Use when after duplicate filtering and fragment length prediction (d) in ChIP-Seq analysis, when you need to convert discrete read alignments into continuous coverage signal for…
Use when you have clustered single-cell RNA-seq data (via Leiden, Louvain, or equivalent) and a k-nearest neighbor graph computed in PCA space, and you want to abstract cell-level…
Use when building or extending a data extraction and conversion system (such as MESSES) where tabular data is transformed via conversion directives into JSON intermediate formats…
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 after running retention-order prediction experiments on a test or held-out evaluation dataset.
Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation…
Use when you have a collection of deconvolved mass spectra (in MGF or mzTab format) from GC-MS analysis and need to group them into a molecular network to identify structural…
Use when when preparing augmented training data for a Siamese rescore model that must learn to rank correct molecular formulas above incorrect ones;
Use when you have a combined EI mass spectral library (MSP format) lacking experimental RI values, access to NIST ri.dat and USER.
Use when when you have quantitative lipidomics data (either from Skyline CSV export or numerical matrix format) with sample annotations and a biological grouping variable (e.
Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate…
Use when constructing HPLC column feature vectors from raw metadata that includes additive composition flags (e.g., presence/absence or concentration of formic acid, acetic acid,…
Use when you have completed a ViMMS simulation run or processed real LC-MS/MS data and need to quantitatively assess whether one DDA controller (e.g., WeightedDEWController with…
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 you have a feature table from untargeted metabolomics (with m/z, retention time, and p-values from differential abundance testing) but lack or wish to bypass metabolite…
Use when immediately after importing raw LC-MS peak tables (e.g., Progenesis format) and before applying group or replicability filters.
Use when when beginning an untargeted LC-MS analysis and either (1) the dataset characteristics (sample complexity, instrument platform, or polarity) differ from previously…
Use when after LDA topic inference has assigned dominant topic labels to mass spectra, and before those labels are passed to MLP or GNN multi-task training.
Use when you have generated a .hic contact map from Hi-C raw sequencing data and need to identify topologically associating domains (TADs) or other chromatin structural boundaries.
Use when you have ion-mobility mass spectrometry metabolomics data with putative metabolite identifications (e.g., from database matching) and want to reduce false positives by…
Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend.
Use when your input is a single-cell gene expression matrix too large to fit in RAM, or you are working in a resource-constrained environment (e.g., shared compute cluster, laptop…
Use when when you have access to the source code of a chemo-informatics tool (e.
Use when when running a ViMMS Environment simulation with save_eval flag enabled and you need to correlate fragmentation events in the output mzML file back to their originating…
Use when when you have loaded centroided .mzML files into a Spectra object and plan to use TARDIS (tardisPeaks) with an MsExperiment object rather than file paths, and you need…
Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures…
Use when you have normalized or voom-transformed gene expression counts/intensities indexed by gene and sample, along with an experimental design matrix specifying condition,…
Use when after generating ranked predictions of chemical formulas or subformulas for MS/MS spectra (from a neural network model like MIST-CF's formula transformer), compare…
Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity…
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 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 after generating a tile matrix or feature count matrix from single-cell ATAC-seq, RNA-seq, Hi-C, or methylation data, before clustering or UMAP visualization, when you…
Use when when initializing an mWISE annotation pipeline with a new or custom KEGG database, or when you need to reconstruct the Cpd.Add matching table with modified…
Use when you have detected features in LC- or GC-HRMS data (via pyOpenMS or custom feature tables) and need to systematically rank them for likelihood of being PFAS compounds.
Use when you have an unknown MS/MS spectrum (query spectrum with m/z and intensity pairs) and a reference spectral library (local or public: GNPS, MASSBANK, DrugBANK), and you…
Use when you have replicate MS/MS spectra with labeled fragment recurrence frequencies and need to select an optimal frequency threshold (beyond the default 0.1) that maximizes…
Use when after drift correction in non-targeted LC-MS metabolomics workflows, when you need to decide which molecular features are sufficiently reproducible (low instrument/QC…
Use when after XCMS feature detection, retention time correction, regrouping, and missing value imputation have produced an aligned feature table with multiple signals per…
Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C-labeled yeast extract, measured CCS values for both labeled and unlabeled lipids, and need to quantify…
Use when you have high-resolution MS2 data (.ms2 format) from tandem mass spectrometry analysis of lipid A-containing samples and need to perform automated structure annotation…
Use when you have extracted metadata or spectral information from a Thermo Fisher Scientific .
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 pre-computed dense embeddings for query spectra (unknown compounds) and reference spectra (spectral library), and you need to rank library entries by…
Use when when you have completed DESeq2 differential expression analysis on RNA-seq count data and obtained p-values for each gene, use IHW if you want to improve power to detect…
Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to…
Use when when you need to aggregate values from multiple records in a JSON input document into a single concatenated string field (e.
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 when a trained Siamese neural network model makes predictions on new spectrum pairs and you need to identify and exclude high-uncertainty predictions to improve RMSE.
Use when when you have a curated list of chemical compounds (real or virtual), a defined fragmentation strategy (e.g., Top-N, exclusion lists), and need to simulate how that…
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 when you have CE-MS data with migration times that vary between runs due to electroosmotic flow drift, but you possess a reliable internal standard with a known effective…
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 you have LC-MS data processed through XCMS grouping that shows signs of RT drift (e.g., data acquired over extended periods or across many samples) and you suspect…
Use when when you need to validate that MSI software (e.g., LipidQMap) achieves documented processing speeds on your target hardware, or when you need to establish a performance…
Use when after loading centroided .mzML LC-MS data and defining a target list (compound ID, name, m/z, RT, polarity) when you need to: (1) automatically locate and integrate peaks…
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 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 when you need to verify that a wrapper package (e.g., rawrr) correctly bridges R and a managed .NET assembly (such as RawFileReader), specifically to confirm that…
Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you wish to group features that represent the same metabolite at different — from…
Use when you have loaded MSI data with an extracted peak list and need to annotate matrix-related signals, particularly when the dataset may contain isobaric ions or peaks with…