Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular…
Use when when you have SWATH-MS raw data (mzML or vendor format) containing multiplexed MS/MS spectra from multiple co-eluting precursor ions and need to separate these spectra…
Use when when you have raw mzML files and a feature table (CSV from mzMine or XCMS) with labeled peaks of unequal class sizes (e.g., fewer false positives than true positives) and…
Use when when you have seed metabolite structures (SMILES or MOL format) from metabolomics data and a curated biotransformation rule database (each rule specifying reactant…
Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
Use when you have raw gas or liquid chromatography–mass spectrometry data (in NetCDF or mzML format) and need to detect features, align them across samples by retention time and…
Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating…
Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
Use when when you have generated multiple 3D conformations for a molecule or set of ionized adducts (e.g., via RDKit) and need to retain only the most energetically favorable…
Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
Use when when you need to confirm that a published Docker image (e.g., hosted on Docker Hub) can be pulled and instantiated successfully, and when the target tool has a defined…
Use when when you have aligned peak data from molecular networking (with m/z, intensity, retention time, and alignment quality metrics across multiple spectra) and need to…
Use when when annotating .msp mass spectrometry files with chemical structure metadata and you need fast, offline molecular transformations (SMILES↔InChI, canonical SMILES…
Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .
Use when when preprocessing a public MS/MS spectral library (e.g., GNPS) for machine learning and you discover discrepancies between expected and observed compound counts after…
Use when after peak detection and feature extraction have produced a composite feature table with m/z, retention time, and intensity values for individual samples.
Use when after fitting a polynomial calibration model to tunemix reference data in DEIMoS, assess whether the model explains sufficient variance in the m/z–drift-time–CCS…
Use when after anchor feature pairs (m/z and retention time values) have been selected from two disparately-acquired LC-MS datasets, and you need to correct for systematic…
Use when you have loaded mzML.gz or HDF5-formatted raw LC-IMS-MS/MS data and need to identify discrete peaks before feature alignment.
Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench
Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical…
Use when when you have run the same mass spectrum through molecular formula assignment under different parameter settings (e.
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 when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to…
Use when when processing open mass spectrometry library (OMSL) data that may contain duplicate spectral records (e.
Use when when you have raw LC-MS data files and need to identify which compounds were actually detected at high abundance during a gradient run, prior to evaluating whether the…
Use when when you have limited real GC-MS overlapped peak data but need thousands of labeled examples to train a deep learning model for mass spectral deconvolution.
Use when you have SWATH-MS raw data (mzML or vendor format) from an untargeted metabolomics experiment and need to identify metabolites.
Use when you have raw Hi-C FASTQ data and need to generate contact maps at kilobase resolution, or you have pre-generated .hic files and need to annotate structural features…
Use when you have computed pairwise similarity or mass difference scores between all fragment ions across two tandem mass spectra and need to select the non-overlapping set of ion…
Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or…
Use when you have a fitted alignment model (e.g., metabCombiner object with pre-aligned feature pair candidates and RT spline mapping) and known shared compound identities (ground…
Use when when two mapping implementations (or versions of the same mapper) show disagreement on per-read mapping status—e.g., one mapper leaves reads fully unmapped that the other…
Use when you have intracellular metabolomics abundance data (absolute or relative concentrations) for multiple cell lines or conditions, a constraint-based stoichiometric…
Use when after batch correction of a metabolomics dataset using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to…
Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did…
Use when you have a feature table from LC-MS analysis (containing m/z, retention time, and intensity values) and need to identify which detected features represent the same…
Use when when implementing or validating a lossy numeric codec for mass-spectrometry
Use when you have a pre-trained MS/MS spectral embedding model and need to validate that it achieves strong and consistent retrieval performance on curated spectral libraries that…
Use when after successfully reading and validating a tab-delimited metabolomics file (containing mandatory columns: aliquot, compound, area, type, injection_time, batch) using…
Use when working with raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains low-abundance background noise, isolated high-intensity artifacts, or jagged peaks…
Use when when you have completed an initial ModiFinder analysis on a compound pair (known compound + modified analog with unknown structure), and you subsequently acquire or…
Use when you have mzML/mzXML chromatogram files from Thermo, Waters, or Bruker instruments and need to extract MS1 and MS2 scans matching both a target m/z value AND a known 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 CE-MS raw data (mzML or netCDF format) containing a known target analyte with a precise m/z value, and you need to isolate its signal within a defined effective…
Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
Use when when you have raw mass spectrometry imaging data (full m/z profiles with intensity arrays) and want to classify spatial regions (e.
Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed…
Use when when you have preprocessed mass spectrometry ion images (single-channel
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 you have raw Hi-C FASTQ files from a Hi-C wet-lab protocol and need to convert them into processed Hi-C contact maps (.hic files) for loop detection, TAD identification,…
Use when you have an annotated LC-MS feature table with KEGG candidate matches and adduct assignments (output from the matching stage), and you need to disambiguate which features…
Use when you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak…
Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal…
Use when you have real LC-MS/MS data (mzML) from a complex sample (e.g., beer, metabolomics extract) and need to prototype or validate a new data-dependent acquisition (DDA)…
Use when after isotope correction when you have extracted intensity matrices from imzML or HDF5 MSI data and need to convert raw or isotope-corrected ion-image intensities into…
Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate) and need to find their -matched structural analogues within a reference library — from…
Use when a Shiny application or R package is confirmed to work on one OS (e.g., Windows only) but fails to initialize or run on others due to unresolved file path conventions,…
Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may…
Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.