Use when a machine learning model produces multiple ranked predictions (each with an associated confidence score) for a single input, and you need to quantify how often the…
Use when when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages,…
Use when after bias correction of ATAC-seq reads (via ATACorrect) when you have a bias-corrected bigWig file and need to measure transcription factor footprint strength within…
Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
Use when at the start of an untargeted LC-MS annotation pipeline when you have a KEGG database with exact masses and need to prepare a mass-matching reference.
Use when a mass spectrum calibration procedure initialized with a narrow ppm window (e.g., ±1.0 or ±5.0 ppm) finds fewer than 5 reference m/z matches.
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 you need to create a synthetic feature table with known, ground-truth condition effects for method validation when: (1) testing normalization or batch-correction…
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 nuclear magnetic resonance (NMR) peak data (1H and 13C measurements) that you need to classify using a deployed SMART 3 model, and you want to submit peaks…
Use when when you have labeled mass-spectrometry spectral data (precursor m/z and fragment m/z–intensity pairs) paired with known molecular structures (as InChIKeys or SMILES),…
Use when after querying a formula database (KEGG, PubChem, or user-supplied) with neutral mass values derived from observed m/z peaks and adduct transformations, when multiple…
Use when you have a feature table from untargeted LC-MS (m/z, retention time, intensity) and need to annotate which observed m/z values correspond to isotopologues and adducts of…
Use when after frequency-based denoising and sample-level aggregation of replicate MS/MS spectra, when you need to export denoised spectra to a standardized, vendor-independent…
Use when you have a raw metabolite count data frame (e.g., c57_nos2KO_mouse_countDF)
Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated…
Use when after anchor selection and retention-time spline mapping have produced a candidate list of feature pair alignments, but before final scoring and reduction of the combined…
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 you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1,…
Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it…
Use when after executing a molecular structure prediction model on spectroscopic
Use when you have a user-supplied metabolite set file (CSV or JSON) defining custom groupings of metabolites (e.
Use when you have molecular structures (SMILES or SDF format) that need to be matched against MS/MS spectra, or you need to compute similarity between query spectra and a…
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 you have matched multiomics data (genomics, epigenomics, transcriptomics,
Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z…
Use when you have DDA LC-MS/MS raw data (mzML format) with detected chromatographic
Use when you have raw SMILES strings from a chemical database (e.g., CCSBase, METLIN, or custom sources) and need to feed them into a graph neural network model.
Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a…
Use when you have two or more CSV feature tables from separate metabolomic experiments (each containing mass, retention time, intensity, isotope, and adduct columns), and you need…
Use when when you have raw GC–MS or LC–MS data (m/z vs retention time chromatography-mass spectrometry maps) and need to identify analyte signals and marker features without…
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 when generating augmented variants of single-channel or multi-channel ion images for contrastive learning in mass spectrometry imaging analysis.
Use when you have multiple CDF files containing mass spectrometry imaging data (spectra, m/z arrays, and spatial coordinates) that need to be ingested into MATLAB for the DIMPLE…
Use when you have implemented or are validating a reader/writer library for a mass spectrometry file format (such as mzPeak, mzML, or similar), and need to confirm that data…
Use when you have generated or received a mass spectrometry data file in a structured format (e.g., mzPeak, Parquet-based archive) and need to verify it conforms to the published…
Use when immediately after acquiring raw GCxGC-MS data in NetCDF format (.cdf files) and before any signal enhancement (smoothing, baseline correction) or alignment steps.
Use when you have obtained a raw reference library file (such as the DTCCS_N2 library for U13C labeled lipids) and need to validate its structure, verify that all expected lipid…
Use when you have a Sciex Multiquant TXT export file containing a metabolomics or lipidomics analytical sequence and need to locate QCpool samples that were injected at regular…
Use when you have inferred or discovered structured results (e.g., LDA-derived motif sets with mass compositions, neutral-loss patterns, and ranked database matches) that must be…
Use when you have a ranked candidate list (e.g., BGCs sorted by IOKR or strain-correlation score) for each test spectrum, a known ground-truth BGC for each spectrum, and you want…
Use when when implementing or reverse-engineering a custom binary file format (e.
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when after executing a spatial statistics function (e.g., squidpy.gr.sepal) on a spatial transcriptomics dataset in AnnData format, and before using the computed rankings or…
Use when after implementing or modifying a cross-language integration layer that wraps Python mass spectrometry functions (e.g., spectral matching, peak detection, normalization…
Use when when you have a GTF genome annotation and need to identify all local alternative splicing events (SE, RI, A5/A3, MX, AF/AL) or transcript-level isoform events for a given…
Use when you have individual MS/MS spectra or batch .mgf files from untargeted metabolomics experiments and need to search them against domain-specific reference libraries (e.
Use when you have untargeted MS2 spectral data (from LC-MS/MS or similar instruments) and need to assign metabolic pathway context to detected compounds when standard spectral…
Use when you have completed LC-MS/MS data processing and feature alignment in MZmine2 or Optimus, generated a feature quantification matrix and MGF file, and now need to format…
Use when after loading an MSP spectral library file into memory using mssearchr's MSP parser, when you need to verify that each spectrum record contains complete and valid…
Use when you have a parent compound (or set of compounds) in SMILES, MOL, or SDF format and need to predict plausible metabolite structures and pathways in a specific biological…
Use when when evaluating how well mass spectral similarity scores correlate with actual chemical structure for annotated spectral pairs (e.g., spectra with InChIKey metadata).
Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts…
Use when you have a set of candidate transformed structures generated by biotransformation rules (e.
Use when when you have imported MSI data (imzML or vendor format) loaded into the napari plugin environment and need to organize raw spectral m/z and intensity arrays prior to…
Use when you have CpG methylation call files (from Bismark or MethylDackel) and need to load them into R for differential methylation analysis, but anticipate memory constraints…
Use when you have transcript quantification output (TPM or raw counts) from a pseudo-aligner (Salmon or kallisto) and an ioe/ioi event definition file from SUPPA2's generateEvents…
Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered…
Use when you have sampled feasible flux distributions from multiple constraint-based
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…