Use when when you need to evaluate how a specific algorithm parameter (such as SearchMolecularFormulas first_hit mode) affects the quantity and quality of molecular formula…
Use when you have a trained NeatMS neural network model and a labelled validation dataset of MS1 peaks (annotated as 'High_quality' or 'Low_quality'), and you need to identify the…
Use when apply IOKR when you have BGCs with structural predictions based on MIBiG homology (cumulative BLAST score ≥10,000) and you wish to rank hypothetical BGC–spectrum links…
Use when you have a trained PS2MS deep learning model, a set of evaluation compounds (especially novel NPS analogues), and want to understand whether prediction confidence…
Use when when training or validating a deep learning model for molecular formula prediction from tandem MS/MS spectra, use this metric to track whether the model's predicted…
Use when you have completed Tn5 insertion bias correction on ATAC-seq reads and now need to quantify footprint signal strength (signal depletion around TF-bound sites) across…
Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before…
Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to…
Use when you have a set of candidate transformed structures generated by biotransformation rules (e.
Use when when processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution.
Use when you have transcript abundance files (e.g., Salmon quant.sf.gz, kallisto abundance.h5, RSEM .isoforms.results) from a quantification tool and need to construct a…
Use when after performing peak detection on centroided .mzML LC-MS data with screening_mode=FALSE in TARDIS.
Use when you have raw mass-spectrometry data (precursor m/z, ionization mode, and fragment m/z–intensity pairs) and need to feed it into a CNN-based metabolite annotation pipeline.
Use when when you have a list of lipids identified by different database identifiers (e.
Use when you have a normalized abundance matrix from LC-MS/MS profiling with sample class assignments (e.g., phenotypic groups, disease states, treatment conditions) and need to…
Use when you have raw metabolomics mass spectrometry data in mzML or mzXML format and need to extract, align, and normalize metabolic features across multiple samples or…
Use when when you have raw MS2 spectra (m/z and intensity pairs) and a curated reference peak list from a large training dataset (e.
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 integrating with an external API (such as TensorFlow Serving) where changes to the response schema could break dependent code, or when model metadata must be extracted…
Use when you have a collection of molecular structures intended for CypReact-based
Use when when you have a scientific software tool (e.g., Met-ID) that is architected to support plugins or configuration-driven modules, and you need to register and apply a novel…
Use when you have preprocessed MS/MS spectra (noise-filtered, normalized) and need to compute pairwise similarity or distance scores for compound library matching, when your goal…
Use when you have acquired EI or MS2 library files in MSP format (e.g., from NIST via Lib2NIST export, RIKEN, MoNA, SWGDRUG, or GNPS) and need to read them into R to assign…
Use when when setting up imzML Writer for the first time on a new machine, or when raw vendor mass spectrometry file conversion fails with ''msconvert not found'' or Docker image…
Use when you need to validate that a repository's automated build, test, or publish pipeline is functioning correctly on a target branch (e.g., release branch); when you want to…
Use when when comparing mapping performance between two mapper implementations (e.g., C++ salmon vs. Rust salmon), validating that a bug fix or algorithmic change did not degrade…
Use when processing raw GC-MS data in NetCDF format where peaks have been detected but lack standardized retention indices.
Use when you have LC-HRMS profile-mode data with detected local maxima (from gradient-descent peak finding) and need to prepare them as input for a convolutional neural network…
Use when when you have tandem mass spectra data and need to predict a binary molecular property (e.g., presence of a functional group like a sulfo group) while maintaining full…
Use when after database search algorithms have scored unknown MS samples against reference species, and you need to visually inspect and confirm species assignments or identify…
Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table…
Use when when you need to verify that a GitHub Actions workflow (e.g., main.yml) executes successfully on your local machine, reproduce a reported passing or failing CI build…
Use when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to systematically identify and annotate lipid A molecular structures.
Use when you have completed Hi-C map generation (producing .hic files from aligned reads) and need to detect and annotate topological features such as chromatin loops,…
Use when when you have high-resolution LC-MS/MS data for an unknown metabolite or small molecule, have computed or measured the molecular ion mass and fragmentation spectrum, and…
Use when you have centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format) and wish to identify peptidic natural products or ribosomally synthesized and post-t — from…
Use when after discovering Mass2Motifs through LDA topic modeling of MS/MS fragmentation data, when you need to assign chemical meaning (substructure classes, candidate…
Use when after filtering retention time and drift time ranges on raw GCIMS samples but before decimation and alignment.
Use when after submitting an LC-MS/MS fragmentation spectrum to the MSNovelist web service and receiving a JSON response containing ranked de-novo structure candidates.
Use when when you have an LC-MS feature table with m/z and retention time columns and need to identify which observed ions correspond to the same neutral compound under different…
Use when you have performed lazy dask-backed feature extraction on an ImageContainer using im.calculate_image_features and need to persist the computed spatial features into the…
Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type,…
Use when you have trained predictive models (e.g., MiMeNet neural networks) on microbiome-metabolome paired data using k-fold cross-validation, held out test folds for each…
Use when after converting or loading a Keras model to HDF5 TensorFlow 2.3.0 format, especially when the model will be served through a pipeline (e.g., NP Classifier) that expects…
Use when you have paired MS/MS spectra and molecular structures (SMILES or SDF format) and need to perform compound identification by retrieving the correct structure for an…
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 when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries,…
Use when when you have multiple CDF files from mass spectrometry imaging experiments (e.g., root tissue MALDI-MS data) that need to be ingested into Matlab for linear imaging…
Use when after peak clustering has been performed on aligned GCIMS samples and a peak table matrix has been constructed, but the matrix contains NA values because some samples did…
Use when working with natural product molecules where conventional synthetic-molecule
Use when you have a curated dataset of molecular structures (or molecular descriptors) paired with experimentally measured or reference collision cross section values, and you…
Use when you have fingerprint or spectrum data that requires compound-class annotation but prefer not to run SIRIUS locally, or need to integrate predictions into an automated…
Use when when you have a trained molecular classifier (like BitterPredict) that accepts structured descriptor input, and you need to understand which chemical descriptor subgroups…
Use when you have completed the MS2LDA LDA modeling phase and possess motifset.json or motifset_optimized.json files containing inferred Mass2Motifs.
Use when you need to determine the full scope of hardware and methodological compatibility for a bioinformatics tool before designing an analytical workflow.
Use when you have centroid mzML files from LC-MS experiments (converted from Thermo .raw or other vendor formats) and need to identify and quantify individual chemical features…
Use when you have raw or processed arrival-time data from a TWIM-MS instrument and need to convert it to CCS values for comparison across experiments or biomolecular classes.
Use when your input is a SummarizedExperiment containing multiple batches or injection sequences of metabolomics samples (study samples, QC replicates, calibration lines) with…
Use when processing heterogeneous mass spectrometry libraries (e.g., from OMSLs) where chemical identifiers are unevenly populated across records.