Use when when you need to execute a multi-backend visualization library (e.g., pyOpenMS-Viz with matplotlib, Bokeh, and Plotly) and must measure or validate execution times,…
Use when working with mass spectrometry spectral libraries (GNPS, MoNA, MTBLS1572, MassBank) that have been preprocessed by prior teams but may contain formatting errors or…
Use when you have newly assayed 1H-NMR metabolomics data from Nightingale Health (CSV or TSV format) and need to apply one or more published metabolic risk scores (Deelen et al.
Use when after starting a TensorFlow Serving instance (e.g., via docker-compose)
Use when after mass-to-charge matching has produced a large table of candidate KEGG metabolites with multiple adduct assignments per feature.
Use when when converting MS/MS spectra from .msp format library files (e.g., MassBank) into a custom fragment library for metabolite annotation, and the source spectra are tagged…
Use when you have imaging mass spectrometry (IMS) datasets with peak intensity features organized as spatial graphs (nodes = pixels/voxels, edges = spatial adjacency), and you…
Use when when you have parallel mass spectra and molecular structure data (e.g., CANOPUS or MassSpecGym datasets) and aim to train a single encoder-decoder model (e.g., BART) that…
Use when you have tandem MS spectra from structurally related or known compounds and need to decide which similarity metric will maximize correct ranking of related molecules in a…
Use when you have obtained MobiLipid or a similar IM-MS lipidomics package that bundles a CCS reference library for labeled lipids, and you need to verify library integrity,…
Use when when implementing or extending file format parsers in a spectral data pipeline, you need unit tests to ensure that format-specific parsers correctly instantiate spectrum…
Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
Use when you have raw FASTQ sequencing reads (single-end or paired-end) and a reference transcriptome FASTA file, and you need to determine which transcript(s) each read aligns to…
Use when you have implemented both CPU and GPU versions of a spectral search algorithm (e.g., approximate nearest neighbor indexing with cascade filtering) and need to validate…
Use when you have measured execution times from multiple scripts that exercise different combinations of categorical variables (e.g., plot types: chromatogram, mobilogram,…
Use when after chromatographic peak detection on preprocessed LC-MS data when you have an xcms result object (XcmsExperiment or xcmsSet) with detected peaks and need to collapse…
Use when you have a known compound structure with validated MS/MS spectrum and a structural analog (modified version) with its own MS/MS spectrum, and you need to assess whether a…
Use when you have loaded a collection of molecular fingerprint vectors (such as biosynfoni fingerprints from a deposited dataset) and need to characterize their statistical and…
Use when after loading raw Agilent Unknowns Analysis CSV output and when you need to convert tentative compound identifications (matched only by GC-MS library cosine similarity or…
Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct infusion MS (DI-MS), ASAP-MS, or other high-throughput ambient ionization methods, an — 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 integrating with an external API (such as TensorFlow Serving) where changes to the response schema could break dependent code, or when model metadata must be extracted…
Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex…
Use when after structural cluster assignment and correlation clustering are complete, and you need to represent the full set of structural relationships (isotopologues, adducts,…
Use when after implementing or modifying utility functions in a library subpackage (e.g., cooltools.
Use when you have extracted quantitative genomic features (e.g., insulation scores, boundary annotations) as a pandas DataFrame with bin coordinates and boolean or numeric…
Use when when you need to verify that a research software package (e.g., MassQL) maintains functional correctness over time, assess the reliability of a tool before integration…
Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
Use when when extending a multi-service project (like MAGMa with its four subproject components) to container orchestration, and you need to ensure each microservice (magmaweb,…
Use when when training a fresh CNN model from scratch on labeled LCMS data (e.g., MS1 peak classification in NeatMS), particularly when aiming for a specific performance target…
Use when after calling buildExperiment on metabolomics data to construct a SummarizedExperiment object, before performing batch correction, outlier detection, or other QC…
Use when you receive a JSON response from a REST API endpoint (e.g., TensorFlow Serving /model/metadata) and need to extract and validate specific fields such as model input…
Use when after inferring Mass2Motif definitions from LDA modeling when you need to build a network representation of motif relationships.
Use when you have a SpaMTP Seurat object with a 'Spatial' assay containing metabolomics features (m/z values) and their associated metadata columns (e.
Use when when annotating full-scan MS or MS imaging data against a metabolite database (e.g., LipidMaps, HMDB) and you need to control the stringency of m/z matching.
Use when after generating a q-value bedgraph track from ChIP-Seq pileup versus local lambda comparison, and you need to identify statistically significant narrow peaks with…
Use when when you have a set of small molecule structures (as SMILES or molecular graphs) and need to predict their elution order in RPLC systems with eluent pH around 2.
Use when you have extracted latent low-dimensional peak features from imaging mass spectrometry (IMS) data using a graph-attention autoencoder and need to identify a ranked subset…
Use when after LDA modeling has produced an inferred motifset (JSON format) containing Mass2Motifs with fragment and neutral-loss patterns.
Use when after sample alignment and isotopologue/adduct grouping are complete, when you need to associate MS2 spectral data (DDA-acquired) with the consolidated feature groups to…
Use when when you have statistically significant features from multi-assay LC-MS metabolomics data (with m/z and retention time annotations) and need to group features that may…
Use when you have transcript-level quantification files (quant.gz, h5, or similar) from a known upstream quantifier (salmon, kallisto, sailfish, oarfish) and need to import them…
Use when after implementing a composite loss function that combines multiple loss terms (e.g., InfoNCE contrastive loss and MSE reconstruction loss) in a PyTorch module, and…
Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic…
Use when you have a filtered set of conformers (100s–1000s) from ASE-ANI that each require independent quantum calculations via QUICK, and you have access to HPC resources with…
Use when you have raw CE-MS instrument output in mzML or netCDF format and need to extract specific ion traces (by m/z value), filter by effective mobility windows, or apply…
Use when when you have run differential methylation analysis in methylKit and need to validate whether overdispersion correction (overdispersion='MN') produces appropriately…
Use when after preprocessing and filtering mass spectra (peak filtering, metadata cleaning) when you need to compare all spectrum pairs within a dataset or between a query set and…
Use when you have centroid-mode LC-MS AIF chromatograms processed through xcms and RAMClustR, a feature table with target m/z and retention time values, and access to fragment…
Use when evaluating whether a mass spectrometry data analysis platform (such as mzmine) provides complete module coverage across all advertised separation and ionisation…
Use when you have paired MS/MS spectra (known compound and its structural analog) with assigned precursor m/z, charge, and SMILES; you want to quantify which parts of the…
Use when when you have Sciex Multiquant TXT export files containing injection sequences from metabolomics or lipidomics studies where pooled QC samples were deliberately injected…
Use when you have paired cdf files (raw mass spectrometry imaging data) and Matlab workspace (.mat) files for the same root sample, and you need to reproduce published linear-axis…
Use when when you have implemented or modified a data ingestion module (e.g., mzML parser) and need to verify that file deserialization produces correct internal representations.
Use when your MSI data is stored in a Cardinal imaging experiment object (version 2.2+) that has already been peak-binned with peakBin(), and you want to run mass2adduct's…
Use when after frequency-based denoising and sample-level aggregation of replicate MS/MS spectra, when you need to export denoised spectra to a standardized, vendor-independent…
Use when you have aligned ATAC-seq BAM files and need to detect transcription factor binding sites via footprint analysis.
Use when you have raw ATAC-seq BAM files and need to perform footprinting analysis to detect transcription factor binding through Tn5 insertion patterns.
Use when when you have a partially documented or undocumented MS analysis pipeline and need to verify its correctness, trace data provenance through multiple processing stages,…
Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon…