Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
Use when after installing a package in development mode (e.g., via `pip install -e .[dev]`) to verify the package functions as intended, or before submitting pull requests to…
Use when after generating in-memory lipid spectra (with m/z, intensity, and metadata such as lipid class, fatty acid composition, and adduct type) when you need to export those…
Use when after generating raw Hi-C contact matrices from aligned reads (post-merge, pre-analysis).
Use when you have generated a peak table or feature list from MZmine, XCMS, MS-DIAL, or Compound Discoverer and need to ingest it into LipidMatch for lipid identification — from…
Use when you have an untargeted metabolomics dataset with a two-layer network topology already constructed (one layer representing biochemical knowledge/pathways, the other…
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 computed Reaction Activity Scores (RAS) from transcriptomics and GPR rules, Reaction Presence Scores (RPS) from RAS normalized flux predictions, and Flux…
Use when you have a raw metabolite abundance matrix (e.g., from MSPrep or another LC-MS/MS pipeline) with many features and samples, and you observe that a substantial fraction of…
Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity…
Use when you have exported lipid identifications from MS-DIAL (version 4 or 5) and need to run LipoCLEAN quality filtering on that output.
Use when you have an unknown sample spectrum (m/z peaks and intensities from DI-MS, ASAP-MS, or other high-throughput mass spectrometry modalities) and a reference species…
Use when you have centroided high-resolution Orbitrap or GC-CI-MS mzML files and a formulaTable of target compounds with known m/z, retention time, and molecular formula, and you…
Use when you have NMR metabolomics measurements paired with pre-analytical metadata (processing delay times, centrifugation timing, sample type such as plasma vs.
Use when you have raw GC-MS or LC-MS data in vendor format (NetCDF, .raw, .d) or generic mass lists, and you need to assign chemical identities to detected peaks.
Use when when implementing a new ComputeConverter subclass for MSMetaEnhancer that performs local chemical structure conversions using RDKit (e.g., SMILES to InChI, canonical…
Use when when applying a series of mpactr filter functions (filter_mispicked_ions,
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 a Thermo Fisher Orbitrap .raw file and need to recover the intensity profile of a specific m/z value or peptide across the LC separation dimension…
Use when you have two independent LC-MS untargeted metabolomic feature tables (e.
Use when you have a set of observed m/z values extracted from a Cardinal MSImagingExperiment object, raw LC-MS data, or similar high-throughput MS dataset, and you need to assign…
Use when when you need to establish a working installation of a Python package in a fresh or isolated environment, particularly when the package is available through multiple…
Use when when you have raw untargeted LC-MS metabolomics data and need to detect low-quality or mis-integrated peaks in an XCMS-processed xcmsSet object before performing…
Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or…
Use when importing MS/MS spectral libraries (particularly from MoNA or GNPS) where SMILES or chemical structure identifiers are embedded in free-text or non-standard Comment…
Use when you have a trained NeatMS neural network model (.h5 format) and need to assess its classification performance at a specific decision threshold (e.g., 0.01) to de — from…
Use when you have a fitted linear model (lmFit object) from microarray or RNA-seq count data and need to compute differential expression statistics, especially when the n — from…
Use when you are preparing to perform effective mobility transformation of CE-MS data and must establish the electrophoretic system's calibration context.
Use when when constructing k-nearest neighbor graphs from spatial coordinates (e.g., microscopy x,y positions or tissue section coordinates) and exact neighbor discovery is…
Use when you have mass spectrometry data arriving through heterogeneous input formats (Task ID from GNPS, Universal Spectrum Identifiers, or Feature-Based Molecular Networking…
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 when you have executed database search pipelines (Dereplicator, VarQuest, or Dereplicator+) on centroided LC-MS/MS spectra in MGF format and obtained match results with…
Use when when you have predictions from one or more metabolite annotation models (MLP baseline, GNN, or ESP ensemble) and need to quantify ranking performance on ESI/LC-MS test…
Use when when contributing code changes to a Python project (fork, feature branch, or pull request) that uses a setup.py-based test suite, before pushing changes to the remote…
Use when when you have run a pathway ranking method (such as PALS/PLAGE) on clean metabolomics data and wish to assess how sensitive the resulting pathway activity rankings are to…
Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100…
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 raw .idat files or a beta-valued matrix from an Illumina HumanMethylation450 or EPIC array experiment and need to import the full probe set into R for downstream…
Use when when you have 512-dimensional (or other fixed-size) representation vectors output from paired encoders processing augmented versions of the same input (e.
Use when when you have observed fragment peak m/z values from tandem mass spectra and need to assign chemical subformulae to them.
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 training Word2Vec embeddings on mass spectra represented as peak-word documents, and you need to preserve the quantitative intensity relationships between fragments…
Use when you have tandem MS data with technical replicates and need to remove features showing high variability between replicates.
Use when you have a tabular file (CSV or Excel) that has been manually or semi-automatically tagged with export tags, and you need to verify tag correctness before running the…
Use when you have raw GC-MS output in CSV format with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.
Use when analyzing differential methylation from bisulfite sequencing data where you suspect overdispersion (variance exceeds binomial expectations), or when comparing uncorrected…
Use when working with raw or minimally processed MS/MS spectra from repositories
Use when you have an indexed gzip–compressed mzML file (mzML.gz with internal index structure) and need to retrieve and work with individual spectra or chromatograms by integer…
Use when when evaluating or designing a mass spectrometry data analysis platform, and you need to verify that every supported separation/ionisation technique (LC, GC, IMS, MS…
Use when you have a GTF annotation file and need to systematically extract all local alternative splicing event coordinates (not transcript isoforms) for downstream PSI…
Use when when reading mzPeak files or other Parquet-backed mass spectrometry archives where spectral m/z and intensity arrays are stored in columnar layouts (point or chunked…
Use when you have a set of in silico-predicted compounds (with SMILES structures) and an experimental metabolomics peak list (m/z values), and you need to filter predictions to…
Use when you have raw MS/MS spectra in multiple formats (.mgf, .msp, .mzML) that contain background noise, instrument artifacts, or low-abundance fragments that would degrade…
Use when you have 512-dimensional representation vectors output from paired ResNet18 encoders processing augmented ion images, and you need to: (1) introduce an intermediate…
Use when when you have peak-abundance .csv files with assigned molecular formulas (elemental composition: C, H, O, N, P, S) from FT-ICR MS or high-resolution MS and need to…
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 predicted BGC-spectrum IOKR scores or other pairwise linking scores, and need to rank genomic clusters (GCFs from BiG-SCAPE) against metabolomic clusters…
Use when when preparing mass tracks for retention-time (RT) alignment across multiple LC-MS samples.
Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment.
Use when you have raw TOF-MS or IM-MS data in Agilent MassHunter (.d) or UIMF format with jagged peaks and low-abundance ions that require signal enhancement, but you need to…