Use when you have CE-MS raw data in OnDiskMSnExp format with both positive and negative polarity acquisitions, migration times that vary due to electroosmotic flow drift, and…
Use when when you need to prototype, test, or benchmark MS1-only acquisition strategies on a defined set of metabolites (e.
Use when when implementing or refactoring a FileInterface._open method or similar polymorphic dispatcher that conditionally instantiates different handler classes based on file…
Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) and need to convert them into normalized, queryable spectral objects for downstream anal — from…
Use when after peak alignment with peakAlign(), when you have an MSImagingExperiment
Use when you are starting a new mass spectrometry analysis task or feature request where the problem scope is unclear, the tool chain (e.g., OpenMS + Python + KNIME integration)…
Use when when you have raw or processed direct-infusion MS (DI-MS) or ASAP-MS spectra as mz/intensity pairs and need to rapidly identify salient peaks for species authentication,…
Use when after molecular formula assignment has been performed on FT-ICR MS peaks and you need to remove assignments with unacceptable mass error before proceeding to…
Use when you have acquired raw MS/MS spectra (in MGF or mzML format) from a mass spectrometry instrument or public repository (e.g., MassIVE, MetaboLights, GNPS) that will be used…
Use when you have completed peak calling and cell annotation in ArchR and want to perform trajectory inference or visualization in STREAM.
Use when you have extracted fragmentation patterns from a collection of MS/MS spectra (using mineMS2) and have partitioned spectra into components via GNPS molecular networking…
Use when when you have mass spectrometry data (mzML, Bruker .d, or CSV) loaded into a Pandas DataFrame with columns for m/z, retention time, ion mobility, or intensity values, and…
Use when after constructing a peak properties dictionary via csv_to_peak_properties
Use when you have Sciex Multiquant text export files from one or more metabolomics or lipidomics analytical sequences and need to identify and locate QCpool (pooled quality…
Use when after running RAMClustR clustering on XCMS-processed metabolomics data, export spectral data when you need to share clustered spectra with external annotation software…
Use when you have a large mass spectrometry dataset stored across multiple mzML, mzXML, or CDF files and need to perform operations (e.g., normalization, filtering, feature…
Use when you have raw or converted spectral data (jcamp, RAW, or mzML format) from NMR, IR, or MS instruments and need to identify individual peaks, extract their properties…
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 you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass…
Use when you have raw GCIMS sample files (from a GC–IMS instrument) and an annotations table (Excel, CSV, or TSV) with sample metadata, and you need to begin the GCIMS…
Use when when you have a web-based visualization of aligned mass spectrometry peaks (m/z, intensity, retention time, alignment quality metrics) and need users to interactively…
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 immediately after executing the MetaboAnalystR 4.0 unified LC-MS workflow (feature detection and quantification module) on raw mzML or netCDF data.
Use when when you have a pre-trained encoder (e.g., TCN spectrum encoder in FIDDLE) that has learned useful representations on a source task (e.g., MS/MS spectrum encoding), and…
Use when you have received chemical annotations from GNPS spectral library matching and need to (1) assess annotation confidence and validity for downstream analysis, (2)…
Use when after running DESeq() and extracting base results with results(), apply shrinkage when you have differential expression estimates and want to reduce the variance of log…
Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields…
Use when when you have access to the MAGMa source code and need to understand or audit how in silico metabolite candidates are enumerated from parent structures.
Use when after RDKit has generated a large ensemble of 3D conformers for a molecule (typically hundreds to thousands), you need to reduce computational burden before…
Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.
Use when when evaluating how well mass spectral similarity scores correlate with actual chemical structure for annotated spectral pairs (e.g., spectra with InChIKey metadata).
Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the…
Use when after sending HTTP requests to API endpoints (such as /classify or /model/metadata on an NP-Classifier server) to verify that the response is parseable JSON and contains…
Use when when preparing a chemical database for virtual or real MS/MS acquisition, and you need to focus on a specific m/z window (e.g., 100–1000) that matches your instrument's…
Use when you have raw or processed arrival-time data from a traveling-wave ion mobility mass spectrometry (TWIM-MS) platform and need to convert it into standardized collision…
Use when you have generated or assembled a lipid spectral library with precursor m/z values, adduct information, and fragmentation patterns, and you need to import those spectra…
Use when you have IM-MS lipidomics data from samples spiked with U13C-labeled internal standards (fully labeled yeast extract) and measured CCS values need bias assessmen — from…
Use when you have translated or raw SMILES strings from a chemical structure curation pipeline and need to remove invalid chemical structures, resolve sanitization errors (e.
Use when after fitting candidate GAM splines with B-spline basis functions across a range of basis dimensions (k values 12–20) to anchor feature pairs (m/z and retention time…
Use when salmon quant is run with the --writeMappings/-z flag and you need to verify that all mapped reads appear in the SAM output file.
Use when after mass track extraction from individual LC-MS samples, when you need to align mass tracks across a cohort to produce a unified feature matrix.
Use when you are designing or optimizing an MsBackend implementation and need to decide whether to pre-populate the @spectraVars slot with all core spectra variable columns (mz,…
Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, call qc_summary() to obtain — from…
Use when when you have a neural network or machine learning model with multiple tunable hyperparameters (layer size, regularization strength, dropout) or design choices (e.
Use when your XCMS-processed LC-MS dataset exhibits retention-time drift or misalignment artifacts—particularly when analyzing hundreds of samples, data acquisition spans longer…
Use when after loading and preprocessing raw scATAC-seq data into an ArchR project object when you need to compute low-dimensional embeddings for clustering, UMAP/tSNE…
Use when when you have peak-abundance .csv files and assigned molecular formula data from FT-ICR MS preprocessing, and you need to verify that a published pipeline's runtime…
Use when you have nuclear magnetic resonance (NMR) peak data (proton 1H and carbon-13 13C measurements) that you need to classify using a deployed deep learning model, and you…
Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final…
Use when you have TSV or CSV files containing structure-organism pairs (with columns for structure identifier and organism identifier) and need to count unique pairs, unique…
Use when a Rust port or alternative implementation of a mapper (e.g., salmon, piscem) consistently maps 2–3% more reads than a C++ reference, especially on short reads.
Use when when training a neural network to predict metabolite abundances from microbiome data (or similar paired multivariate omics prediction tasks) and you need to avoid…
Use when you have mass spectrometry imaging (MSI) data with ion images that need low-dimensional representation learning for downstream tasks like co-localized ion searching or…
Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from…
Use when when a C++ program writes records to an output stream (e.g., SAM alignment file) and the final output file contains fewer records than expected based on upstream counts…
Use when your input is an AnnData object with expression matrix X as a sparse scipy matrix or Dask-backed array, and you need to apply preprocessing functions (normalization, PCA,…
Use when when you have a spatial metabolomics or LC-MS dataset with detected m/z features (as a feature matrix or SpaMTP Seurat object) and need to assign metabolite identities.
Use when when deploying an R package from a non-CRAN repository (e.g., r-universe, Bioconductor, GitHub), or when verifying that a package build is reproducible and meets CRAN…
Use when when you have paired or unpaired MS/MS spectra and need to compute structural similarity scores without explicit molecular fingerprint computation, or when you want to…
Use when when you have uploaded a pre-analytical data table containing sample metadata, processing delay annotations (pre- and post-centrifugation times), and paired NMR…