Use when you have raw molecular datasets (e.g., METLIN-CCS, CCSBase) with SMILES strings, 3D coordinates, adduct information, and ground-truth collision cross section labels, and…
Use when after generating a Chemical Feature Tree artifact (Phylogeny[Rooted]) from q2-qemistree's make-hierarchy method, or when importing a tree from external sources, to…
Use when processing SWATH-MS (Sequential Windowed Acquisition of all Theoretical Mass-spectra) raw data files (mzML or vendor format) for untargeted metabolomics, specifically…
Use when after peak detection in nontargeted LC-MS workflows when you have a feature table with detected peaks and need to assign quality scores or filter low-confidence features.
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 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 loaded raw Agilent Unknowns Analysis CSV output with required columns (Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test…
Use when when annotating large-scale untargeted metabolomics datasets where reference library coverage is incomplete and you need to infer metabolite identities for unannotated…
Use when when preparing raw mass spectrometry imaging (MSI) ion images for deep learning–based representation learning, especially when you need to generate augmented image pairs…
Use when after fitting a linear model with lmFit on voom-transformed or log2-normalized RNA-seq or microarray expression matrices, apply eBayes moderation to moderate gene-wise…
Use when you have two or more independently processed MemoMatrix objects (each generated from a separate sample set) and your analysis goal requires direct comparison of MS2…
Use when after sample alignment and feature grouping in untargeted LC-MS workflows, when the aligned feature table contains missing intensity values (NA or zero entries) due to…
Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing.
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 you have aligned single-cell ATAC-seq data as BAM files or fragment files (TSV format with genomic coordinates) and need to prepare it for spectral embedding, clustering,…
Use when you have a set of query chemicals (chemical names or structures) and need to match them against a reference chemical library organized by type or category, with the goal…
Use when you have IM-MS lipidomics data acquired on samples spiked with fully labeled U13C lipid standards (e.g., U13C yeast extract), and you need to assess whether systematic…
Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and…
Use when when comparing two implementations of the same RNA-seq mapping algorithm on identical reference indices and read sets, if per-read mapping agreement is <99.8% or the…
Use when a webservice component (like MAGMa's joblauncher) lacks formal API documentation but the source code is accessible, and downstream consumers (web applications, external…
Use when you have completed one or more LC-MS gradient runs, extracted separation efficiency metrics from the resulting MS1 and MS2 spectra, and need to incorporate those real…
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 after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to…
Use when when you have loaded a project JSON document from the Pairing Omics Data Platform and need to identify and document constraint violations (such as whitespace in URL…
Use when after accurate mass searching has assigned multiple detected m/z features to the same metabolite via positive and negative adduct libraries, and before sample-level…
Use when you have a pair of MS/MS spectra—one from a known compound and one from a structurally related modified (unknown) compound—and need to identify which atom(s) in — from…
Use when after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of…
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 you have raw LC-MS/MS spectral data in .mgf format (or vendor-specific raw data that can be converted to .mgf via MZmine or similar tools) and need to prepare it for…
Use when you have intracellular metabolomics concentration measurements across multiple cell lines or conditions, a stoichiometric metabolic network model with reaction-metabolite…
Use when when you have trained a regression model on experimental retention times or similar continuous molecular property predictions and need to quantify its generalization…
Use when when migrating an existing file-based spectral library (stored as JSON, CSV, or binary formats) into a production system that requires frequent subset queries by metadata…
Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification…
Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each…
Use when you have raw GC-MS data (aroma, breath, or other volatile analyte samples) in NetCDF or vendor-native format and need to identify multivariate chemo-/biomarker features…
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 you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including…
Use when immediately after loading raw methylation array data using champ.load() or champ.import() to verify data integrity.
Use when building a multi-source metadata annotation pipeline where converters are organized as dynamically discoverable subclasses in separate packages (e.g.,…
Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to…
Use when when you have computed similarity scores (cosine, modified cosine, Spec2Vec, or other metrics) between a set of query spectra and a reference library with known…
Use when you have MGF or native MS/MS arrays (mz_array, intensity_array, precursor_mz, adduct) and want to predict the most likely molecular formula.
Use when after creating a fresh conda environment from a pinned dependency specification (environment.yml or requirements.txt) and installing packages via conda and/or pip.
Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time…
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 RAMClustR clustering of XCMS-detected features and prior to final compound annotation, when you need to verify the robustness of molecular weight inference or when…
Use when when performing peak detection on Gas Chromatography–Ion Mobility Spectrometry samples where the Reactant Ion Peak (a high-intensity background signal from the ion…
Use when when reading a binary file format with a magic integer or fixed checksum field at a known offset, and endianness is not explicitly declared in file metadata or header…
Use when after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.
Use when when evaluating a regression or similarity prediction model and you need to understand whether prediction error is uniform across the outcome space or concentrated in…
Use when when importing raw mass spectrometry data from instrument vendors or public repositories in one format (e.g., mzML, mzXML) and needing to export it in another format (e.
Use when you have 1H NMR spectral tensors as input and need to extract local features (e.g., peak patterns, signal neighborhoods) before applying attention-based or sequence-level…
Use when developing or reviewing Python code for a scientific package (e.g., cooltools) that targets collaborative development with multiple contributors.
Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural…
Use when when you have computed PCA coordinates from chemical annotation matrices (e.
Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measure — from…
Use when immediately after chromatographic peak detection (findChromPeaks) when you have detected peaks across multiple samples and need to identify which peaks represent the same…
Use when you are converting a processed Cardinal MSImagingExperiment object (containing normalized peaks, optional spatial shrunken centroids segmentation, and feature m/z…