Use when you have a metabolite intensity matrix (rows=metabolites or peaks, columns=samples) paired with metabolite-to-pathway or metabolite-to-feature-group annotations, and you…
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 your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration,…
Use when when building a scientific visualization library that must support multiple plotting backends and needs to avoid backend-specific code duplication.
Use when when you have paired genomics (antiSMASH-detected BGCs with MIBiG homology assignments) and metabolomics data (MS2 spectra from GNPS), and you need to score BGC-spectrum…
Use when you have a GNPS mass spectral molecular network (in graphml or cytoscape format) and want to enrich its nodes with chemical class information derived from GNPS public…
Use when you have raw Hi-C FASTQ files from a high-throughput chromatin conformation capture experiment and need to generate a normalized contact matrix (.hic file) for downstream…
Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project…
Use when when you need to understand how a multi-instrument mass spectrometry platform (like mzmine) decides which processing module receives a given dataset based on its — from…
Use when you need to quantify the degree of match between two MS/MS spectra—either
Use when after noise filtering and baseline correction have been applied to mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other high-throughput MS formats in mzML, mzXML, or…
Use when you have UPLC-HRMS raw data (ThermoFisher, Agilent, or compatible vendor format) from water samples or environmental matrices containing unknown organic pollutants, a…
Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
Use when when processing aligned LC-MS data across multiple samples where the computational bottleneck is repeated peak-detection algorithm calls (one per sample per m/z value).
Use when immediately after executing the MetaboAnalystR 4.0 unified LC-MS workflow (feature detection and quantification module) on raw mzML or netCDF data.
Use when working with mass spectrometry spectral libraries (GNPS, MoNA, MTBLS1572, MassBank) that have been preprocessed by prior teams but may contain formatting errors or…
Use when you are developing or comparing new data-dependent acquisition (DDA) strategies in ViMMS and need to evaluate how well each strategy fragments sampled compounds from the…
Use when you have 1D or 2D NMR spectra (1H and/or 13C) and need to predict unknown molecular structure (formula and connectivity) up to ~19 heavy atoms; or you have a set of…
Use when you have a table of detected chromatographic peaks (e.g., from CentWave peak detection in xcms) and need to isolate a single target m/z (e.g., m/z 304.1131 for a…
Use when you have an unknown mass spectrometry spectrum (acquired experimentally
Use when after installing ENPKG or any component of the workflow via conda/pip dependency manifests and before executing workflow scripts.
Use when you have experimental fragment m/z values from HRMS/MS instruments (Q-Exactive orbitrap, Q-TOF) in CSV or mzML-derived peaklist format, and need to match them against a…
Use when when you need to verify that a research software package (e.g., MassQL) maintains functional correctness over time, assess the reliability of a tool before integration…
Use when when processing raw or centroid mass spectra (e.g., ESI-MS or FT-ICR data from Bruker .d or Thermo .raw formats) and you need to remove instrument noise and low-abundance…
Use when you have untargeted LC-MS metabolomics data preprocessed with XCMS and need to filter out low-quality peak integrations that could introduce false positives or noise into…
Use when you have acquired tunemix data (positive or negative ion mode, in .h5 format) with known CCS reference values and need to construct a calibration function that will later…
Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine…
Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g.,…
Use when you have a pre-trained GNN model checkpoint, a test dataset with molecular representations (SMILES, 3D coordinates, adducts) and ground-truth labels, and need to quantify…
Use when working with GCIMS datasets where retention time spans a wide range (e.g., 0–1500 s) but your analytes of interest are confined to a narrower window (e.g., 0–1100 s).
Use when you have run ORA on simulated metabolite sets with known null conditions (no true pathway enrichment) and need to measure how detection coverage, pathway database size,…
Use when after MS2 fingerprints have been generated by counting MS2 peaks and neutral losses in each sample, and you have aligned them into a MemoMatrix (sample-by-fingerprint…
Use when when preparing NMR datasets for processing in NMRFx and the Dataset.createDataFile() method must choose among competing storage backends.
Use when when you have sum-normalized peak-abundance matrices from FT-ICR MS data with assigned molecular formulas and need to compare metabolite diversity between treatment…
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 raw IM-MS data in UIMF or Agilent MassHunter .d format acquired from a multiplexed (interleaved) ion mobility experiment, and you need to recover indivi — from…
Use when you have multiple mass spectral libraries in different formats (NIST MSP + MOL folder, MoNA MSP, RIKEN MSP, SWGDRUG MSP) and need to merge them into a single,…
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 after computing PLAGE-derived activity scores for pathways or metabolite sets (Molecular Families, Mass2Motifs) from log2-standardized metabolomics intensity data.
Use when when loading or creating an NMR spectral dataset (Dataset.createDataFile)
Use when when converting raw metabolomics data (tab-delimited text files, Sciex OS exports) into a structured object for batch processing, or when you need to organize…
Use when you have loaded normalized methylation data from EPIC or 450k arrays and need to identify differentially methylated blocks rather than individual CpG sites or DMRs.
Use when after using edgeR::DGEListFromTximport with divide=TRUE on tximport output containing Gibbs sample or bootstrap replicates.
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when you have a USI accession (e.g., 'mzspec:MSV000082283:f07074:scan:5475' or 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') pointing to a publicly…
Use when after feature detection has produced a TSV feature table (from Asari or equivalent) containing m/z, retention time, and intensity columns, and before MS1 or MS2…
Use when extracting migration times of specific analyte or reference markers (e.g., Paracetamol EOF marker) from CE-MS files using peak-picking workflows.
Use when you are designing or optimizing an MsBackend implementation and need to decide whether to pre-populate the @spectraVars slot with all core spectra variable columns (mz,…
Use when when building a comprehensive reference spectral library for metabolomics or chemical identification, you have multiple source libraries in different formats (msp, mgf,…
Use when you have a spectral library with structural ground truth (InChIKey or SMILES annotations for ≥50% of spectra) and want to benchmark whether a new or existing spectral…
Use when when you have TCN-predicted candidate formulas with ranked scores and need to train a Siamese rescore model to re-rank those candidates.
Use when you have raw molecular structures in SMILES or SDF format that will feed into BitterPredict.m or other structure-based classifiers.
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 after bias-correcting ATAC-seq cutsite signal (using ATACorrect or equivalent) when you have a set of genomic regions of interest (e.
Use when you have raw MS/MS spectra (in MGF or mzML format) with unscaled peak intensities and noise artifacts, and you plan to rank chemical formulas, predict adducts, or score…
Use when you have Nightingale Health 1H-NMR metabolomics data (feature matrix with named metabolite columns) and need to compute predicted metabolic age for each sample, typically…
Use when apply Leiden clustering after constructing a k-nearest neighbor (kNN) graph from single-cell expression data when you need to partition cells into discrete, biologically…
Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
Use when you need to set up a LipoCLEAN analysis for MS-DIAL lipid identifications and do not yet have a configuration file, or you are switching between MS-DIAL versions 4 and 5…
Use when after batch correction of metabolomics data using pooled study quality control (SQC) samples and calculation of compound/internal standard ratios, when you need to decide…