Use when you have untargeted metabolomics MS/MS spectra from multiple features and need to identify which features belong to the same molecular family or are related by…
Use when you have raw mass-spectrometry files (MGF, BIOM, mzXML, mzML) or feature abundance tables from external tools (MZmine2, peak detection software) and need to convert them…
Use when you have a precomputed expected contact frequency table (TSV format with columns: dist_bp, contact_frequency, n_valid) derived from cooler files and need to compress…
Use when when you have multi-omic TWIM-MS data (raw or processed arrival-time records) and have already assigned features or detected ion features to biomolecular classes (e.
Use when when you have an mzML file that you want to store persistently in a queryable format for repeated access, or when memory constraints prevent loading entire mzML files…
Use when you are preparing to reuse public tandem MS data from MassIVE via ReDU and need to partition files by sample metadata (e.g., organism, tissue type, extraction method,…
Use when when you need to make OpenMS C++ classes, functions, or data structures callable from Python code, or when verifying that a newly bound C++ component can be imported 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 microarray or RNA-seq expression data paired with phenotype/sample metadata describing experimental conditions, treatments, or group assignments, and you…
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 after composite-map peak detection has produced an unfiltered peak list with SNR, peakshape (goodness_fitting), peak_height, and prominence values.
Use when you have a query mass spectrum (or a metabolite reference spectrum from public data) and need to search it against a large-scale spectral repository (≥billions of…
Use when when you have aligned ChIP-Seq reads (single-end BED or paired-end BEDPE format) and need to identify enriched genomic regions by comparing ChIP signal against control…
Use when after MZmine feature detection and molecular networking on a single LC-MS/MS DDA sample, when you have a feature table (with retention time, m/z, fragmentation spectra)…
Use when you have claims in a paper or tool documentation that one peak picking method outperforms others (e.g., 'IDSL.IPA outperforms MZmine 2 and xcms'), but the specific…
Use when you have raw Hi-C FASTQ files from a Hi-C wet-lab protocol and need to convert them into processed Hi-C contact maps (.hic files) for loop detection, TAD identification,…
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 when a tool like TARDIS extends its API to accept multiple input types (e.g., both file paths and MsExperiment objects), and you need to confirm that screening-mode…
Use when you have an unknown metabolite with unknown mass spectrum and need to prioritize structural candidates from databases (PubChem, HMDB) by their likelihood of being the…
Use when you have a GC-MS dataset with a Match.Factor column (output from Agilent Unknowns Analysis or equivalent) and need to retain only high-confidence compound identifications.
Use when when you have a feature table from LC-MS preprocessed data (e.g. from asari v1.9.2) and need to annotate ions and infer neutral mass.
Use when when you have a collection of DNA adduct compound structures in SDF format that requires validation for structural integrity and completeness, and you need to generate…
Use when when training a deep neural network on paired MS/MS spectra to predict structural similarity scores, especially when the training dataset is moderate-sized (109,734…
Use when you have fit a linear model to normalized gene expression data (microarray intensities or RNA-seq counts) and need to test for differential expression across experimental…
Use when when you need to validate that MSI software (e.g., LipidQMap) achieves documented processing speeds on your target hardware, or when you need to establish a performance…
Use when when you have raw GC–MS data in two-dimensional m/z × retention time format (NetCDF or proprietary binary) and need to identify marker features across aroma or breath…
Use when you are setting up HiC-Pro or a similar multi-tool pipeline for the first time, or you need to validate that all required dependencies are installed and discoverable.
Use when when preparing to send peak data (1H and 13C NMR measurements) to a machine learning classification endpoint and you need to verify the current model's input/output names…
Use when after running GNPS molecular networking, SIRIUS compound identification,
Use when after constructing initial data bins from mzTree (indexed by int(mz × 1000)), determine whether a single bin contains one or multiple mass tracks.
Use when you need to validate that a repository's automated build and publish pipeline is functioning correctly on a release or target branch, particularly when assessing the…
Use when you have independent LC-MS assays (e.g., positive and negative ionization modes, different lipid profiling assays, or different chromatographic methods) analyzed on the…
Use when when you have prediction scores (softmax probabilities, uncertainties) from a trained deep learning model evaluated on a heterogeneous dataset and you need to determine…
Use when working with untransformed metabolomics count data (e.g., c57_nos2KO_mouse_countDF)
Use when you have raw or minimally processed single-cell RNA-seq expression data loaded into an AnnData object (dense, sparse, or Dask-backed array as X), and you need to apply…
Use when when you have paired microbiome-metabolome datasets where only a subset of metabolites carry curated biochemical annotations (e.
Use when you have pre-processed chromatin accessibility data (ATAC-seq or DNAse-seq) with chromVAR deviations already computed for individual cells or bulk samples across multiple…
Use when you have a compressed file format (e.g., igzip) with a custom binary header structure that encodes metadata (index-to-offset mappings) in a fixed layout, and you need to…
Use when when processing a batch of LC-MS samples in mzML or mzXML format where at least one file has been designated as a quality control (QC) file, extract its TIC or BPC before…
Use when when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) that must be fed into a CNN model for metabolite annotation…
Use when you have paired genomic (BGCs clustered into GCFs via BiG-SCAPE) and metabolomic data (MS2 spectra grouped into MFs), with strain/sample co-occurrence patterns and…
Use when you are repeatedly querying or iterating over multidimensional MS data stored in MZA HDF5 format (retention time, drift time, m/z dimensions) and profiling shows that…
Use when after you have partitioned a feature network into connected subnetworks (each containing ion features linked by isotope or adduct mass differences).
Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which…
Use when you have received new or updated MassBank records (in plain-text or structured format) that must be integrated into the MassBank-data repository and you need to ensure…
Use when you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (as metabData objects) acquired under different conditions or at differen — from…
Use when you have .msp spectral library files with compound names but lack standardized chemical identifiers (SMILES, InChI, InChI Key, CAS number, IUPAC names, or molecular…
Use when after peak detection on composite mass tracks when you need to evaluate whether a detected peak represents a pure, interference-free signal on its m/z channel.
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 completed a GNPS1 (METABOLOMICS-SNETS, METABOLOMICS-SNETS-V2, FEATURE-BASED-MOLECULAR-NETWORKING) or GNPS2 (classical_networking_workflow,…
Use when when designing a library that needs to support multiple plotting backends (e.g., matplotlib, bokeh, plotly) and you want to avoid reimplementing parameter validation,…
Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible
Use when you have loaded raw MS intensity tables into QuantyFey and observe or suspect intensity drift artifacts across your measurement sequence.
Use when you have GCIMS samples exhibiting misalignment across drift time (typically 5–16 ms range) and retention time (typically 0–1100 s range) caused by pressure/temperature…
Use when you have a collection of molecular structures intended for CypReact-based
Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide…
Use when you have a 1D ¹H NMR spectrum (as chemical shift vs. intensity) and a corresponding peak list (chemical shift values), and you need to identify which metabolites are…
Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final…
Use when deploying the ipbhalle/metfragweb container and you need to supply custom MetFrag settings (ChemSpider tokens, proxy servers, local database connections) without…
Use when you have a raw LC–MS compound metadata file (xlsx or csv) with heterogeneous column names and column order, and you need to prepare it for targeted peak detection in…