Use when a Shiny application or similar cross-platform tool is restricted to a single operating system (e.
Use when you have a lipid identification or library-generation task that requires you to define a target chemical space bounded by lipid classes (e.g., phosphatidylcholine,…
Use when after executing a spatial analysis function (e.g., squidpy.gr.sepal) that modifies or augments a data object, verify that the expected output fields exist with correct…
Use when a GitHub repository displays a CI workflow badge (e.g., passing/failing status in README) and you need to verify that the reported status is accurate, reproduce the CI…
Use when when you have an existing real mzML file from a metabolomics LC-MS/MS acquisition (e.g., beer or urine samples) and need to populate a virtual mass spectrometer with the…
Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on…
Use when when you need to create in silico LC-MS/MS experiments with diverse chemical backgrounds for testing fragmentation strategies or acquisition controllers, and you want the…
Use when when processing mass spectrometry imaging (MSI) data in positive ion mode where both [M+H]+ and [M+Na]+ adducts are present for the same lipid species, and you observe…
Use when you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including…
Use when you have a Thermo Fisher Scientific .raw file containing PRM data and need to verify that acquisition of a specific precursor ion (e.g., LGGNEQVTR++ at m/z 487.2567) is…
Use when when preparing MS/MS spectral data for training word-embedding models (Word2Vec, Skip-gram, CBOW) that will learn relationships between fragment ions and neutral losses.
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 you have SWATH-MS data (mzML or vendor binary format) where precursor isolation windows intentionally capture multiple co-eluting compounds, resulting in multiplexed…
Use when training neural networks on MS/MS spectra (or similar scientific data) where you need to preserve model states that improve validation performance.
Use when when you have a calibrated FT-ICR mass spectrum (e.g., ESI-NEG mode) and need to decide between rapid single-assignment (first_hit=True) and exhaustive multi-assignment…
Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples…
Use when when you have a pre-trained Casanovo model, annotated MS/MS spectra in MGF format, and want to benchmark whether beam search decoding improves peptide prediction quality…
Use when you have a user-defined reference list of isolated, high-confidence chromatographic peaks (ground-truth) matched across multiple LC-HRMS samples, and you need to produce…
Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts…
Use when when implementing new scoring components (inchikey score, neighbourhood
Use when when ingesting or updating MassBank records in plain-text or structured format, and you need to verify that metadata fields (accession, name, formula, mass, spectrum…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological — from…
Use when when you have a generic constraint-based metabolic model, cell-line-specific
Use when when you have LC-IM-MS/MS data with measured collision cross section (CCS) values and m/z assignments, and you need to disambiguate sterol isomers (particularly N-Me…
Use when after merging separate vocabularies for distinct data modalities (e.g., spectral tokens for m/z values and intensities, structural tokens for SMILES or graphs) and before…
Use when analyzing GC-MS data containing overlapping chromatographic peaks—a common scenario in untargeted metabolomics and environmental screening where sample complexity or…
Use when after normalizing total UMI counts per cell using normalize_total, and before PCA or feature selection.
Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
Use when you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.
Use when you have a raw or Seurat object-backed scRNA-seq expression matrix and need to: (1) stabilize variance across genes with SCTransform normalization, (2) extract feature…
Use when after running XCMS getEIC() to generate xcmsEIC objects and fillPeaks() to produce a filled xcmsSet object, before computing the 12 peak-quality metrics (Apex…
Use when running targeted peak detection on LC-MS data acquired with multiple overlapping m/z scan windows and observing distorted or periodically discontinuous peak profiles in…
Use when when preparing to run Over-representation Analysis (ORA) on metabolomics pathway data, after you have loaded both a metabolomics pathway database (e.g., KEGG, MetExplore)…
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 a web application receives mass spectrometry data through heterogeneous
Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise…
Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.
Use when when you need to reproduce a computational workflow described in a GitHub repository, validate CI/CD pipeline definitions (e.g., GitHub Actions workflows), inspect source…
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 a preprocessed unknown sample spectrum (m/z peaks and intensities) from high-throughput mass spectrometry (DI-MS, ASAP-MS, or ambient ionization methods — from…
Use when a Python package has been relocated to a new repository location, reorganized to conform to new organizational standards (e.g., metabolomics-cloud conventions), or its…
Use when when you have mass spectrometry raw data (DI-MS or ASAP-MS format) from plant samples that are easily confused due to morphological similarity, or when you need to verify…
Use when after identifying statistically significant LC-MS features (e.g., via MB-VIP with p < 0.01 and permutation testing), when you need to consolidate multiple ionization and…
Use when you have CE-MS test files archived in the msdata Bioconductor package and need to load them into an in-memory or on-disk R representation to extract ion…
Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs,…
Use when you have two independent LC-MS untargeted metabolomic feature datasets (each with retention time and m/z values) and need to identify which features in one dataset…
Use when when you have detected multiple features from non-targeted mass spectrometry and need to group them by putative compound origin.
Use when after implementing or modifying utility functions in a library subpackage (e.g., cooltools.
Use when when you have known metabolite concentrations and their spin-system coupling constants (J-values) and need to generate synthetic ¹H NMR spectra for method validation,…
Use when you have large spectral libraries (thousands to millions of spectra) and need to search query spectra against them for peptide identification with tolerance for…
Use when you have filtered ATAC-seq peak counts, matched motifs to those peaks, and want to measure which transcription factor motifs show elevated or reduced accessibility…
Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in . — from HolobiomicsLab/asb-skill-collections
Use when you have a Thermo Fisher Scientific .raw file from an Orbitrap instrument and need to programmatically retrieve MS1 spectral attributes (base-peak m/z, intensity,…
Use when after spreadOut() has converted raw CSV peak data into a structured list, when you have one or more Compound.Name entries from GC-MS that may be ambiguous, non-canonical,…
Use when you have GNPS molecular networking output (from GNPS1 at https://gnps.ucsd.edu
Use when when you have generated a set of predicted metabolite structures from BioTransformer's metabolism prediction engine and need to assign identity to observed compounds from…
Use when you need to persist and communicate the health status of multiple external web services queried during an annotation run.
Use when you have Thermo Fisher Scientific .raw files from an LC-MS experiment and need to extract spectral features (base-peak m/z, intensity, scan-level properties) indexed by…
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 after RAMClustR clustering and molecular weight inference via do.findmain, when you need to export deconvoluted cluster spectra for import into external annotation tools…