Use when when you have raw GC–MS data in two-dimensional m/z × retention time format (NetCDF or proprietary binary) and need to identify marker features across aroma or breath…
Use when when processing LC-MS data from isotope labeling experiments where the tracer (13C, 2H, 15N, 18O, or 34S) has known isotopic impurity and you observe discrepancies…
Use when when deploying a Word2Vec-based spectral similarity model (such as Spec2Vec) on a new mass spectrometry dataset and needing to assess whether the pre-trained model's…
Use when you have constructed a NetworkX graph with LC-MS features as nodes and need to annotate each node with metadata derived from the MamsiStructSearch output (assay source,…
Use when after duplicate filtering of MZmine-exported MGF and CSV files, when you have combined spectra from multiple samples in a single MGF and need to segregate them by sample…
Use when you have centroided LC-MS data (.mzML format) and a curated list of targeted metabolites or lipids (with m/z, retention time, and polarity) that you want to quantify and…
Use when you have extracted ion chromatogram (EIC) candidate data from untargeted LC/HRMS files (mzXML, mzML, or netCDF format) and need to identify genuine peaks within each EIC.
Use when you have a query electron ionization (EI) mass spectrum and need to search it against a library of known EI mass spectra to identify unknown compounds.
Use when you have extracted a list of candidate molecular formulae for a given m/z value and need to rank them by plausibility.
Use when when you have LC-MS peak table data in Excel format (e.g., from MS-DIAL peak picking) with separate compartments for sample information, feature properties, and intensity…
Use when when you have an ArchR project object with processed single-cell ATAC-seq data and want to infer developmental or cell-state trajectories.
Use when when exporting in-memory generated spectra as MSP-format spectral libraries, you must first map each spectrum record to required MSP fields (NAME, PRECURSORMZ, SPECTRUM)…
Use when you have modified the Scanpy codebase (e.g., added a feature or bugfix) and need to confirm that all unit and integration tests pass before submitting a pull request, or…
Use when after applying a configuration fix (e.g., adding an instrument type to an allowlist, updating filtering thresholds) to a dataset preprocessing pipeline, you need to…
Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, m — from…
Use when you need to map computed per-bin metrics (insulation scores, boundary calls, contact frequencies) back to genomic coordinates for export to BED/GFF format,…
Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers,…
Use when you have an annotated list of metabolite compounds (with associated m/z features or compound IDs) and want to determine which KEGG metabolic pathways are significantly…
Use when you have acquired LC-IMS-MS/MS data (or equivalent multidimensional MS/MS acquisition) in mzML or mzML.gz format and need to disambiguate overlapping fragmentation…
Use when you have raw mass spectrometry spectra from an unknown analyte or a synthetic compound library and need to feed them into PS2MS or similar deep learning classifiers for…
Use when you have an m/z-resolved feature list from LC- or GC-HRMS analysis (either detected by pyOpenMS or provided as a custom Excel table) and need to prioritize potential PFAS…
Use when you have a SummarizedExperiment object containing NMR or MS metabolomic data with aligned phenotype information (BMI, disease status, age, gender), and you need to…
Use when you have preprocessed single-cell RNA-seq data (normalized and dimensionality-reduced via PCA) and need to establish cell-to-cell connectivity for trajectory inference,…
Use when when you have a list of lipids identified by different database identifiers (e.
Use when you have a bioinformatics pipeline (like HiC-Pro) with mixed Python, R, and compiled tool dependencies, and you need to ensure consistent reproducibility across machines…
Use when after batch effect removal and sample integration, when you have a normalized feature-by-sample abundance matrix (finalData) with corresponding sample group labels…
Use when when you have a large collection of reference MS/MS spectra (spectral library) and need to search unknown query spectra against it rapidly, particularly for open…
Use when when you have experimental MS/MS data (peak lists, precursor m/z, charge state, adduct type) paired with a chemical structure (SMILES or structural identifier), and need…
Use when you have measured intracellular metabolite concentrations (e.g., via LC–MS/MS) across multiple cell lines or samples and want to predict which metabolic reactions are…
Use when when beginning a MEMO analysis workflow with raw or unaligned MS2 spectra files and needing to extract fragmentation data and precursor information before counting MS2…
Use when you have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around TF-bound sites) across…
Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine,…
Use when after feature detection and alignment (XCMS or equivalent), when you have a CSV feature table with m/z and retention time columns and need to group features derived from…
Use when when you have aligned mass tracks (extracted ion chromatograms) across multiple LC-MS samples consolidated into a composite map and need to detect reproducible elution…
Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
Use when when you have raw MS/MS spectra in MSP format (or similar) with m/z–intensity peak pairs and need to prepare them for neural embedding models that require fixed-size…
Use when apply peak-count capping when preprocessing tandem mass spectrometry (MS/MS) spectra for peptide identification or spectral library matching, particularly when working…
Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of…
Use when your input is a corpus of MS/MS spectra with annotated molecular formulas and adduct types that represent a new ionisation mode, instrument type, or adduct chemistry not…
Use when after XCMS feature detection and retention time correction, when you need to group features derived from the same compound.
Use when after isotopologue and adduct grouping has been completed and you need to associate MS2 spectra with consolidated feature groups in DDA LC-MS experiments.
Use when you have a query mass spectrum and a set of candidate molecular structures, and you need to prioritize candidates by their likelihood of matching the query.
Use when when you need to understand the modular structure of a multi-component research software project—particularly when integrating, documenting, or extending a system whose…
Use when you have multiple independent implementations of the same data format reader (e.g., Rust, Python, R versions) and need to verify they produce identical or equivalent…
Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (as metabData objects) acquired under different conditions or at differen — from…
Use when you are building a visualization library that must support multiple plot kinds (chromatogram, spectrum, mobilogram, peakmap) across multiple rendering backends…
Use when when developing or validating a DNA methylation array analysis pipeline using ChAMP, you need an independent ground-truth dataset to confirm that DMR detection is working…
Use when when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode…
Use when when reproducing a prior software release (especially one generated by automated versioning tools like Semantic Release), you need to confirm that the artifacts produced…
Use when when deploying containerized versions of a multi-variant application (e.g., CLI, development, Linux, and Windows flavors) and you need to verify that each built image…
Use when when performing m/z domain calibration on FT-ICR or high-resolution MS data and the initial calibration attempt finds fewer than 5 reference m/z matches within the…
Use when you have two or more CSV feature tables from independent metabolomic experiments (each with RT, m/z, intensity, isotope, and adduct columns), and you need to merge them…
Use when you need to transfer retention time predictions from one chromatographic method to another, but have access to only a small number (≥10) of molecules with known retention…
Use when when you need to confirm that a generated or retrieved release artifact from a version control system (e.g., git tag v1.0.0) produces byte-for-byte or functionally…
Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
Use when you have located a workflow definition file (YAML or JSON) in a versioned release or commit and need to verify that it conforms to the schema specification for that…
Use when you have performed lazy dask-backed feature extraction on an ImageContainer using im.calculate_image_features and need to persist the computed spatial features into the…
Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin…
Use when when you have spatial molecular data (e.g., Visium, imaging-based cytometry) stored in an AnnData object with coordinate information in .
Use when you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.