Use when after defining a transformer encoder architecture with multi-head self-attention and positional encoding, and before training or inference on mass spectrometry data.
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 after constructing a SummarizedExperiment object from raw metabolomics data via buildExperiment, or after batch correction and ratio computation steps, inspect rowData,…
Use when you have a repository of structured records (e.g., mass spectrometry data, metadata, or domain-specific formats) and need to enforce validation rules systematically…
Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
Use when you have LC-MS/MS DDA metabolomics data (positive and/or negative ionization modes) and sample metadata (originating taxon) for one or more samples, and you need to…
Use when you have computed multiple independent scoring functions (e.g., standardised strain correlation and IOKR) for a large set of potential genomic–metabolomic links and wish…
Use when after peak filtering (by m/z, isotopic presence, formula assignment error, and sample prevalence) and before multivariate analysis (PCA, NMDS, PERMANOVA) when comparing…
Use when when you have vendor mass spectrometry raw files (e.g., .raw format) that must be converted to an open format (Aird) using a Windows .
Use when after completing feature m/z grouping and pairwise alignment detection on two LC-MS datasets acquired under non-identical conditions.
Use when you have generated PSI matrices for alternative splicing events or transcripts across two or more biological conditions using SUPPA's psiPerEvent or psiPerIsoform…
Use when you have raw peak area or intensity measurements for both compounds and their corresponding internal standards across all study samples (including QC and calibration…
Use when you have deployed a TensorFlow model via TensorFlow Serving in a containerized environment (e.
Use when working with imaging mass spectrometry (IMS) datasets where you need to (1) automatically identify marker ions without manual annotation, (2) reduce peak intensity…
Use when when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you…
Use when when designing or integrating a file parser for mass spectrometry formats (.raw Thermo RAW format, .mzml XML-based format) in a metabolomics processing pipeline, or when…
Use when when beginning ChIP-Seq analysis with single-end BED/SAM input and no prior knowledge of the library's fragment length.
Use when after structural clustering (isotopologue grouping, adduct detection, cross-assay linking) and correlation clustering of LC-MS features, when you need to inspect and…
Use when you have raw GC-MS data in netCDF or vendor-specific binary format and need to separate co-eluting compounds and extract clean mass spectra for each individual chemical…
Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
Use when you have executed batch spectral searches against two or more domain-specific MASST tools and received heterogeneous output formats (domain-specific HTML trees, JSON…
Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness,…
Use when you have raw LC-MS/MS data files (mzML/mzXML format from Thermo, Waters, or Bruker instruments) and a list of target compounds defined by precursor m/z values (and…
Use when training a DNN on retention time prediction or similar continuous regression tasks where: (1) the feature space is very high-dimensional (thousands of molecular…
Use when after collecting observed separation efficiency scores at sampled gradient conditions and you need to propose the next gradient to evaluate.
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 designing a metabolite annotation workflow that must simultaneously leverage established biochemical knowledge (pathway databases, reaction networks) and experimental…
Use when you have loaded an MS2 library (from NIST, GNPS, or other sources via read_lib()) that contains both positive and negative ionization modes mixed in a single file, and…
Use when when you have a training set of MS2 spectra with known chemical structures (e.
Use when when processing collections of in-silico mass spectra from OMSLs (Open Mass Spectra Libraries) where the adduct field is absent, null, or not explicitly specified in the…
Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.
Use when when you have executed database search pipelines (Dereplicator, VarQuest, or Dereplicator+) on centroided LC-MS/MS spectra in MGF format and obtained match results with…
Use when after feature extraction and peak recognition have produced detected MS/MS spectra (precursor m/z, charge, retention time, and fragment ion peaks), and you need to export…
Use when when you need to confirm that a generated or retrieved release artifact from a version control system (e.g., git tag v1.0.0) produces byte-for-byte or functionally…
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 when you have deposited a collection of JSON project documents in a platform and need to verify that all conform to the published schema before public release or — from…
Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by…
Use when you have completed DESeq differential expression analysis on a DESeqDataSet and obtained raw results with p-values across all genes.
Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm…
Use when you have extracted a peak list from MSI data and need to annotate matrix-related signals, but overlapping peaks or isobaric ions (ions with identical or near-identical…
Use when you have mzPeak files stored as Parquet tables within a ZIP archive and need to load spectrum metadata, chromatogram metadata, signal data (profile or centroid), or peaks…
Use when when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzML, mzXML, or mzData format) paired with either genome sequences or precursor peptide predictions, and you…
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 when you have raw molecular structures in SMILES or SDF format that must be prepared as input to a descriptor-based classifier (e.g., BitterPredict).
Use when you have retention time predictions from a source chromatographic method and need to predict retention times for a target chromatographic method, but have limited…
Use when you have trained a new machine learning model for chemical formula or adduct assignment from MS/MS spectra and need to assess whether it offers genuine performance gains…
Use when when you have constructed a two-layer metabolite annotation network (knowledge-driven and data-driven) and need to propagate initial seed annotations (e.
Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating…
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 multiple MSP or spectral library files (e.g., one per batch of analytical standards, or organized in a directory structure) that need to be read and merged into…
Use when when you have a mass spectrometry data file (such as mzPeak) that has been read by two or more independent implementations (e.g., Rust, Python/pyarrow, R/arrow) and need…
Use when you have raw MS/MS spectral data in one or more standard mass spectrometry file formats (.mgf, .msp, or .mzML) and need to convert them into a standardized…
Use when you have LC-HRMS raw data files (.mzML or .abf format) from metabolomics experiments and need to extract, align, and annotate features in a reproducible manner across…
Use when you have trained two or more graph neural network models on the same CCS dataset split (using identical hyperparameters, loss functions, and optimization settings) and…
Use when you have IM-MS lipidomics data acquired on samples spiked with fully labeled U13C lipid standards (e.g., U13C yeast extract), and you need to assess whether systematic…
Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or…
Use when after feature extraction (Asari) has produced a full feature table from mzML data, but before normalization and annotation.
Use when when you have raw mass spectrometry data (from mzML, Bruker .d, or CSV format) loaded into a Pandas DataFrame and need to ensure it has the correct column structure (m/z,…
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 after NPFimg's automated detection algorithm has identified marker features from a two-dimensional MS map (m/z vs retention time), especially when you need to validate…