Use when after loading fragment counts into a SummarizedExperiment object (e.g., via getCounts) but before motif matching or deviation computation.
Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the…
Use when you have completed cross-validation tuning of one or more machine-learning
Use when after running PERMANOVA on distance matrices derived from FT-ICR MS metabolite peak intensities or other high-dimensional compositional data, when p-values indicate…
Use when when you need to extract m/z and intensity peak values from a Spectra object backed by MsBackendMzR or similar on-disk backends; when analyzing subsets of spectra without…
Use when when validating a metabolomics pathway analysis method (particularly decomposition-based approaches like PLAGE) against data quality degradation, or when comparing…
Use when you have a connected subnetwork of LC-MS features that matched isotope or adduct patterns, and you need to establish a canonical tree representation with a single neutral…
Use when when you have an aligned GCIMS dataset and need to configure the findPeaks function with CWT algorithm to detect peaks across retention time and drift time dimensions.
Use when after running XCMS getEIC() to generate xcmsEIC objects and fillPeaks() to produce a filled xcmsSet object, before computing the 12 peak-quality metrics (Apex…
Use when a spatial metabolomics dataset contains semicolon-delimited isomer name annotations (e.g., 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to collapse…
Use when you need to validate that a scientific software project's continuous integration pipeline is functional and producing reproducible builds—particularly before releasing…
Use when you need to verify that a GitHub Actions workflow (such as a Build and Publish pipeline) executes successfully on a specific branch (e.g., release branch) and produces a…
Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST indices and need to integrate the resulting match outputs into a single — from…
Use when when analyzing DNA methylation data from bisulfite sequencing (RRBS, target-capture, or whole-genome) and the dataset is too large to fit comfortably in memory, or when…
Use when when a C++ program writes records to an output stream (e.g., SAM alignment file) and the final output file contains fewer records than expected based on upstream counts…
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 peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS…
Use when a Rust port or alternative implementation of a mapper (e.g., salmon, piscem) consistently maps 2–3% more reads than a C++ reference, especially on short reads.
Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values,…
Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of…
Use when you have IM-MS measurements of samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract) and need to assess whether measured CCS values…
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 implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
Use when you have preprocessed metabolomics data stored in a SummarizedExperiment
Use when after running DESeq() and extracting raw results with results(), when you have log fold change estimates with high variance and wish to improve their precision.
Use when when you have 1H-NMR metabolite measurements from Nightingale Health assayed on a new cohort and wish to compute risk scores (e.g., all-cause mortality, cardiovascular…
Use when after starting a TensorFlow Serving instance (e.g., via docker-compose)
Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or…
Use when after matching mass-to-charge ratios to a KEGG database and obtaining multiple candidate metabolites per feature, but before filtering quasi-molecular adducts.
Use when after invoking pp.make_fragment_file to convert a coordinate-sorted BAM file (e.g., from 10X ATAC or standard alignment) into a compressed fragment file.
Use when you have a SummarizedExperiment object containing pooled quality control samples with measured compound and internal standard peak areas.
Use when you have real mzML LC-MS/MS data (e.g., from a Beer sample or HMDB reference set) and want to test whether a proposed TopN DDA strategy (or variant) can accurately…
Use when you have a MetaboLights dataset identifier (e.g., MTBLS1124) and need to download a specific mzML file (e.g., QC07.mzML) from the public repository for visualization,…
Use when after feature table normalization and imputation are complete, immediately before MS1 and MS2 annotation.
Use when you have raw GCxGC-MS chromatogram data in NetCDF (CDF) format from an instrument and need to load it into R for preprocessing (smoothing, baseline correction, peak…
Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an…
Use when you have raw 1D ¹H NMR spectroscopy output consisting of (1) a CSV file with chemical shift and intensity columns and (2) a TXT file listing detected peak chemical…
Use when when you need to confirm that a research tool or package maintains a functioning test suite, especially before adopting it for downstream analysis or before contributing…
Use when you have computed raw p-values from partial Spearman correlations (or other univariate tests) between each metabolite in a SummarizedExperiment object and a phenotype of…
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 when processing in-silico or experimental MS spectra records from databases with incomplete metadata, specifically when the adduct field is null or absent but the ionmode…
Use when you have positive- or negative-mode tunemix reference data (with known CCS values, m/z, and measured drift times) and need to establish a calibration model for converting…
Use when you have molecular identifiers (SMILES strings or molecular structure files) that need to be converted into node-edge graph tensors for input to message passing neural…
Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d)
Use when when analyzing high-resolution mass spectrometry data from natural-abundance
Use when after fitting candidate GAM splines with B-spline basis functions across a range of basis dimensions (k values 12–20) to anchor feature pairs (m/z and retention time…
Use when when comparing two preprocessed MS/MS spectra for compound identification
Use when before constructing a DESeqDataSet from count data or tximport output, when you have raw RNA-seq samples that need to be annotated with experimental conditions, treatment…
Use when you have a defined set of lipid species (identified by class and fatty acid composition) and need to create a high-throughput spectral library for mass spectrometry-based…
Use when when you have MS/MS spectral data (raw or intermediate format) that must be fed into the Mass2SMILES Docker container or similar deep learning models for…
Use when after integratePeaks has been executed with a chosen integration method (e.g., fixed_size with RIP saturation threshold of 0.1) on a clustered, baseline-corrected GC-IMS…
Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that…
Use when you have RNA-seq count matrices (from alignment, transcript quantification, or HTSeq-count files) and need to test for differential expression between two or more…
Use when you have co-registered IMC (protein imaging mass cytometry) and SIMS (secondary ion mass spectrometry for metabolites) data from the same tissue regions, cell…
Use when when you have a trained deep learning model (e.g., PS2MS) and an evaluation dataset of compounds, and you need to assess how prediction confidence varies across…
Use when when you have large sequential media files (mzML spectra, text chapters, or similar) and need to enable both random access by ID and sequential iteration without loading…
Use when you are implementing ORA for metabolomics pathway analysis and must decide which metabolites constitute the statistical background against which to test your experimental…