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 beginning an LC-MS data analysis pipeline and you need to rapidly inspect instrument metadata, acquisition parameters, or scan statistics from proprietary Thermo .raw…
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 after rewriting or refactoring a Python module (such as calculate_feature_overlap.py
Use when you are in the Bayesian optimization loop after fitting a Gaussian Process model to observed LC gradient runs, and you need to propose the next gradient to evaluate.
Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a…
Use when when you have .msp mass spectrometry metadata containing chemical identifiers (e.g., compound names or SMILES strings) and need to compute derived chemical properties…
Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators)…
Use when you have loaded an MS2 library (from NIST, GNPS, or other sources via read_lib()) that contains both positive and negative ionization modes mixed in a single file, and…
Use when you have XCMS-aligned feature tables with retention time values and need to compute pairwise feature similarity.
Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by…
Use when after sample alignment and grouping of isotopologues and adducts have been completed, when the aligned feature table contains NA or zero entries (missing intensities) for…
Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to ident — from…
Use when you have preprocessed 1H NMR spectral data with compound labels and need to identify multiple compounds in a flavor mixture where both local spectral patterns (handled by…
Use when you have raw line-scan mass spectrometry imaging data from nano-DESI or other line-scan acquisition modes and need to produce a georeferenced 3D pixel array.
Use when when working with feature abundance tables (rows=features, columns=samples)
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 you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo…
Use when you have loaded an FT-ICR raw spectrum (e.g., ESI_NEG_SRFA.d in Bruker or ThermoFisher .raw format) and need to identify the m/z positions and intensities of individual…
Use when when you need to confirm that a publicly hosted academic web service (such as molDiscovery) is live and responding at a documented endpoint URL, or when troubleshooting…
Use when you have generated or obtained a two-dimensional mass-spectrometry intensity matrix (m/z × retention time scan points) with simulated or experimental peak shapes, noise,…
Use when when you need to verify the current operational status of a software project across multiple dimensions (CI/CD, code quality, test coverage, containerization, archival)…
Use when you have an untargeted metabolomics dataset with partial metabolite annotations (from database matching or prior curation) and need to extend annotation coverage to…
Use when you have raw GC-MS output in CSV format (with Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.Name columns) and need to systematically…
Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb,…
Use when you have raw mzML files and feature tables (CSV from mzMine or XCMS) for LCMS data, have generated training/validation/test batches with known class imbalance, and need…
Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign…
Use when you have preprocessed, normalized beta-value matrices from EPIC or 450k methylation arrays with at least two sample groups (case/control, treatment/untreated, or similar…
Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites…
Use when when you have a repository containing hundreds or thousands of structured records (e.g., MassBank records in standardized format) that must be validated for correctness…
Use when when you have received Sciex Multiquant TXT export files from a completed metabolomics or lipidomics analytical run and need to verify that QC pool samples were injected…
Use when when deploying a multi-container application stack using docker-compose
Use when you have transcript-level abundance estimates and count matrices from tximport (derived from Salmon, Sailfish, or kallisto output) and need to prepare them for…
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 batch effect removal and data integration, when you have a feature-by-sample matrix (finalData) and wish to separate and visualize sample groups by their…
Use when you have LC-HRMS chromatograms in retention time × m/z matrix format and need to automatically localize chromatographic peak positions and extents prior to matching…
Use when when you need to establish a reproducible inventory of compounds for LC-MS/MS simulation studies, particularly to determine how many unique molecular formulas fall within…
Use when you need to generate a set of candidate chemical formulas for LC-MS/MS simulation—specifically when you want to populate a virtual mass spectrometer with realistic…
Use when after executing a molecular networking workflow on GC-MS data that has been processed through auto-deconvolution, and a published reference network exists from a prior…
Use when you have a Mass Spectrum Point (MSP) file containing electron ionization mass spectral records with header fields and peak intensity pairs, and you need to load it into…
Use when you have a C# GUI application targeting .NET Framework 4.8 (Windows-only)
Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass…
Use when you have a trained multitask model checkpoint and preprocessed spectral inputs (1D NMR spectra, 1H-only, 13C-only, or combined 1H+13C), and you need to generate…
Use when you have an existing mass spectrometry data file in a vendor or standard format (mzML, NetCDF, etc.) and need to convert it to mzPeak format for downstream analysis,…
Use when you have a sparse pairwise distance matrix derived from nearest neighbor indexing of MS/MS spectra (or similar high-dimensional objects) and need to partition spectra…
Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
Use when when you have raw tandem mass spectrometry peak data (m/z and intensity pairs), precursor m/z, charge state, and adduct annotation for one or more compounds, and need to…
Use when you have a cleaned organism table (with validated, deduplicated organism names from sources like NCBI, manual curation, or previous cleaning steps) and need to annotate…
Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to…
Use when you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on…
Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment…
Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and…
Use when after identifying statistically significant LC-MS features (e.g. via MB-VIP permutation testing) when you need to consolidate redundant measurements of the same…
Use when when you have generated spectral embeddings for a query set and a reference spectral library, computed pairwise cosine similarity scores between them, and need to…
Use when you have transcript-level abundance estimates from salmon, sailfish, or kallisto quantification and need gene-level count matrices for differential expression analysis.
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 apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection…
Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover…
Use when when beginning peak calling on ChIP-Seq data: you have raw single-end or paired-end BED/BEDPE alignment files for both ChIP and control samples and need to remove…
Use when you have processed LC-MS/MS spectral data (as a .mgf file with feature identifiers) and computed pairwise ms2deepscore similarity scores, and you need to create a 2-D…