Use when you have a preprocessed unknown sample spectrum (m/z peaks and intensities) and need to identify the most likely species or reference entries by scoring it again — from…
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 you have raw MS intensity data paired with measurements from known concentration standards, and you need to produce absolute quantified concentration values rather than…
Use when after composite-map peak detection (scipy.signal.find_peaks) has identified candidate peaks on aligned mass tracks, but before compiling the final feature table.
Use when when processing OMSLs (Open Mass Spectra Libraries) with heterogeneous data quality, inconsistent annotations, or mixed ionmode/chromatographic modes (LC/GC), and you…
Use when building a transformer-based neural network for chemical formula ranking or classification from mass spectrometry spectra, and you need to encode categorical chemical…
Use when you have a metabolomics count table (rows=metabolites, columns=samples)
Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified…
Use when you have a genome annotation GTF file and need to identify all transcript-level alternative splicing events (exon skipping, intron retention, alternative splice sites,…
Use when at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers.
Use when you have PSI (percent-spliced-in) matrices for multiple samples grouped into two or more biological conditions, along with corresponding transcript expression…
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 your input is raw .idat files or a beta-valued matrix from Illumina HumanMethylation450 or EPIC arrays, and you need to remove unreliable probes (those with detection…
Use when when you have extracted a raw Orbitrap scan from a .raw file and need to verify that the instrument operated within expected parameters and that observed peptide fragment…
Use when when you have extracted retention times from the top detected MS1 features in a LC-MS run and need to evaluate whether the gradient spreads those compounds efficiently…
Use when when processing centroided .mzML LC–MS runs with a multi-polarity target list (i.e., some targets ionize in positive mode, others in negative mode, or both) and you need…
Use when you have received new or updated MassBank records (in plain-text or structured format) that must be integrated into the MassBank-data repository and you need to ensure…
Use when when you have pre-computed embeddings for query and reference MS/MS spectra, computed their cosine similarity matrix, and need to measure retrieval success by verifying…
Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) from one or more metabolomics samples, and you need to prepare them for MS2 fingerprint — from…
Use when after executing annotateRC to match six or more lipidomics/metabolomics features against ion fragment databases (e.
Use when you have execution-time data for the same set of plotting operations (e.g., chromatogram, spectrum, peakmap rendering) across two or more backend implementations (e.
Use when you need to understand or validate whether calling filter_mispicked_ions() (or similar R6 filter methods) with different copy_object settings will mutate your original…
Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental…
Use when you have applied two or more competing analysis workflows to the same RNA-seq or microarray dataset and need to assess whether they yield consistent or divergent…
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 after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for…
Use when you have a query mass spectrum matched to multiple candidate metabolites (by accurate mass, database lookup, or spectral similarity), and you possess or can train a DNN…
Use when you have a set of candidate transformed structures generated by biotransformation rules (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 you have a log2-transformed, standardized peak intensity matrix (rows = metabolite features, columns = samples) with compound annotations mapped to curated pathway…
Use when you have a set of small-molecule structures (SMILES, InChI, or SDF format) and need to predict their chromatographic retention times for a specific method, either to…
Use when a Shiny application or R-based tool is known to run on only one operating system (e.g., Windows-only), and you need to identify the root causes preventing execution on…
Use when when you need to understand the computational structure of a modular scientific application (especially one with multiple subprojects or plug-in architectures) and static…
Use when you have an existing mass spectrometry data file in a vendor or standard format (mzML, NetCDF, etc.) and need to convert it to mzPeak format for downstream analysis,…
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 observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by…
Use when your input consists of multiple large MSP files (hundreds of megabytes) with associated structure folders containing hundreds of thousands of MOL or SDF files that…
Use when apply this filter after batch correction of compound/internal-standard ratios when you have pooled study quality control (SQC) samples and need to determine which…
Use when when integrating LC-MS/MS data from diverse sources (e.g., public repositories like MSV000080102, instrument outputs, or precomputed workflows) into NPDtools pipelines.
Use when when you have computed per-bin insulation scores from a Hi-C cooler file using cooltools.insulation and need to identify discrete genomic boundaries that separate…
Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C labeled internal standards (e.g., fully labeled yeast extract) and need to quantify and correct…
Use when when processing open mass spectrometry library (OMSL) data that may contain duplicate spectral records (e.
Use when you have an unknown MS/MS spectrum (tandem mass spectrum) with a measured precursor m/z and fragment peaks, and you need to assign the most likely molecular formula and…
Use when when you have retention times measured on one chromatographic method and need to predict or map them to another method with minimal or no overlap in measured molecules.
Use when processing LC-MS metabolomics studies with >10 samples where sample count and memory constraints make pairwise mass alignment infeasible.
Use when when you have mzPeak format spectrum files and need to work with spectrum metadata, intensity/m/z arrays, or precursor information in a tabular, columnar, or vectorized…
Use when developing or reviewing Python code for a scientific package (e.g., cooltools) that targets collaborative development with multiple contributors.
Use when you have a large collection of preprocessed MS/MS spectra (typically >10,000 spectra) with diverse chemical structures and you need to learn embeddings that capture…
Use when you have MS2 fragmentation spectra from multiple samples (in .mgf, .mzML, or .mzXML format) and want to compare them despite poor feature overlap, strong RT shifts…
Use when you have annotated metabolite structures (with SMILES strings) from a reference library (e.
Use when you have output from a biotransformation rules module (candidate transformed structures linked to anchor molecules) and untargeted MS/MS spectral data, and you want to…
Use when when preparing ion image data from mass spectrometry imaging for contrastive self-supervised representation learning, and you need to generate augmented image pairs that…
Use when when you have XCMS-preprocessed LC-MS metabolomics data with a peak table and an accompanying covariate/metadata file that contains a 'SampleType' column, and you plan to…
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 after computing a pairwise sample distance matrix from aligned MS2 fingerprint vectors and you need to visualize sample relationships, clustering, or separation by group…
Use when after computing expected adduct ions for a metabolite using a derivatizing matrix ruleset, validate the predicted m/z values and adduct formulas against a curated…
Use when when processing paired augmented versions of the same input (e.g., two augmented ion images in COL or ISO mode) and you need to learn meaningful low-dimensional…
Use when after identifying precursor peptides from genome assemblies via BGC mining, when you need to enumerate the chemical space of PTM variants (lantibiotic, lassopeptide,…
Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a…
Use when when you have raw feature tables exported from a tandem LC-MS/MS preprocessing tool (e.g., Progenesis QI, MS-DIAL, Bruker Metaboscape) and need to combine them with…