Use when xCMS grouping has been performed on LC-MS data from studies with hundreds of samples or data acquisition periods longer than a week, where retention time drift structures…
Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method…
Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared…
Use when when you have a metabolomics abundance table with missing values and need to decide which imputation method to apply, or when designing a simulation to evaluate…
Use when after implementing or modifying an mzML parser module that converts mzML files into MS-DIAL's internal data model, and before integrating the parser into the production…
Use when when you have raw MS2 spectra (m/z and intensity pairs) and a curated reference peak list from a large training dataset (e.
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 after accurate mass searching has assigned multiple detected m/z features to the same metabolite via positive and negative adduct libraries, and before sample-level…
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 you have preprocessed (smoothed and baseline-corrected) 2D-GCxGC-MS chromatograms from multiple samples and need to align their peak positions to a common reference…
Use when after auditing and optionally rescaling a mass track (composite mass chromatogram) when you need to subtract background signal and set dynamic prominence thresholds for…
Use when before invoking any Python module in a multi-step Hi-C processing pipeline, or when a dependency has been freshly installed or reinstalled.
Use when you have RNA-seq read count data and a metabolic model with GPR rules, and you need to assess how differential gene expression translates into differential metabolic…
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 you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer…
Use when when you have a mzPeak file (uncompressed ZIP archive containing Parquet tables) and need to access decoded spectral data arrays (m/z, intensity), spectrum metadata (scan…
Use when you have a baseline GNN model for predicting a continuous molecular property (e.
Use when you have LC-IM-MS/MS experimental data (raw mzML or vendor format) containing signals from N-Me derived unsaturated sterol lipids and need to assign double-bond positions…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute stable variance estimates and differential expression sta — from…
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 exported lipid identifications from MS-DIAL (version 4 or 5) and need to run LipoCLEAN quality filtering on that output.
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 when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages,…
Use when when you have a raw or minimally processed scRNA-seq dataset (e.g., a Seurat object loaded from GEO) and need to prepare it for pathway enrichment or coregulation…
Use when you have paired measurements (e.g., gene expression counts, protein abundance, or sampled flux distributions) from two cell lines or conditions and need to assign a…
Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
Use when you have an m/z-resolved feature list from LC- or GC-HRMS analysis (either detected by pyOpenMS or provided as a custom Excel table) and need to prioritize potential PFAS…
Use when you have a metabolomic SummarizedExperiment object with replicate QC (quality control) samples and need to remove non-reproducible metabolic features before phenotype…
Use when you are implementing a custom MsBackend subclass for the Spectra package and need to ensure that spectraData() returns all core spectra variables (e.g., centroided,…
Use when when a Shiny application is documented or observed to run only on Windows, blocking deployment to Linux or macOS users.
Use when you have (1) spatial omics data loaded in AnnData format with a pre-built spatial neighbor graph (from squidpy.gr.spatial_neighbors() or similar), (2) a categorical…
Use when after generating or filtering transformation products using generateTPs() or filter(), when you need to annotate MS/MS spectra using MetFrag and require a database of…
Use when you have a set of metabolites or chemical formulas to analyze and want to evaluate how different MS/MS fragmentation strategies (e.g., TopN, exclusion lists, dynamic…
Use when after anchor feature pairs (m/z and retention time values) have been selected from two disparately-acquired LC-MS datasets, and you need to correct for systematic…
Use when after completing a multi-stage Docker build targeting a compiled runtime environment (e.g., airdpro:cli produced from a Wine + .NET Framework 4.8 + Ubuntu 22.
Use when you have acquired raw mass spectrometry data in vendor-proprietary formats (ThermoFisher, Agilent, or equivalent) and need to analyze it using MSThunder for unknown…
Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it…
Use when after loading and formatting raw peak-picked LC-MS metabolomics data frames (via metabData constructor) when you need to eliminate features with poor sample coverage…
Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality.
Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational…
Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture…
Use when when you have a webservice codebase (Python, Java, etc.) with HTTP route definitions, parameter handling, and serialization logic, and you need to generate an OpenAPI 3.
Use when you have raw electron ionization mass spectra (m/z and intensity pairs) that you intend to match against a library using the Identity (EI Normal) or Similarity (EI…
Use when after preprocessing and normalizing count matrices from transcriptomics
Use when after chromatographic peak detection on preprocessed LC-MS data, when you have hundreds or thousands of individual m/z × retention-time peaks and need to associa — from…
Use when you have paired-end RNA-seq reads (FASTQ) and a reference transcriptome (FASTA), and you need to estimate transcript-level expression (NumReads and TPM).
Use when you have a feature table from nontargeted LC-MS peak detection (containing m/z, retention time, and intensity values) and need to disambiguate whether detected features…
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 when you have a ranked list of GCF-MF (genomic cluster family–molecular feature) link predictions from one or more scoring functions, a curated set of known validated…
Use when after frequency-based denoising has been applied to individual replicate spectra within each feature (via generate_denoised_spectra), you have a collection of denoised…
Use when evaluating alternative implementations of data storage or retrieval strategies in R objects—specifically when deciding whether to eagerly populate all columns in a data…
Use when when building or extending a mass spectrometry data parser that must support multiple mzML storage formats (plain .mzML, indexed .mzML.gz, standard-compressed .mzML.
Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional…
Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular…
Use when you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct…
Use when when you have m/z values from spatially-resolved mass spectrometry imaging (MSI) and need to predict their molecular formulae with high precision.
Use when when beginning an untargeted LC-MS annotation workflow, before attempting to match experimental m/z peaks to metabolite identities.
Use when you have tandem MS data with technical replicates and need to remove features showing high variability between replicates.
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 when you have mass spectral libraries from multiple sources (NIST, MoNA, RIKEN, GNPS) in disparate formats (MSP, MGF, MOL folder structures) or with misaligned metadata…