Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical s — from…
Use when you have a genome annotation GTF file and need to identify all transcript-level alternative splicing events (exon skipping, intron retention, alternative splice sites,…
Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
Use when you have raw or preprocessed MS/MS spectra in one of the supported formats (MGF, mzML, mzXML, JSON, MSP, mzXML, pickled matchms objects, or USI) and need to extract peak…
Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final…
Use when after drift correction and before missing value imputation when your LC-MS peak table contains features with variable detection rates across samples.
Use when you have implemented or are validating a reader/writer library for a mass spectrometry file format (such as mzPeak, mzML, or similar), and need to confirm that data…
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 when you have Sciex Multiquant TXT export files containing injection sequences from metabolomics or lipidomics studies where pooled QC samples were deliberately injected…
Use when analyzing MALDI-mass spectrometry imaging data in which sodium or other alkali metal contamination is suspected, or when peak lists show unexplained mass differences in…
Use when when you have deployed NP Classifier using Docker Compose and need to confirm that both the server and TensorFlow Serving containers are running and healthy before…
Use when you have a large indexed gzip file (igz format) with metadata encoded in the gzip header comment field, and you need to retrieve specific blocks or spectra by integer…
Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid…
Use when you have a curated relational dataset (structure-organism pairs) and need to quantify how structures distribute across a categorical variable (e.g., organism prevalence).
Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire…
Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that…
Use when when you have a binned Hi-C cooler file, an associated eigenvector track (from prior eigs_cis calculation), and need to measure how strongly the genome is partitioned…
Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided,…
Use when when you have a spatial molecular dataset (e.g., Visium, MERFISH) with categorical cell-type or feature annotations and want to test whether specific categories are…
Use when after feature clustering has been applied to co-eluting LC-MS features and mass-to-charge ratio matching to KEGG has produced an annotated table with adduct assignments.
Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical…
Use when your goal is to assess whether a pretrained NMR2Struct model trained on molecules ≤19 heavy atoms can generalize to larger, more complex molecules, or whether accuracy…
Use when you have mass spectrometry spectral data (m/z and intensity pairs, precursor m/z, MS level, and metadata) in R memory or in a file format (mzML, mzXML, CDF, MGF, MSP),…
Use when when you have raw profile LC-MS data in .mzML format and need to prepare regions of interest (ROI) as input for a CNN-Transformer peak detection network.
Use when after peak detection on LC/HRMS data (mzXML, mzML, netCDF formats) when m/z values require refinement for improved mass accuracy in untargeted metabolomics workflows.
Use when starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z,…
Use when you have a SummarizedExperiment object containing peak counts from single-cell or bulk ATAC-seq/DNAse-seq data and need to prepare it for unbiased motif deviation…
Use when you have a collection of annotated MS/MS spectra with precursor m/z values and fragment peak lists, and you aim to train or apply a spectral similarity model (such as…
Use when you have cloned a scientific Python project (e.g., scverse/scanpy) and need to verify that your local development environment matches the CI specification before…
Use when you have observed mapping rate or quantification disagreement (e.g., >0.1% divergence in mapping rate or Pearson r < 0.
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 you have consensus metabolic reconstructions for all members of a microbial or plant community (e.
Use when you have raw MS/MS spectra in MGF or other standard formats that need to be ingested into a machine learning pipeline for cross-modal matching against molecular…
Use when when working with JSON project documents that must conform to a schema-defined structure, and you need to apply type-specific validation, sanitization, or transformation…
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 you have a chemical substrate and need to predict its biotransformation
Use when after running macs3 callpeak with the -f BEDPE flag on paired-end ChIP-Seq data (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.
Use when you have downloaded or cloned a fragmentation library repository (such as LipidMatch) and need to verify that it contains the expected breadth of coverage across both…
Use when your metabolomics dataset (LC/MS or GC/MS) contains missing values encoded as NA or zero that represent compounds below the instrument's limit of detection (LOD) or limit…
Use when when you need to verify or retrieve package-internal metadata about compiled .NET assembly location and version before processing raw mass spectrometry files, or when…
Use when you are preparing to run LipoCLEAN on MS-DIAL output and need to create or update a configuration file, or you have switched between MS-DIAL 4 and MS-DIAL 5 data and need…
Use when you have per-feature CV values from quality control analysis of NMR or MS metabolomic data and need to: (1) establish whether your dataset meets FDA reproducibility…
Use when : (1) you have metabolomic data (NMR or MS-derived) and a continuous phenotype variable; (2) you need to quantify associations while controlling for known confounders…
Use when after applying one or more intensity drift correction strategies (Internal Standard correction, statistical drift correction, custom or weighted bracketing) within…
Use when when preparing MS/MS spectra from .msp files for transformer-based deep learning models in IDSL_MINT.
Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived…
Use when when you have a table of execution times or performance metrics indexed by two or more categorical dimensions (e.g., plot_type × backend, or sample × condition), and you…
Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
Use when you have processed and quantified MSI data from one or more imzML files in LipidQMap and need to export them as a unified, standards-compliant HDF5 container that…
Use when you have raw .idat files or beta-valued matrices from Illumina HumanMethylation450 (450K) or EPIC array experiments and need to import them into R for quality control and…
Use when you have developed a new machine learning model for predicting metabolomic profiles from microbiome data and need to quantify its performance improvement over existing…
Use when after extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument…
Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment…
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 a tandem mass spectrum (MSMS) of a known or hypothesized peptide, along with its ProForma 2.
Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment…
Use when when you have Thermo Fisher Scientific .raw files from Orbitrap instruments and need to build a quantitative summary of MS1 acquisition intensity dynamics across a…
Use when after deploying a TensorFlow-backed classification service, you need to verify that the model's input layer names ('input_2048' and 'input_4096') and output layer name…
Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs.
Use when after peak picking across individual spectra in an MSImagingExperiment,