Use when you have MS-DIAL lipid identification results (alignment exports in msp/txt format) and need to distinguish correct from incorrect lipid IDs before downstream analysis.
Use when after retention-time and m/z-based peak alignment has been completed across a cohort of LC-MS samples, and you need to create a unified quantitative matrix for…
Use when when you have a GTF genome annotation and need to catalog all transcript isoforms and local alternative splicing event variants (exon skipping, intron retention,…
Use when you have a peak-picked feature table (HDF5 format with m/z, drift_time, retention_time, intensity columns) and need to identify and label isotopic signatures within…
Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to…
Use when you have a trained NeatMS neural network model (.h5 format) and need to select an operating threshold for peak classification on your LCMS dataset.
Use when when you need to create synthetic noisy MS/MS spectra for benchmarking or validating denoising algorithms.
Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
Use when adding a new converter class to MSMetaEnhancer or when modifying an existing converter's __init__ method to add/remove conversions.
Use when you have trained predictive models (e.g., MiMeNet neural networks) on microbiome-metabolome paired data using k-fold cross-validation, held out test folds for each…
Use when after completing PCA and k-nearest neighbor graph construction on preprocessed, log-normalized, highly-variable-gene-filtered single-cell RNA-seq data (stored in an…
Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence detection, before reporting features in the final feature table — from…
Use when when you have a preprocessed bag-of-fragments corpus from tandem mass spectrometry spectra and need to train an MS2LDA model to discover Mass2Motifs.
Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field…
Use when you have raw DIA mass spectrometry data files (.raw, .d, or .wiff formats) from timsTOF, TripleTOF, or Orbitrap instruments and need to extract precursor ion…
Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table…
Use when you have a batch of mass spectra records in .msp format that lack standardized metadata fields (SMILES, InChI, CAS numbers, molecular formula, IUPAC names) and need to…
Use when after executing Formation formatting on processed feature tables (output from Blueshift or Gravity modules).
Use when when you have raw LC-MS all-ion fragmentation (AIF) chromatograms in centroid mode and need to prepare them for metabolite annotation using fragment ion matching.
Use when after completing sample alignment in JPA (Part 5) or when ingesting a peaklist or aligned feature matrix from prior peak-picking runs, parse feature metadata to enable…
Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and measured CCS values need bias assessmen — from…
Use when when you have a loaded metabolite database (e.g., hmdb_compounds.p pickle file) and need to constrain the chemical space to a specific instrumental m/z range (e.
Use when you have calibrated m/z peak lists, configured adduct transformations (e.g., [M+H]+, [M+Na]+, [M-H]−), and need to annotate peaks with molecular formulae from KEGG,…
Use when when a software tool is distributed as a Docker image and you need to confirm it is available on a registry (e.g., Docker Hub), that the image pulls without corruption,…
Use when when you have run a pathway ranking method (such as PALS/PLAGE) on clean metabolomics data and wish to assess how sensitive the resulting pathway activity rankings are to…
Use when you have developed or adapted a peak detection method for chromatography–mass
Use when your Hi-C data is stored in cooler format (a binary HDF5-based sparse matrix with associated genomic bins and genomic tracks); you need to programmatically access the…
Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs.
Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
Use when after executing memo_from_unaligned or memo_from_aligned functions to generate a MemoMatrix object from MS2 spectra or aligned feature tables.
Use when when preparing to run Over-representation Analysis (ORA) on a metabolomics study, after constructing the background set but before running the enrichment test.
Use when when you have multiple file format variants (compressed indexed gzip, standard gzip, SQLite database, uncompressed mzML) that all need to be read via a unified interface,…
Use when you have processed the same set of untargeted LC/HRMS files (mzXML, mzML, or netCDF format) with two or more peak-picking tools and need to validate which tool produces…
Use when after running spectral networking on tandem MS data and obtaining a network graph, when you need to assess which spectra cluster together, determine cluster…
Use when you have an isotope-corrected or raw MSI dataset stored in HDF5 format following Cardinal::HDF5 conventions, a user-provided internal standard definition (sample…
Use when your raw TOF-MS data (Agilent MassHunter .d format) exhibits jagged, artifact-prone peaks in low-abundance ions that compromise peak quality assessment or when you need…
Use when you have a GC-MS dataset with a Match.Factor column (or equivalent quality metric) and need to evaluate how many unique compounds are retained at different confidence…
Use when after cluster-based filtering has produced a set of candidate KEGG compounds for each feature cluster in untargeted LC-MS data, and you need to rank these candidates by…
Use when after peak detection in GCIMS when you need to group detected peaks across multiple samples into reproducible clusters.
Use when you have predicted structural similarity scores (e.g., Tanimoto or Dice scores) for a large set of spectrum pairs and need to assess prediction accuracy across the full…
Use when when preparing to read Thermo Fisher Scientific .raw files using rawrr functions (readFileHeader, readSpectrum, readChromatogram, readIndex), or when retrieving cached…
Use when you have tandem mass spectra for compounds with known binary or categorical molecular properties (e.
Use when you have a set of query chemicals and a reference library (organized by type or group), and you need to determine which reference compounds most closely resemble each…
Use when when you need to compare the computational efficiency of different mass spectrometry libraries on identical data and processing pipelines, or when you want to establish…
Use when you have a set of small-molecule compounds (e.g., from MS/MS library matching or database annotation) that require retention time validation or ranking to resolve…
Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction…
Use when when you have imported raw mass spectrometry spectral data (in formats like mzML, mzXML, msp, MGF, or JSON) and need to clean peak lists before metadata validation,…
Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment…
Use when you have a tab-delimited feature table (m/z, retention time, intensities) from LC-MS preprocessing and need to group related ions (isotopologues, adducts, in-source…
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 raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize…
Use when you have developed a predictive model and need to compare its performance against established baselines (e.g., linear regression, Random Forest, Canonical Correlation…
Use when you have loaded normalized methylation beta-value matrices from Illumina EPIC or 450k arrays and need to move beyond single-CpG differential methylation testing to…
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 removing invalid or malformed entries (e.g., SMILES validation, format errors) from large spectral datasets (GNPS, MoNA, MTBLS1572, MassBank).
Use when when you need to reproduce or validate a specific historical release artifact (e.g., a Semantic Release v1.0.
Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared…
Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or…