Use when your workflow fetches data from multiple external web services (e.g., CIR, CTS, PubChem, IDSM, BridgeDb) asynchronously and you need to track which services are…
Use when after loading and preprocessing raw scATAC-seq data into an ArchR project object when you need to compute low-dimensional embeddings for clustering, UMAP/tSNE…
Use when after calling squidpy.gr.spatial_neighbors on an AnnData object containing spatial coordinates in obsm.
Use when after peak picking, sample alignment, and isotopologue/adduct grouping steps have been completed in an untargeted LC-MS workflow.
Use when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all-pairs or many-to-many…
Use when you have a GNPS-generated classical or feature-based mass spectral molecular network (graphml or JSON format) and a corresponding MS2LDA experiment with Mass2Motif…
Use when you have a normalized gene expression matrix (bulk RNA-seq or microarray) from a time-course or multi-condition experiment and need to quantify whether known gene sets…
Use when you are starting a new mass spectrometry analysis task or feature request where the problem scope is unclear, the tool chain (e.g., OpenMS + Python + KNIME integration)…
Use when when ingesting spectra from multiple open mass spectrometry libraries (OMSLs) in .mgf, .msp, .json, or .csv format and you observe mixed experimental protocols,…
Use when you have TWIM-MS data (arrival time and m/z values) from a multi-omic sample and need to: (1) establish a CCS calibration curve from known standards, (2) assign…
Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those…
Use when when a research software project is decomposed into distinct subproject components (e.
Use when analyzing differential methylation from bisulfite sequencing data where you suspect overdispersion (variance exceeds binomial expectations), or when comparing uncorrected…
Use when immediately after parsing and validating raw LC-MS/MS data files (mzML, mzXML, or vendor formats) when you need to prepare spectral data for fragmentation tree…
Use when using Casanovo for de novo peptide sequencing on high-stakes datasets (immunopeptidomics, paleoproteomics, or monoclonal antibody discovery) where missing the correct…
Use when when you have mass spectrometry imaging root datasets paired with accompanying .mat workspace files (as in the B73 and Oaxacan Green genotypes from Sama et al.
Use when when you need to validate that a development build release workflow (such as dev_build_release.yml for a mass spectrometry data processing project) executes without…
Use when after peak detection and MS1 feature extraction from FIA-MS, GC-MS, LC-MS(/MS), or CE-MS data, when you need to identify unknown metabolites by matching observed m/z…
Use when you have preprocessed MS/MS spectra with measured precursor m/z values but the ionization adduct type is unknown or ambiguous—particularly in metabolomics workflows where…
Use when you have a processed ArchR project object (containing peak calls, cell barcodes, and quality control metadata) and need to: (1) reduce dimensionality of the peak matrix…
Use when after invoking the saveAnnotations function on a MetaboAnnotatoR annotations object to confirm that all four expected output file types (global results file, ranked…
Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS — from…
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 you have a peak table from XCMS preprocessing with intensity measurements for the same set of metabolites across multiple QC replicate injections (samples marked…
Use when when you have SMILES strings representing neutral organic molecules and need to enumerate the likely protonated (e.g., [M+H]+) and deprotonated (e.
Use when when you have a SummarizedExperiment containing metabolomic abundances and a corresponding vector of quality metrics (e.g., coefficient of variation computed across QC…
Use when when processing large collections of mass spectra from multiple Open Mass Spectra Libraries (OMSLs) or databases that may contain redundant spectral records with…
Use when you have a set of natural product molecules (or suspected natural products) in SMILES, InChI, or SDF format and need a chemical representation suitable for biosynthetic…
Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability…
Use when you have a large single-cell count matrix (≥10 million cells) in CSR format and need to verify whether the matrix-free spectral embedding in SnapATAC2 achieves its…
Use when you have a large collection of tandem mass spectra (mzML, mzXML, or MGF format) and want to group similar spectra into clusters to identify redundancy, discover novel…
Use when you have extracted metadata or spectral information from a Thermo Fisher Scientific .
Use when you have a curated relational dataset (structure-organism pairs) and need to quantify how structures distribute across a categorical variable (e.g., organism prevalence).
Use when you have a trained multitask machine learning model for structure prediction, test set molecules with paired ¹H and ¹³C NMR spectra, and need to understand the marginal…
Use when you have raw GC–MS or LC–MS data represented as a two-dimensional map (m/z axis vs. retention time axis) and need to identify chemo-/biomarker features across multiple…
Use when when you have IM-MS lipidomics data acquired on samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and need to quantify systematic CCS bias…
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 after loading raw m/z peak data (in MetaboAnalyst, MetaboShiny native, or Metabolights format) and merging it with sample metadata (batch IDs, concentration values,…
Use when you have ATAC-seq BAM alignments with classified motif sites (bound vs. unbound based on chromatin accessibility or binding thresholds) and wish to detect and visualize…
Use when when you have a pre-trained GNN checkpoint and a smaller, task-specific
Use when you have a preprocessed feature table (tab-delimited: feature ID, m/z, retention time, intensity columns) from LC-MS data and need to annotate which observed features…
Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real…
Use when building a multi-source metadata annotation pipeline where converters are organized as dynamically discoverable subclasses in separate packages (e.g.,…
Use when when beginning peak calling on ChIP-Seq data: you have raw single-end or paired-end BED/BEDPE alignment files for both ChIP and control samples and need to remove…
Use when when you have partitioned public MS/MS files from MassIVE using the ReDU File Selector into one or more filtered groups (G1–G6) and need to verify that each group's file…
Use when you have acquired Bruker Solarix FT-ICR-MS raw data (e.g., ESI_NEG_SRFA.d)
Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation timestamps or duration), and — from…
Use when you have a GitHub repository with published CI workflow badges (e.g., unit test or package test badges in the README) and need to independently verify that the workflows…
Use when you have raw or processed arrival-time data from a traveling-wave ion mobility mass spectrometry (TWIM-MS) platform and need to convert it into standardized collision…
Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties…
Use when when you need to understand or modify how MS2Query routes query spectra through its dual-pathway architecture, or when integrating MS2Query into another tool and need to…
Use when you suspect XCMS grouping contains misaligned features due to suboptimal parameter settings or insufficient samples.
Use when you have paired microbiome and metabolomic (or similar compositional) data with a new regression model and want to rigorously demonstrate its predictive advantage over…
Use when you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak…
Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire…
Use when when comparing quantification results between two versions of a tool (e.g., salmon 2.0 Rust rewrite vs.
Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root…
Use when you need to assess MS1-level ionization efficiency, peak detection sensitivity, and chromatographic separation without the overhead of MS/MS fragmentation.
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 you have raw LC-IM-MS/MS data files from sterol lipid analysis and need to identify unsaturated sterol isomers by matching experimental collision cross section values…