQC for heteronuclear correlations) from parsed metabolite concentration and…
Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be…
Use when when you have loaded an unprocessed Cardinal object from MS imaging data (e.g., from Zenodo or native formats) containing thousands of m/z features across many spectra,…
Use when when training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments…
Use when you have sampled flux distributions from two or more constraint-based metabolic models representing different biological conditions (e.
Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.
Use when when you have aligned paired scATAC-seq and scRNA-seq data from the same cells (multiome data) and need to create a single reduced-dimension coordinate space that…
Use when after computing pairwise mass-difference transformations between FT-ICR MS peaks and matching them to a reference biochemical transformation key, you have putative edge…
Use when when working with mass spectrometry imaging data from metabolites treated with derivatizing matrices (e.
Use when you have a sparse pairwise distance matrix derived from nearest neighbor indexing of MS/MS spectra (or similar high-dimensional objects) and need to partition spectra…
Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with…
Use when after sample alignment in untargeted LC-MS workflows, when the aligned feature table contains missing (NA or zero) intensity entries for features that are detected in…
Use when when implementing fragment ion annotation in proteomics workflows and needing to determine whether neutral loss annotation (e.g., H2O: -18.010565, NH3: -17.026549) should…
Use when immediately after loading metabolomics measurements into a SummarizedExperiment
Use when after constructing a kNN graph (via pp.neighbors) on preprocessed, scaled, and PCA-reduced single-cell expression data.
Use when when you have an unknown MSMS spectrum (precursor m/z and fragment ions) and need to discover structurally related compounds from a spectral library.
Use when you have a Sciex Multiquant (≥v3.0.3) txt export containing QCpool sample measurements at multiple timepoints within a sequence, and you need to flag compounds with high…
Use when you have experimental RT measurements from a source chromatographic method and need to predict RTs for the same molecules on a target chromatographic method, but lack a…
Use when after fitting a Gaussian Process regression model to prior LC-MS gradient runs (retention times, separation efficiency scores, or compound identification counts) — from…
Use when when you have paired NMR metabolite measurements and corresponding processing metadata (pre-centrifugation delay, post-centrifugation delay, sample type, cohort) for a…
Use when when you have large sequential media files (mzML spectra, text chapters, or similar) and need to enable both random access by ID and sequential iteration without loading…
Use when when you have: (1) a collection of molecules represented as molecular graphs (nodes=atoms, edges=bonds with chirality/order attributes); (2) structured metadata…
Use when you have preprocessed GCF-MF link pairs from paired genomics–metabolomics
Use when you have MS/MS fragmentation spectra (from Orbitrap or Q-TOF instruments) in MGF format with known precursor m/z, adduct type, and collision energy, and you need to…
Use when you are preparing to run a complex multi-tool bioinformatics pipeline (such as HiC-Pro) on a new system or cluster, and need to confirm that all required binaries exist…
Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature…
Use when you have a user-defined reference list of isolated, high-confidence chromatographic peaks (ground-truth) matched across multiple LC-HRMS samples, and you need to produce…
Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile)
Use when you need to measure how much a specific model capability or architectural feature contributes to prediction performance, especially when that capability is non-obvious or…
Use when when you need to validate that a .NET assembly (such as ThermoFisher.CommonCore.RawFileReader) is correctly installed and accessible before attempting data reading…
Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest it into LipidMatch for lipid identification — from…
Use when you have an untargeted metabolomics feature table (with m/z and retention time columns) and a metabolic network database with compound chemical formulas, and you want to…
Use when when you have a resolved spectrum file (mzML, mzXML) and need to visualize where MS2 precursor scans occur on an XIC display.
Use when your MetaboSet object contains missing values (marked as NA) in the expression matrix after quality flagging, but you need complete data for multivariate analysis.
Use when when preparing to process raw LC-HRMS metabolomics data (.mzML or .abf files) with MS-DIAL within a Nextflow pipeline, before executing peak detection and chromatogram…
Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform…
Use when when you have a .msp mass spectra file with incomplete or missing chemical metadata fields (SMILES, InChI, CAS number, formula, InChIKey, IUPAC name) and need to populate…