Use when when you have raw or centroid-mode LC-MS All-ion fragmentation (AIF) spectra and need to generate or match against ion fragment databases.
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 after applying one or more mpactr filters (mispicked, group, cv, insource) to an mpactr object and generating a qc_summary() data.
Use when when you have high-throughput mass spectrometry data (DI-MS, ASAP-MS, LDI-MS, or other ambient ionization formats) from unknown biological samples and need to determine…
Use when when you have RNA-seq count matrices (from HTSeq, featureCounts, Salmon, kallisto, or RSEM quantification) and need to test for differential expression between two or…
Use when when constructing a reference mass-matching framework for untargeted metabolomics or isotope-tracing LC-MS data, before pattern-matching observed features to isotopic and…
Use when you have merged methylation call data across multiple biological replicates (samples per group ≥2) with base-pair-level coverage information, and you need to identify…
Use when when you have a set of candidate LC gradients (parameter combinations) that you wish to evaluate with a Gaussian process model, or when you need to convert raw gradient…
Use when when processing a multi-sample LC-MS metabolomics project after mass-track extraction and retention-time calibration have been applied to all individual samples, and you…
Use when you have received a validated dataset (e.g., interim/tables/4_analysed/platinum.tsv.
Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage…
Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry
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 you need to understand how a Java application routes input data to processing modules based on declared data types, conditionally branches on instrument or format…
Use when you have paired microbiome (16S rRNA, metagenomic) and metabolomic (LC-MS, GC-MS) abundance tables from the same biosamples, and you want to predict which metabolites are…
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 after RDKit has generated multiple conformations for a molecule in an SDF or XYZ format, and you need to reduce the conformational ensemble to a tractable size (by…
Use when you have a collection of molecular fragments (e.g., from molecular decomposition, retrosynthesis, or synthetic planning) that must be matched to known fragment libraries…
Use when you have raw LC-MS or GC-MS data files from a mass spectrometer (in mzML, NetCDF, or mzXML format) and need to detect chromatographic peaks, correct m/z bias via mass…
Use when you have a curated dataset of ≤10,000 molecular structures with known collision cross section values for training, a target set of ≤10,000 molecules requiring CCS…
Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a…
Use when you need to verify whether a GitHub Actions workflow badge (e.g., main.yml) accurately reports the CI pipeline's true pass/fail status.
Use when you have a spatial omics dataset (AnnData object with coordinate columns like 'x', 'y', 'z') and an associated tissue image file (e.g., TIFF, PNG, or HE-stained…
Use when when evaluating a trained spectral embedding model on publicly available datasets (GNPS, MoNA, MTBLS1572, MassBank, or MassSpecGym) and you need to report averaged…
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 SMILES strings of molecules at specific ionization states (e.g., protonated or deprotonated adducts) and need to predict collision cross section values for mass…
Use when when beginning a new mass spectrometry analysis workflow with raw spectral data files in mzML, mzXML, msp, MGF, or JSON format.
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
Use when you have obtained a raw reference library file (such as the DTCCS_N2 library for U13C labeled lipids) and need to validate its structure, verify that all expected lipid…
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 you have intensity measurements (peak features, protein intensities, or gene expression values) with compound or gene annotations (KEGG IDs, ChEBI IDs, UniProt IDs, or…
Use when you need to build a comprehensive EI spectral reference library for GC-MS compound identification in MS-DIAL, starting from raw downloads of NIST, RIKEN, MoNA, or SWGDRUG…
Use when when you have a neural network layer definition (parameters, weight initialization, embedding dimension) from a trained or pretrained model checkpoint and need to…
Use when you have transcript-level quantification output files (quant.sf, quant.gz) from salmon, kallisto, sailfish, or oarfish and need to produce gene-level count matrices,…
Use when after generating collision cross section predictions on a validation or test set using a trained graph neural network model, and you need to quantify prediction accuracy…
Use when when processing LC-MS mass tracks (EICs) and you need to identify genuine chromatographic peaks rather than noise artifacts.
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 a single-cell count matrix with 10 million or more cells that must be processed through dimension reduction, clustering, or integration pipelines.
Use when you have completed XCMS preprocessing (getEIC() and fillPeaks()) on untargeted LC-MS metabolomics data and need to assign per-peak quality scores prior to manual…
Use when when you have raw metabolomics measurements in tab-delimited text format (e.g., from Sciex OS exports) and need to load them into R for quality control analysis.
Use when you have IM-MS lipidomic data from samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract), measured CCS values stratified by lipid class…
Use when after log-transformation and missing-value imputation of a metabolomics
Use when when you have raw LC-MS chromatographic data (mzML or vendor format) and need to identify and characterize all detectable peaks across the full retention time range for…
Use when when building or modifying an asynchronous annotation pipeline that dispatches metadata enrichment requests to multiple heterogeneous web services and must verify that…
Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically…
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 matched multiomics data (genomics, epigenomics, transcriptomics,
Use when you have raw MS/MS spectra (in formats like mzML, json, mgf, msp, mzxml) that contain background noise or numerous low-intensity peaks before running MS2Query library…
Use when after kNN imputation of metabolite measurements but before variance-stabilizing
Use when you have a collection of compound structures in SDF format (e.g., DNA adduct structures) and need to systematically generate predicted fragment spectra across a defined…
Use when after converting existing mass spectrometry formats (mzML, vendor formats) into mzPeak using command-line tools or when receiving mzPeak files from external sources.
Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert individual spectra into fixed-dimensional vector — from…
Use when when you have a pre-trained Casanovo model, annotated MS/MS spectra in MGF format, and want to benchmark whether beam search decoding improves peptide prediction quality…
Use when you have latent low-dimension peak features extracted by a Graph-attention
Use when when ingesting heterogeneous MS spectral data from multiple open-access libraries (OMS libraries) where metadata completeness and correctness are uncertain.
Use when after sample alignment and peak picking have produced an aligned feature table with m/z and retention time coordinates.
Use when you have LC-HRMS profile-mode data (e.g., netCDF or mzML format) and need to convert detected or reference chromatographic peaks into fixed-size 2D arrays (rt × mz…
Use when you have draft metabolic reconstructions (in SBML or equivalent format) for multiple organisms sampled from a single ecological community (e.
Use when when claiming that one mass spectrometry processing library achieves higher throughput than competitors, or when evaluating whether a new or optimized implementation…
Use when you have a metabolomics dataset (LC/MS or GC/MS) with missing values and need to determine which are below the limit of detection (LOD) or limit of quantification (LOQ).