Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph…
Use when when you have partitioned public MS/MS files from MassIVE using the ReDU File Selector into one or more filtered groups (G1–G6) and need to verify that each group's file…
Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time…
Use when a spatial metabolomics dataset contains semicolon-delimited isomer name annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to collapse…
Use when you have completed the MS2LDA LDA modeling phase and possess motifset.json or motifset_optimized.json files containing inferred Mass2Motifs.
Use when when deploying a new Python package in a reproducible analysis environment or continuous integration pipeline, and you need to confirm that all required core modules…
Use when you have collected MS/MS spectra from a microbial sample (pure culture, environmental isolate, or mixed community) and need to assign chemical identities to observed m/z…
Use when you have a domain-specific language (DSL) grammar specification and raw query strings that must be converted into structured intermediate representations for validation,…
Use when you have a curated training dataset of molecular structures with known CCS values, a target set of ≤10,000 molecules requiring CCS predictions, and need to apply a…
Use when when implementing a custom MsBackend subclass and need to verify that spectra variables (e.g., precursor m/z, retention time, MS level) conform to expected data types…
Use when you have aligned ATAC-seq BAM files and peak annotations from two or more experimental conditions (e.
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 you are implementing ORA for metabolomics pathway analysis and must decide which metabolites constitute the statistical background against which to test your experimental…
Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak…
Use when after training a GNN-RT model on preprocessed molecular graph data (from Train.py) or after applying transfer learning to an in-house dataset (from Transferlearning.
Use when you have a peak table from XCMS preprocessing with intensity measurements for the same set of metabolites across multiple QC replicate injections (samples marked…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single — from…
Use when you have a trained decision tree model on ChemEcho sparse feature vectors and need to convert a specific decision path (root to leaf) into a deployable query.
Use when you have experimental retention times measured on a source chromatographic
Use when when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including…
Use when you have m/z values from mass spectrometry imaging (or similar MSI experiments) and need to assign molecular formulae to them.
Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
Use when you have a compiled EI or MS2 library object (from read_lib or c() combination of multiple sources) and a local NIST library installation with accessible ri.dat and…
Use when you have an aligned feature table from untargeted LC-MS with missing intensity values (NA or zero entries) for features that are present in some samples but fell below…
Use when you have imaging mass spectrometry (IMS) data preprocessed into an h5py-backed feature matrix, and a trained graph-attention autoencoder has already extracted latent…
Use when you have selected a subset of public tandem MS files from ReDU/MassIVE that have been processed through GNPS spectral library matching, and you need to organize their…
Use when you have retrieved multiple candidate structures from a molecular structure database (e.g., PubChem, HMDB) for an unknown compound, and you have predictions of…
Use when a Shiny application or similar cross-platform tool is restricted to a single operating system (e.
Use when when executing a multi-converter annotation workflow on mass spectra metadata (.
Use when when processing untargeted LC-MS data with SLAW and observing incomplete feature detection across the sample cohort—i.e., features present in some samples but with…
Use when you have a sparse chromatin accessibility matrix (ATAC-seq or DNAse-seq counts per peak per sample), matched peak-annotation assignments (e.
Use when when you have unknown MS/MS spectra with observed precursor m/z values and want to infer the molecular formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de…
Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
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…
Use when when a new version or variant of a tool claims performance improvements
Use when you have raw LC-MS fractional abundances (FAM) data from isotope labeling experiments and need to obtain true mass distribution vectors (MDV) that represent only the…
Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the…
Use when you have loaded raw mass spectrometry spectral data (in MGF, MSP, mzML, or mzXML format) and need to decide which intensity threshold(s) to use for filtering out noise…
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 you have one or more vendor mass spectrometry raw files (Thermo .raw, Agilent .d, Sciex .wiff2, or other MSConvert-supported formats) that must be converted to Aird…
Use when you need to support multiple plotting backends for the same data visualization task, and you want to centralize backend selection logic so that users can specify their…
Use when when implementing new scoring components (inchikey score, neighbourhood
Use when you have LC-HRMS profile-mode data (retention time × m/z matrix format) and need to automatically identify chromatographic peak locations and boundaries prior to feature…
Use when after PCA dimensionality reduction and scaling of normalized, log-transformed gene expression data, when you need to identify local cell neighborhoods (typically with…
Use when you have raw mzML files and corresponding feature tables (CSV format, mzmine-formatted) from untargeted LCMS experiments, and you need to convert them into…
Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
Use when when building a neural network to map between mass spectrometry spectra and molecular properties (e.g., fingerprints, SMILES, or fragment ions) where sequential or…
Use when you have a large compressed scientific data file (e.g., indexed gzip mzML) where you need to retrieve specific spectra, chapters, or records by integer ID without loading…
Use when you have a molecular structure (SMILES, InChI, or chemical formula) and need to predict which fragments will appear with high intensity in a tandem MS spectrum, or when…
Use when you have 1H NMR spectral data from complex mixtures and need to identify component compounds, but a single architecture (CNN or Transformer alone) fails to capture both…
Use when a paired omics project JSON document contains genome identifiers (e.g. IMG IDs, NCBI accessions) but lacks corresponding organism names.
Use when you have raw or processed FT-ICR MS spectra with detected peaks (m/z values) and need to: (1) assign elemental compositions to each peak, (2) filter assignments by mass…
Use when you have a pre-trained DNN RT predictor (e.g., trained on METLIN SMRT with 80,038 experimental RTs) and need to adapt it to predict retention times in a new or external…
Use when when analyzing untargeted LC/HRMS data from population-scale projects (n > 500) spanning multiple sample batches or instrument runs, peaks with identical or…
Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g.,…
Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures…
Use when you have built multiple Docker image variants (e.g., cli, dev, linux, windows) from a multi-stage Dockerfile and need to verify that their uncompressed and compressed…
Use when when you have raw GCxGC-MS data imported from NetCDF into a 2D-TIC chromatogram object and need to remove chemical and instrumental noise (column bleeding, baseline…
Use when configuring a new injection-plate design template in InjectionDesign if you have multiple QC types to position on a plate and need to visually distinguish them in the…
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…