Use when you have precomputed expected contact frequency tables (TSV format with columns like dist_bp, contact_frequency, n_valid) and need to apply log-binning and smoothing to…
Use when you have a mass-spectrometry query string written in MassQL (or similar domain-specific SQL-inspired syntax) that must be converted into structured form for execution.
Use when you have tunemix reference data acquired in both positive and negative ion modes and need to establish independent CCS calibration curves for each mode.
Use when you have a fitted linear model (lmFit object) from microarray, RNA-seq, qPCR, or proteomics data and need to test for differential expression across genes while…
Use when when you have loaded a MoNA mass spectral library (GC-MS or LC-MS/MS) in MSP format and observe that SMILES strings are present in the Comment field rather than in a…
Use when after peaks have been detected in aligned GCIMS samples using findPeaks with CWT parameters and peaks have been clustered across samples, and you need to integrate peak…
Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax
Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment…
Use when you have a set of conformers that have already been filtered by ASE-ANI neural network potentials and need to extract quantum-mechanical electronic properties…
Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, m — from…
Use when you have aligned ATAC-seq BAM files and want to discriminate between transcription factor binding sites that are actually occupied by protein versus sites with matching…
Use when after executing a molecular structure prediction model on spectroscopic
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 after peak detection in untargeted LC/HRMS workflows, when you have a list of candidate peaks with signal intensity profiles and need to filter them according to data…
Use when processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
Use when when you have query chemicals identified by GC-MS (with Match.Factor values) and need to verify structural similarity against a reference chemical library to confirm…
Use when you have LC-MS/MS DDA data from one or more samples and need to organize fragmentation spectra by similarity relationships to support compound annotation, enable…
Use when building or maintaining a system that fetches metadata from multiple independent external web services and needs to diagnose why annotation runs fail or slow down.
Use when when reproducing or validating a tandem mass spectrometry denoising pipeline on mzML files with known feature precursor m/z and RT coordinates, compare pre- and…
Use when before running any R function that wraps compiled C# methods or system executables (e.g., rawrr::readSpectrum), especially when the package depends on language runtimes…
Use when when processing centroided .mzML LC–MS runs with a multi-polarity target list (i.e., some targets ionize in positive mode, others in negative mode, or both) and you need…
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 have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
Use when when you need to constrain a large metabolite database to a specific instrumental range (e.g., m/z 100–1000) before generating virtual chemical mixtures for LC-MS/MS…
Use when you have a set of in silico-predicted compounds (with SMILES structures) and an experimental metabolomics peak list (m/z values), and you need to filter predictions to…
Use when when you have a set of molecular structures (N-Me derived unsaturated sterol lipids or structurally similar organic molecules with C=C bonds) represented as SMILES or…
Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect…
Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run…
Use when you have paired-end or single-end RNA-seq reads (FASTQ format) and a reference transcriptome (FASTA), and you need to estimate transcript-level abundances (NumReads and…
Use when when identifying landmark peaks for retention time alignment in multi-sample LC-MS metabolomics workflows.
Use when you have acquired LC-IMS-MS/MS data (or equivalent multidimensional MS/MS acquisition) in mzML or mzML.gz format and need to disambiguate overlapping fragmentation…
Use when immediately after loading metabolomics measurements into a SummarizedExperiment
Use when after completing peak calling and cell annotation in an ArchR project, when you intend to perform trajectory analysis using STREAM rather than ArchR's native monocle3 or…
Use when you have executed a binary classifier (such as BitterPredict.m) on a set of molecules with chemical structure descriptors and need to translate the raw predictions into a…
Use when you have vendor-independent centroided mzML files from data-dependent acquisition (ddMS2) HRMS experiments and need to extract a reproducible feature list with mass,…
Use when you have MS2 spectra data (MGF/mzML format) and aligned feature tables, and your analysis goal is to compare samples that may have poor MS1 feature overlap, strong…
Use when you have raw GC-MS output exported as CSV (containing columns: Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
Use when you have N-methyl-derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict their MS/MS fragmentation behavior before…
Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each…
Use when you have a raw metabolite abundance matrix (e.g., from MSPrep or another LC-MS/MS pipeline) with many features and samples, and you observe that a substantial fraction of…
Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name,…
Use when your input is a spatial dataset (AnnData object with coordinate metadata) paired with a large tissue image, and you need to extract spatial features (via…
Use when after generating combined or alternative scores for a set of BGC-metabolite (GCF-MF) link candidates, you need to evaluate whether a scoring function preferentially ranks…
Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic…
Use when when you have completed feature detection in MZmine3 or similar tools and produced a feature quantification table (rows = features, columns = samples with intensity…
Use when after installing an R package from a non-CRAN repository (such as r-universe) to confirm the package build is sound, dependencies resolve correctly, and no warnings or…
Use when when you have obtained an R-based bioinformatic program (such as DNMS2Purifier.
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…
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 after marker identification or metabolite annotation has produced a curated list of compound IDs (e.g., KEGG IDs or CAS numbers) and you need to determine which metabolic…
Use when you have multiple mass spectral library files in different formats (MSP, MGF, MOL folders) from sources like NIST, MoNA, RIKEN, or GNPS, and need to produce a single…
Use when you have a normalized gene expression matrix (bulk RNA-seq or microarray) from a time-course or multi-condition experiment and need to quantify whether known gene sets…
Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS…
Use when you have acquired a mass spectrum from an unknown suspected illicit drug analyte and need to compare it against a synthetic NPS database to rank candidate identities by…
Use when after completing peak picking, sample alignment, and before final MS2 spectrum extraction, when you have identified individual ion peaks across samples and need to link…
Use when after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table…
Use when you have a tandem mass spectrum with observed m/z peaks and a known peptide sequence (as a ProForma string, optionally with post-translational modifications), and you…
Use when you have downloaded raw LC-MS spectral peak data from a public repository (e.g., DOI 10.25345/C5FD2F) and need to ingest it into memory and prepare it in the format…
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 you have annotated metabolite structures (with SMILES strings) from a reference library (e.