Use when you have a GTF annotation file and need to systematically extract all local alternative splicing event coordinates (not transcript isoforms) for downstream PSI…
Use when you have RNA-seq count matrices (from alignment, transcript quantification, or HTSeq-count files) and need to test for differential expression between two or more…
Use when you have paired GCF and MF datasets with strain membership information and need to rank candidate GCF–MF links to identify which biosynthetic gene clusters likely produce…
Use when when you have structural clusters from multiple LC-MS assays (e.g., positive and negative ion modes, or reversed-phase and HILIC methods) and need to identify which…
Use when you are composing multiple containerized services that have data dependencies—e.g., a web application that launches calculation jobs, a calculation engine that consumes a…
Use when after mass tracks have been aligned across all samples into a MassGrid (via sample-wise or centroid-based alignment), you have a unified set of m/z features tracked…
Use when you have computed RAS (Reaction Activity Scores) from transcriptomics and GPR rules, RPS (Reaction Propensity Scores) from intracellular metabolomics via mass-action…
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 when you have mass spectrometry data (chromatograms, spectra, mobilograms, or peak maps) in a Pandas DataFrame and need to generate the same visualization in multiple…
Use when you have custom lipid species (not covered by the 500,000+ built-in LipidMatch entries) that you need to match against experimental MS/MS data, or you are extending…
Use when when you have tandem mass spectra from ribosomally synthesized peptides (RiPPs) and suspect the presence of unknown or non-standard post-translational modifications that…
Use when when you need to validate that a package's periodic integration test suite (distinct from unit tests) passes as expected, or when you must collect and communicate…
Use when you have received an mzPeak archive (a ZIP file containing Parquet tables) and need to understand its internal structure, validate that spectrum metadata aligns with…
Use when after constructing individual mass tracks from mzTree data bins and before alignment across samples.
Use when when you have salmon quant.sf.gz output files from pseudoalignment-based transcript quantification and need to convert transcript-level abundance estimates and counts…
Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that…
Use when you have a preprocessed GC-MS dataset (from spreadOut) with standardized column names (Compound.Name, Component.RT, Base.Peak.MZ, Component.Area, Match.Factor) and a…
Use when when you have Thermo Orbitrap .raw files containing known reference peptides (e.
Use when after generating a corpus/features JSON file from raw MS2 fragmentation
Use when you have a tandem mass spectrum (MsmsSpectrum) from a known peptide and need to determine what fraction of observed peaks can be explained by expected fragment ions.
Use when you have a Thermo Fisher Orbitrap .raw file and need to programmatically
Use when you have raw GC-MS data (in netCDF or vendor format) containing overlapping chromatographic peaks from complex mixtures where individual compound spectra cannot be…
Use when you have a Thermo Fisher Scientific .raw file and need to (1) enumerate all scans and their metadata, (2) identify which scans are MS1 vs.
Use when you have a collection of chemical structures (SMILES, InChI, SDF, or mol formats) and need to train or apply a machine learning model for retention time prediction or…
Use when immediately after loading raw .idat files or beta-value matrices from HumanMethylation450 or EPIC arrays when you need to exclude probes that fail quality control.
Use when after isotope correction has been applied to MSI ion images, when you have sprayed or identified a reference lipid standard of known amount (pmol/mm²) and need to…
Use when when you have aligned peak-alignment data from a preceding molecular networking task (structured as a table with peak intensity, m/z, retention time, and alignment…
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 when comparing two MS/MS spectra (query and reference) to quantify their spectral resemblance for compound identification or molecular networking, particularly when you…
Use when after peak picking and alignment have been performed on MSImagingArrays
Use when you have vendor-specific raw mass spectrometry data (ThermoFisher .raw, Agilent .
Use when during MS/MS spectral preprocessing when converting raw spectra from .mgf, .msp, or .mzML formats into a bag-of-fragments corpus for LDA modeling.
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 spatial metabolomics data with semicolon-delimited isomer name annotations (such as the 'all_IsomerNames' column in SpaMTP Seurat objects) and you need to reduce…
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 after generating large feasible flux distributions (e.g., 1 million sampled solutions per cell line) from constrained metabolic models, apply t-SNE when you need to…
Use when when you have access to annotated MS/MS spectra from a specific ionization mode (e.g., negative ESI) or adduct class (e.
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 after RDKit has generated a large set of 3D conformers for a molecule in SDF or XYZ format, and before submitting conformers to computationally expensive quantum-chemical…
Use when you have MS imaging or LC-MS data with pre-annotated m/z values that include multiple isomer or metabolite names per m/z (stored as semicolon-delimited or multi-record…
Use when you have received MSBERT-preprocessed spectral data from GNPS, MoNA, or MTBLS1572 and need to ensure data integrity before training a spectral embedding model.
Use when you have (1) peak-picked LC-MS AIF features in a feature table with m/z and retention time, (2) corresponding xcmsSet and RAMClustR pseudo-MS/MS spectral objects from…
Use when you have annotated MS/MS spectra in MGF format and need to identify peptide sequences that may not exist in reference protein databases—such as in immunopeptidomics,…
Use when your TWIM-MS dataset contains ions with multiple charge states (e.g., +1, +2, +3 for the same molecular species) and you need CCS values that correctly account for the…
Use when you have a Docker image published to a registry (e.g., docker://stravsm/msnovelist6),
Use when after downloading an mzML file from a remote repository (e.g., MetaboLights, MassIVE, GNPS) via USI resolution, before attempting to parse it into a spectrum container or…
Use when after frequency-based denoising of MS/MS spectra, when you need to validate that denoising improves metabolite identifications and quantify the trade-off between signal…
Use when you have raw HPLC column metadata arrays containing Tanaka parameter blocks that will be fed into a featurizer for machine learning on retention times.
Use when you have a heterogeneous feature matrix combining molecular descriptors (from RDKit/mordred) and chromatographic metadata (column length, temperature, pH, flow rate,…
Use when you have completed cross-validation tuning of one or more machine-learning
Use when you have observed metabolites (from LC-MS/MS, chromatography, or spectroscopy) whose identities are unknown, and you wish to constrain the candidate pool by leveraging…
Use when you have predicted retention times from one or more machine learning models (DNN, Gaussian Process, or ensemble) applied to small-molecule chromatography data, along with…
Use when you have a dashboard_data.json file (JSON export from the msFeaST pipeline) and need to interactively explore quantification tables, metadata, and spectral data on a…
Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g.,…
Use when when training a neural network to predict metabolite abundances from microbiome data (or similar paired multivariate omics prediction tasks) and you need to avoid…
Use when when you need to create synthetic noisy MS/MS spectra for benchmarking or validating denoising algorithms.
Use when you have centroided MS2 spectra from data-dependent acquisition (ddMS2) in mzML format and seek to prioritize potential PFAS features by detecting diagnostic fragment…
Use when when you have raw or minimally processed microarray expression data (e.g., from GEO) with intensity values that exhibit sample-to-sample distributional differences and…
Use when before constructing a DESeqDataSet from count data or tximport output, when you have raw RNA-seq samples that need to be annotated with experimental conditions, treatment…
Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.