Use when after peak picking has generated a peaklist of experimental fragment m/z values (from Q-Exactive orbitrap, Agilent/Bruker/SCIEX Q-TOF UHPLC-HRMS/MS, or direct…
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 when implementing or reverse-engineering a custom binary file format (e.
Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
Use when when you have downloaded or cloned a lipidomics library repository (such as LipidMatch) and need to audit the breadth of lipid-type coverage to ensure the library meets…
Use when when you have raw mzML files and a corresponding feature table (CSV format, e.g., from mzmine) and need to generate peak matrices with fixed dimensions (e.g., 2 × 120)…
Use when you have raw or archived MSP spectral library files and need to load them into R for library searching, spectral matching, or batch reprocessing.
Use when you have an indexed gzip–compressed mzML file (mzML.gz with internal index structure) and need to retrieve and work with individual spectra or chromatograms by integer…
Use when you have Sciex Multiquant txt exports containing signal intensities from QCpool samples injected at regular intervals (e.g., every 10–20 samples) during one or more…
Use when you have a high-resolution LC-MS/MS spectrum or pre-computed molecular fingerprint from a small-molecule sample and need to retrieve a systematic structural…
Use when after completing sample alignment in JPA (Part 5) or when ingesting a peaklist or aligned feature matrix from prior peak-picking runs, parse feature metadata to enable…
Use when you have executed an end-to-end SnapATAC2 pipeline on the pbmc10k_multiome dataset (or a similar single-cell ATAC-seq dataset with a published reference) and need to…
Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE barocycler-based concurrent multiomics method and need to perform integrative prepr — from…
Use when you have a GNPS-generated molecular network (classical or feature-based
Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually…
Use when you have multiple mass spectral libraries in different formats (NIST MSP + MOL folder, MoNA MSP, RIKEN MSP, SWGDRUG MSP) and need to merge them into a single,…
Use when when designing a dataset storage layer that must handle variable dataset sizes, block layouts, and platform-specific constraints (e.g., Windows vs. non-Windows).
Use when you have intracellular metabolomics abundance data (absolute or relative concentrations) for multiple cell lines or conditions, a constraint-based stoichiometric…
Use when you have raw LC-MS data in mzML or mzXML format and need to extract reproducible, high-quality metabolite features (m/z, retention time, intensity) for global…
Use when comparing mapping outputs from two different salmon versions or implementations (e.g., C++ 1.12.0 vs.
Use when when you have executed the MultiModalSpectralTransformer architecture on a set of multi-modal spectroscopic inputs (NMR, HSQC, COSY, IR) and obtained predicted molecular…
Use when when you have a binned MS/MS spectrum vector (e.g., 9948-dimensional input from 10,000 equally-spaced m/z bins in the 10–1000 Da range) and need to compress it into a…
Use when when you need to validate that a Python package (or update to it) is accessible to end users through official distribution channels, or when you are preparing a release…
Use when you have raw or curated mass spectrometry data (MS1, MS2, or MSMS) in mzML, mzXML, CDF, MGF, MSP formats, or from a MassBank/MetaboLights repository, and need to convert…
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 after feature detection has produced a TSV feature table (from Asari or equivalent) containing m/z, retention time, and intensity columns, and before MS1 or MS2…
Use when when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform untargeted feature detection with chromatographic alignment across multiple…
Use when when comparing raw link scores (strain correlation or IOKR) across different GCF-MF or BGC-spectrum pairs and you need to distinguish true positive links from background…
Use when you have a USI accession (e.g., 'mzspec:MSV000082283:f07074:scan:5475' or 'mzspec:PXD000561:Adult_Frontalcortex_bRP_Elite_85_f09:scan:17555') pointing to a publicly…
Use when when building reproducible Python-based computational workflows that must serve both beginner and expert users; when the analysis requires interactive parameter tuning,…
Use when you have a new or draft file format specification (e.g., mzPeak) with multiple independent language implementations, and you need to verify that all readers agree on the…
Use when after performing peak detection on centroided .mzML LC-MS data with screening_mode=FALSE in TARDIS.
Use when you have retrieved chemical formulae and metadata from two or more of HMDB, ChEMBL, or PubChem and need to merge them into a single searchable database without formula…
Use when you have an untargeted metabolomics feature table with m/z values, retention times, intensity measurements, and p-values from statistical testing, but lack or wi — from…
Use when you have a peak-abundance matrix from FT-ICR MS (peaks as rows, samples as columns with raw peak intensities) and need to compute abundance-based diversity indices or…
Use when after matching mass-to-charge ratios to a compound database (e.g., KEGG) and assigning adduct/fragment types, when you have an annotated feature table with retention…
Use when when you have loaded a raw or processed Cardinal MSImagingExperiment object from MS imaging data and need to (1) extract spectral intensities and m/z feature information…
Use when you have training LC-HRMS chromatograms (rt × m/z matrix format) from which you have already extracted peak candidates using smoothing and gradient-descent peak…
Use when when you have computed Spec2Vec similarity scores (typically cosine similarity in [0, 1] range) between discovered Mass2Motifs and a spectral library, and need to decide…
Use when when executing a multi-converter annotation workflow on mass spectra metadata (.
Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per…
Use when you have normalized or voom-transformed gene expression counts/intensities indexed by gene and sample, along with an experimental design matrix specifying condition,…
Use when when you have an unknown mass spectrum (query spectrum) and need to search it against a reference database of billions of spectra to find matching or structurally related…
Use when after matrix annotation has been performed on mass spectrometry imaging (MSI) data when you need to identify and document ions whose m/z values overlap with or are…
Use when when a Python package is being relocated to a new GitHub organization (e.
Use when you have retrieved a complete set of project JSON documents from a data platform and need to verify that each document's structure, field types, and required properties…
Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate…
Use when after peak detection in nontargeted LC-MS workflows when you have a feature table with detected peaks and need to assign quality scores or filter low-confidence features.
Use when you have a combined EI library (from multiple sources such as NIST, RIKEN, MoNA) and access to NIST RI database files (ri.dat and USER.
Use when when you have run ORA on a metabolomics dataset and obtained p-values for pathway enrichment, but you need to assess whether observed significance is genuine or an…
Use when you have a feature intensity matrix (peak vector) and a corresponding set of QC sample indices from a multi-batch LC/GC-MS experiment, and you need to establish…
Use when after loading an MS-DIAL feature table when you need to separate features into two disjoint groups: one meeting a quantitative threshold (e.g., m/z decimal values outside…
Use when when training a dual-encoder architecture (bi-encoder + cross-encoder) on NMR spectral data where independent encoding and joint pair processing produce competing or…
Use when you have raw GC–MS or LC–MS data in two-dimensional m/z vs retention time format and need to identify marker features at parts-per-billion sensitivity without relying on…
Use when when you have mass spectrometry spectra in one of the six supported formats (mzML, mzXML, msp, metabolomics-USI, MGF, JSON) and need to convert them to a different format…
Use when you have an experimental MS/MS spectrum (e.g., from MassBank or acquired data) for a single metabolite with known accurate precursor m/z and adduct type, and you need to…
Use when after you have (1) corrected ATAC-seq BAM files for Tn5 insertion bias using ATACorrect, (2) computed per-base footprint scores using ScoreBigwig, (3) obtained a motif…
Use when processing raw GC-MS data in NetCDF format where peaks have been detected but lack standardized retention indices.
Use when you have an unknown mass spectrometry spectrum (acquired experimentally
Use when you have performed spectral dimension reduction on single-cell omics count matrices and wish to partition cells into discrete populations.