Use when you have CE-MS raw data (mzML or netCDF format) containing a known target analyte with a precise m/z value, and you need to isolate its signal within a defined effective…
Use when when deploying a metabolomics processing tool (such as asari) and needing to predict resource requirements or validate claimed scalability on laptop-class hardware (≤16…
Use when you have metabolomic data (e.g., from LC-MS or GC-MS comparing patient to controls) showing differential abundant metabolites (DAMs), candidate genes from exome…
Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable,…
Use when you have experimental retention times (RTs) for a small set of calibration molecules (≥10) measured on both a source chromatographic method and a target method, and you…
Use when reading mass spectral library files (particularly MoNA EI or MS2 libraries) where structural metadata like SMILES information is embedded in general-purpose fields (e.g.,…
Use when after bias-corrected ATAC-seq signal tracks (bigWig files) have been generated and you need to quantify transcription factor binding strength within open chromatin…
Use when you have quantification output from two versions or implementations of the same tool (e.g., C++ vs.
Use when after merging methylation call files across all samples into a unified methylBase object (via unite()), when you need to assess whether biological replicates cluster…
Use when when you need to support multiple plotting library backends (static or interactive) for the same data visualization domain (e.
Use when when implementing or reverse-engineering a custom binary file format (e.
Use when when processing untargeted LC-MS metabolomics data with XCMS and need to identify low-quality peak integrations that may introduce noise or bias into subsequent compound…
Use when you have raw or preprocessed mass spectrometry feature matrices (e.g., from low mass resolution or sparse acquisition) and want to enhance signal quality and spatial…
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 you have a precomputed expected contact frequency table (TSV with columns: dist_bp, contact_frequency, n_valid) derived from cooler Hi-C matrices and need to generate a…
Use when you have tandem MS/MS spectrum data in standard peak file formats (mzML, mzXML, or MGF) and need to cluster spectra based on precursor mass and fragment ion similarity.
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 when you have baseline MS/MS peak annotations from a known compound but need to refine them using newly available structural information (e.
Use when when a research software project is decomposed into distinct subproject components (e.
Use when setting up a LipidMatch analysis run and you need to select among three mutually-exclusive analysis modes (PFAS, Lipid, or Tween-positive detection).
Use when after running annotateRC on LC–MS AIF data when you need to inspect whether a feature has multiple plausible annotations (e.g., isobaric lipids, isomers with the same…
Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g.,…
Use when when you have a real mzML file from an untargeted metabolomics LC-MS/MS experiment and need to extract the chemical features it contains—either to simulate a…
Use when when you have an unknown compound's mass spectrum (m/z peaks and intensities in .mgf or equivalent format with mandatory PRECURSOR_MZ and IONMODE tags) and need — from…
Use when you have a collection of preprocessed mass spectra (in mzML, mzXML, msp, MGF, or JSON format) and need to quantify similarity relationships across all pairs—for instance,…
Use when when you have coordinate-sorted BAM files from single-cell ATAC-seq experiments (e.g., 10X Genomics scATAC-seq) and need to generate a compressed fragment file for…
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 your workflow fetches data from multiple external web services (e.g., CIR, CTS, PubChem, IDSM, BridgeDb) asynchronously and you need to track which services are…
Use when after generating large feasible flux distributions (e.g., 1 million sampled solutions per cell line) from constrained metabolic models, apply t-SNE when you need to…
Use when when you have pre-computed Word2vec spectrum embeddings and need to perform fast approximate nearest-neighbor retrieval from a library of millions of spectra (e.g., NIST…
Use when after a ViMMS Environment.run() simulation completes with save_eval flag enabled, you have collected EvaluationData containing chemical compounds, their generated scans,…
Use when you have a GNPS molecular network (in GML or GraphML format) and a completed MS2LDA experiment on ms2lda.org, and you want to annotate network nodes with detected…
Use when you have detected and clustered unknown MS features from untargeted xenobiotic metabolomics data, computed fragmentation pattern similarity scores between features and…
Use when after identifying putative BGC-encoded precursor peptides from a genome assembly via MetaMiner's BGC identifier, when preparing a RiPP structure database for downstream…
Use when when you have loaded a cooler file containing Hi-C contact matrices and need to quantify how contact probability decays with genomic distance within a single chromosome.
Use when when you have acquired ion mobility–mass spectrometry data (drift time and m/z dimensions) and need to convert observed drift times into calibrated CCS values.
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 after peak alignment with peakAlign(), when you have an MSImagingExperiment
Use when when implementing new scoring components (inchikey score, neighbourhood
Use when you have a precomputed expected contact frequency table (TSV format with columns: dist_bp, contact_frequency, n_valid) derived from cooler files and need to compress…
Use when you have a filtered set of non-overlapping peaks from ATAC-seq data and a collection of motifs (typically from JASPAR or similar databases), and you need to identify…
Use when when benchmarking or validating a pathway analysis method (such as PALS, ORA, or GSEA) on metabolomics data, you need quantitative evidence that the method's pathway…
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 domain-specific language (DSL) grammar specification and raw query strings that must be converted into structured intermediate representations for validation,…
Use when you have a pre-trained MS/MS spectral embedding model evaluated on one or more source datasets (GNPS, MoNA, MTBLS1572) and need to verify that it performs well on…
Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct…
Use when you have a compressed mzML file (mzML.gz or indexed gzip format) and need to extract a single spectrum or a small subset of spectra by their known numeric identifiers,…
Use when at the start of an untargeted LC-MS annotation pipeline when you have a KEGG database with exact masses and need to prepare a mass-matching reference.
Use when after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table…
Use when raw MS quantification data (feature-by-sample intensity matrix) shows systematic variation in detector response across the run sequence—i.e., when the same analyte…
Use when when you have a pre-computed hierarchical dendrogram from structural clustering (e.g., of LC-MS features based on m/z and retention time) and want to compare or validate…
Use when you have pseudo-MS/MS spectra from LC-MS all-ion fragmentation (AIF) data that have been matched against one or more ion fragment databases (e.g., LipidPos, MassBank),…
Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert…
Use when you have preprocessed single-cell ATAC-seq fragment files or count matrices and need to identify open chromatin regions (peaks) to support downstream differential…
Use when when you have metabolite structures (as SMILES strings) and need to predict their observable m/z ions under non-standard ionization conditions imposed by a derivatizing…
Use when before running HiC-Pro or similar multi-stage pipelines on a new system or environment, especially when dependency installation is not automated (e.g., not in a conda…
Use when you have a multi-cluster single-cell RNA-seq dataset with cell-type annotations and you want to test whether known biological pathways (e.g., KEGG or MSigDB gene sets)…
Use when when you have a GitHub-hosted Python project (or other supported language) with an existing test suite and want to gate code contributions on multiple quality dimensions…
Use when you suspect XCMS grouping contains misaligned features due to suboptimal parameter settings or insufficient samples.
Use when you have per-sample metabolite abundance data and a metabolite-to-pathway