Use when you have aligned features characterized across multiple dimensions (m/z, drift time, retention time) and need to: (1) resolve MS/MS spectra that may contain fragments…
Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.
Use when you have raw or processed mass spectrometry data in HDF5 (.h5) or mzML format and need to ingest it into DEIMoS for multi-dimensional analysis.
Use when after constructing MetaboSet objects from Excel-formatted LC-MS peak tables and before drift correction or quality flagging.
Use when you have a set of candidate metabolites for an unknown compound detected in a liquid chromatography–mass spectrometry (LC-MS) experiment, predicted RTs from a trained DNN…
Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.
Use when when processing mass spectrometry imaging data with multiple adduct forms of the same lipid species, and you need to correct one adduct form (e.g.
Use when you have tabular data (CSV or Excel) with column headers annotated using MESSES tagging syntax (#<table_name>.id for record identifiers, #.
Use when you have a large collection of MS/MS spectra (hundreds of thousands to millions) that need to be clustered, you have already constructed nearest neighbor indexes on…
Use when you have trained a multitask NMR-to-structure model and need to quantify its predictive accuracy on held-out test molecules.
Use when you have statistically significant features from multiple LC-MS assays with different ionization modes (e.g., positive and negative ESI) and need to collapse redundant…
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 after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax
Use when you have a set of molecular structures in SMILES format that require CCS prediction for metabolite annotation in untargeted mass spectrometry workflows.
Use when when you have deposited or archived biosynfoni fingerprint vectors (such as from Zenodo 10.5281/zenodo.14822624) and need to ingest them into a Python workflow to compute…
Use when when you have built a new tool implementation or major version and need to verify it produces equivalent results to a reference implementation on the same input data and…
Use when when you have extracted intermediate JSON conforming to the Experiment Description Specification and need to restructure, filter, sort, or aggregate records (e.
Use when when raw MS/MS spectra from GNPS or similar databases contain variable-scale peak intensities, missing metadata, or inconsistent m/z calibration, and you intend to feed…
Use when you have implemented or modified a tandem mass spectrometry formula inference model and need to measure whether a specific architectural change (e.
Use when after training multiple neural network models via k-fold cross-validation
Use when you have raw mass spectrometry data from an instrument not yet validated in your pipeline (e.
Use when you have a mass spectral library (EI or MS2 format) loaded into R via read_lib() and possess either MOL files (from Lib2NIST export) or an SDF file containing the…
Use when you have a raw metabolite count data frame (e.g., c57_nos2KO_mouse_countDF)
Use when your ChIP-Seq input is paired-end sequencing data stored in BEDPE format (e.g., CTCF_PE_ChIP_chr22_50k.bedpe.gz), and you need to estimate fragment length and call peaks…
Use when you are deploying a Windows .NET application (e.g., AirdPro CLI) inside a Docker container on a non-Windows host and need to understand whether Wine initialization…
Use when you have retrieved multiple candidate structures from a molecular structure database (e.g., PubChem, HMDB) for an unknown compound, and you have predictions of…
Use when when you have an experimental tandem mass spectrum (peaks with m/z and intensity values) and wish to identify which fragments or chemical subformulae each peak…
Use when you have a ranked list of metabolite identifiers (PubChemCIDs, KEGG IDs, or chemical names) from differential abundance or ANOVA testing and need to determine which…
Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the…
Use when when XCMS or other DTW-based aligners have produced misaligned LC-MS feature groups across hundreds of samples or long acquisition periods (>1 week), particularly when…
Use when you have mzPeak files stored as Parquet tables within a ZIP archive and need to load spectrum metadata, chromatogram metadata, signal data (profile or centroid), or peaks…
Use when after MS2Deepscore has selected the top 2000 candidate spectra from a library based on spectral similarity, and you need to re-rank these candidates to surface the single…
Use when when generating synthetic LC/GC-MS .mzML files with companion ground-truth peak tables for method validation, you need to calculate the absolute maximum intensity that…
Use when you have extracted peaks from multiple LC/HRMS batches (n > 1) with their m/z and RT values, and you need to identify and align peaks representing the same compound…
Use when when you have preprocessed mass spectrometry ion images (single-channel
Use when you have a mass-spectrometry query string written in MassQL (or similar domain-specific SQL-inspired syntax) that must be converted into structured form for execution.
Use when when you have a GTF genome annotation and need to identify all local alternative splicing events (SE, RI, A5/A3, MX, AF/AL) or transcript-level isoform events for a given…
Use when when training or validating a deep learning model for molecular formula prediction from tandem MS/MS spectra, use this metric to track whether the model's predicted…
Use when when you need to compare the computational efficiency of different mass spectrometry libraries on identical data and processing pipelines, or when you want to establish…
Use when a web application receives mass spectrometry data through heterogeneous
Use when before running HiC-Pro's normalization stage on aligned Hi-C BAM files. Specifically, when you have SAM/BAM-formatted aligned Hi-C reads that need bias correction and…
Use when when you have access to Rust source code in a repository with a Cargo manifest (Cargo.toml) and need to verify that a library's read and write APIs produce…
Use when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform peak detection, feature alignment, and metabolite annotation in a reproducible,…
Use when when you have modifications to propose for a shared codebase (e.g., bug fixes, new features, or documentation updates) and need to integrate them without disrupting the…
Use when you have identified a published method (e.g., MIST-CF for chemical formula ranking from mass spectra) whose source code and trained weights are available in a public…
Use when you have raw metabolomics data in mzML or mzXML format and need to convert it into a normalized feature table (CSV or mzTab) via automated batch processing.
Use when when you have raw strain correlation scores (or similar overlap-based metrics) computed across genomic cluster family (GCF) and molecular family (MF) pairs of varying…
Use when after constructing candidate feature pair alignments and retention-time
Use when you have LC-MS feature tables (with m/z and retention time columns) paired with raw .mzXML or .mzML files, and you need to automatically validate which detected features…
Use when when compiling EI or MS/MS spectral libraries from multiple gigabyte-scale sources (e.
Use when when you have NMR metabolite measurements paired with documented pre-centrifugation and post-centrifugation delay times, and need to assess how processing delays affect…
Use when when you have received chemical annotations from GNPS spectral library matching workflow and need to assess their reliability before downstream analysis (e.g., chemical…
Use when you have raw or semi-curated mass spectrometry spectral data in JSON, CSV, MSP, or MGF format from multiple open mass spectra libraries (OMSLs) and need to standardize…
Use when after converting or loading a Keras model to HDF5 TensorFlow 2.3.0 format, especially when the model will be served through a pipeline (e.g., NP Classifier) that expects…
Use when after rewriting or modifying a Python module (such as calculate_feature_overlap.py
Use when you have a raw NV file from NMRViewJ or compatible NMR acquisition software and need to extract header metadata before processing spectroscopic data.
Use when you have Nightingale Health 1H-NMR metabolomics assay output (metabolite concentrations in a samples × features matrix) and you want to compute a published metabolic risk…
Use when you have acquired one or more tandem MS/MS spectra and need to identify metabolites against a reference library filtered by biological domain (e.
Use when after reading in per-sample methylation call files with methRead() and obtaining methylRawList objects, but before calculating differential methylation or performing…
Use when designing multi-batch LC/GC-MS experiments where samples belong to multiple groups or conditions and you need to ensure that each injection plate receives a balanced…