Use when when building an extensible converter framework where new converter implementations (e.g., WebConverters or ComputeConverters for external chemical services) should be…
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 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 need to represent natural product molecules as fixed-length bit vectors for downstream machine learning (e.
Use when you have transcript-level abundance estimates from salmon, sailfish, or kallisto quantification and need gene-level count matrices for differential expression analysis.
Use when when you have loaded both a known compound and its modified analog with MS/MS spectra, initially generated baseline modification probability scores, and then obtained or…
Use when after a machine learning model has generated predicted molecular structures (connectivity graphs and molecular formulas) from 1D NMR spectra.
Use when you need to automate testing and quality checks on code changes—specifically when pull requests or commits are made to a repository and you want to verify that builds…
Use when you have an annotated LC-MS feature table with KEGG candidate matches and adduct assignments (output from the matching stage), and you need to disambiguate which features…
Use when when you have mass spectrometry data with ion mobility (drift time or 1/K₀) measurements as a continuous dimension and want to visualize intensity distributions across…
Use when when integrating an R package that wraps a compiled .NET assembly (such as rawrr), you need to verify that the internal dispatch mechanism between the R layer and the C#…
Use when you have downloaded raw HMDB data (hmdb_metabolites.zip or pickle file) and need to generate a representative set of chemical objects for simulating LC-MS/MS acquisition…
Use when designing a contrastive learning pipeline for ion images or other data modalities where you need to process multiple augmented versions of the same input through an…
Use when you have acquired EI or MS/MS spectral libraries from multiple public sources (NIST, RIKEN, MoNA, SWGDRUG, GNPS) with inconsistent metadata field layouts, missing or…
Use when after peak detection on mass track segments using find_peaks, when you need to distinguish genuine chromatographic peaks from noise-induced false positives or irregular…
Use when you have a versioned workflow definition file (YAML or JSON) from a specific release commit and need to verify it conforms to the project's schema specification, validate…
Use when you have mzML-format mass spectrometry data files and need to load them into memory as structured data (pandas DataFrame) to prepare for visualization with pyOpenMS-Viz…
Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that…
Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z and intensity; columns = samples) and need to assign KEGG compound identifiers to observed peaks.
Use when you have completed LC-MS/MS data processing and feature alignment in MZmine2 or Optimus, generated a feature quantification matrix and MGF file, and now need to format…
Use when before invoking pp.make_fragment_file on a BAM file from alignment or external sources, especially when the BAM's sort order is unknown or when integrating BAM files from…
Use when you have a feature quantification table (m/z, retention time, peak areas) and candidate metabolite annotations (chemical identifiers, MS/MS spectra matches, or…
Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z…
Use when when you have downloaded a multi-file .csv library repository (e.g., LipidMatch) and need to verify that it meets minimum thresholds for species diversity (e.g., 500,000+…
Use when when loading gene expression data (e.g., from GEO via getGEO or microarray ExpressionSet objects) that contains duplicate rows mapped to the same Gene ID, missing gene…
Use when when you have a trained BitterPredict classifier, a dataset of molecules with computed descriptors and known bitter/not-bitter labels, and want to understand which…
Use when when you have a generic constraint-based metabolic model, cell-line-specific
Use when when you have computed hierarchical clustering dendrograms on your feature matrix (microbes or metabolites) using Euclidean distance and complete linkage, and need to…
Use when after generating a feature table via mzrtsim() containing simulated peak abundances across samples with condition and batch effects, and you need to expose the abundance…
Use when your CE-MS dataset exhibits migration time drift between runs due to electroosmotic flow (EOF) variation, and you have identified two internal mobility markers (e.g.,…
Use when you have a peak-picked feature table (HDF5 format with m/z, drift_time, retention_time, intensity columns) and need to identify and label isotopic signatures within…
Use when after extracting tabular data into intermediate JSON representation (via tagging), or after manual JSON editing, and before converting to a target format (e.g., mwTab for…
Use when you have instantiated a learned component (embedding layer, encoder, or transformer submodule) from a published codebase and need to verify that its forward pass produces…
Use when you have a peak intensity matrix from LC/GC-MS analysis with known QC sample indices and suspect batch-related systematic variation in feature intensities.
Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist…
Use when when you have deconvolved GC-MS spectra (post-deconvolution output compatible with GNPS_GC input specification) and need to group them by chemical similarity to construct…
Use when you have selected a subset of ReDU public tandem MS files with GNPS chemical annotations (level 2 or 3 spectral library matches) and wish to explore sample relationships…
Use when after baseline correction (e.g., via asymmetric least squares) when raw GCxGC-MS chromatograms still contain high-frequency noise that obscures true signal structure.
Use when you have a comprehensive target list (containing compounds from both positive and negative ionization modes) but need to screen or detect peaks in a single LC-MS run…
Use when after feature detection and alignment in untargeted MS data processing, when you need to filter or rank candidate metabolite annotations by spectral quality before…
Use when you have completed peak picking in MS-DIAL (generating files like Urine_RP_NEG_norm.txt or Urine_RP_POS_norm.txt) and need to load the resulting feature table into R for…
Use when : (1) you have metabolomic data (NMR or MS-derived) and a continuous phenotype variable; (2) you need to quantify associations while controlling for known confounders…
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 when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate, octanal, undecane) and need to evaluate them against reference compound categor — from…
Use when when preparing to run ORA on a metabolomics study: you have a list of detected metabolites from your experiment and need to determine which metabolites from the full…
Use when you have raw, high-resolution MS/MS spectra in mzML, mzXML, or MGF format that need to be prepared for fast similarity searching or clustering.
Use when after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
Use when you have a set of compounds (e.g., novel NPS analogues in an evaluation dataset) and need to classify them as structurally similar to or divergent from a reference set…
Use when after applying the CV_ratio() filtering function to a normalized metabolomic feature matrix (e.g., Urine_RP_NEG_norm.txt) in margheRita, generate retention statistics to…
Use when you have raw or unstructured MS2 spectral data (from untargeted tandem mass spectrometry experiments) and plan to run MS2MP inference for KEGG pathway prediction.
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 after retention-time and m/z-based peak alignment has been completed across a cohort of LC-MS samples, and you need to create a unified quantitative matrix for…
Use when you have collected or parsed 1H and 13C NMR peak data (chemical shift values and intensities) and need to submit it to the SMART 3 /api/smart3/search endpoint or similar…
Use when you have a SummarizedExperiment object containing peak counts from single-cell or bulk ATAC-seq/DNAse-seq data and need to prepare it for unbiased motif deviation…
Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a…
Use when you have loaded individual methylation call files as methylRawList objects from bisulfite sequencing experiments (via methRead()) and need to perform base-level…
Use when you have mass spectrometry data loaded as a Pandas DataFrame with retention time and intensity columns, and you need to visualize the overall or mass-trace-specific…
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 when preparing augmented variants of ion images (single-channel 2D arrays or multi-channel spectral images) for contrastive learning in mass spectrometry imaging tasks.
Use when when you have preprocessed LC-MS/MS data (MGF file with MS1 and MS2 spectra and a feature abundance table from MZmine2 or similar peak detection tool) and need to perform…