Use when you have inferred or discovered structured results (e.g., LDA-derived motif sets with mass compositions, neutral-loss patterns, and ranked database matches) that must be…
Use when after applying Scanpy preprocessing functions (e.g., pp.normalize_total, pp.pca) to a Dask-backed AnnData object, or when performing any operation that could alter matrix…
Use when you have an unknown MS/MS query spectrum with a known or measured precursor m/z value and need to search a spectral library (local or public: GNPS, MASSBANK, DrugBANK) to…
Use when you have high-resolution tandem MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or searched at scale (millions of spectra).
Use when you have paired genomic (BGCs clustered into GCFs via BiG-SCAPE) and metabolomic data (MS2 spectra grouped into MFs), with strain/sample co-occurrence patterns and…
Use when when you have acquired a CCS reference library (such as DTCCSN2 for U13C labeled lipids) and need to verify that it contains the expected lipid classes, CCS values are…
Use when you have deposited mass spectrometry imaging datasets in NetCDF (CDF) format with accompanying MATLAB workspace files (.
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 you need to verify that an S4 replacement method (e.g., `mz<-`) in a bioinformatics backend class correctly validates input data using vectorized operations on…
Use when after ASE-ANI has filtered conformers to remove high-energy geometries, and you need to compute electronic properties required for CCS prediction.
Use when preparing training batches for a neural network classifier on LCMS peak data where class counts are unequal (e.g., more high-quality peaks than low-quality peaks).
Use when when you have raw LC-MS/MS DDA spectral data (positive and/or negative ionization modes) paired with sample metadata (originating taxon), and you need to detect molecular…
Use when you have a trained decision tree model on ChemEcho sparse feature vectors and need to convert a specific decision path (root to leaf) into a deployable query.
Use when when you have completed feature detection in MZmine3 or similar tools and produced a feature quantification table (rows = features, columns = samples with intensity…
Use when after executing Formation formatting on processed feature tables (output from Blueshift or Gravity modules).
Use when when you have received raw MRM lipidomics export files in vendor-specific
Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
Use when after clustering and filtering KEGG candidates for LC-MS features, when you have a ranked set of candidate metabolites per feature and access to a metabolite interaction…
Use when when implementing or extending a DSL parser (lexer + recursive descent or LALR parser) that accepts user-authored query strings.
Use when when you have multiple CDF imaging files (e.g., from mass spectrometry imaging scans of biological samples) that need to be read into a single Matlab workspace with…
Use when you have validated intermediate JSON data (conforming to the Experiment Description Specification) and need to configure how it should be converted to a supported output…
Use when when you have preprocessed mass spectra (peak-filtered, metadata-cleaned) in supported formats (mzML, mzXML, msp, MGF, JSON) and need to compare all or many pairs of…
Use when you have paired metabolomics data (MS/MS spectra and feature quantification) linked to organismal or tissue taxonomy, and you want to reduce false positive annotations…
Use when after generating candidate transformed structures from biotransformation rules and when you have MS/MS spectral feature data that you wish to organize into putative…
Use when when you have a processed or annotated MsmsSpectrum object (from USI loading or direct instantiation) and need to generate a figure showing observed peaks, their…
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 when you have validated SMILES strings or canonical molecule objects from RDKit and need to convert them into the fixed-size numerical tensor format expected by a deep…
Use when when you have loaded (un)targeted metabolite data into a Metaboprep object and need to exclude samples with excessive missing values before quality control or statistical…
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 a preranked gene list (e.g., genes sorted by log2 fold-change, t-statistic, or other continuous metric) and a collection of gene sets or biological pathways, and…
Use when after training a decision tree classifier on ChemEcho sparse feature vectors (representing tandem mass spectra fragmentation patterns), especially when the goal is to…
Use when after loading centroided .mzML LC–MS runs and before executing full peak detection and integration.
Use when you need to verify the scope and completeness of a software platform's analytical capabilities—particularly when the project claims to support multiple input modalities…
Use when after running DESeq() to fit negative binomial GLMs and obtaining raw p-values from results(dds), when you need to reduce false positives from multiple testing across…
Use when when processing multiple LC-MS samples with varying scan numbers or retention-time drift, before constructing composite mass tracks for peak detection.
Use when you have calibrated m/z peak lists, configured adduct transformations (e.g., [M+H]+, [M+Na]+, [M-H]−), and need to annotate peaks with molecular formulae from KEGG,…
Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
Use when when you have a collection of microbial genomes with predicted BGCs (via antiSMASH), a set of MS/MS spectra (e.g.
Use when after feature detection and alignment have produced a feature table with MS/MS spectra, and you have access to a reference spectral database (e.g., xenobiotic reaction…
Use when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/...
Use when you have executed mzExacto() on a preprocessed GC-MS dataset and need to verify that the returned dataframe correctly matches query chemicals to their m/z peaks,…
Use when you have a CSV or Excel file containing chemical structure descriptors for one or more molecules, and you want to obtain binary bitter/not-bitter predictions for each…
Use when when you have extracted file metadata or scan summaries as R list objects from .raw files using readFileHeader(), readIndex(), or readSpectrum(), and need to persist them…
Use when you have two MS/MS spectra from related compounds (e.g., a reference compound and a suspected modified version) and need to quantify where and how their structures differ.
Use when you have antiSMASH v5.0.0 BGC predictions from a set of microbial genomes and you need to integrate those predictions with GNPS metabolomic data (MS2 spectra and…
Use when when a scientific software repository documents multiple standalone tools, web applications, or resources with associated metadata (URLs, publications, taxonomic…
Use when working with large GCIMS matrices where computational speed or memory constraints are a concern, after filtering retention time (e.g., 0–1100 s) and drift time (e.g.,…
Use when you have Thermo Orbitrap .raw files and need to access raw spectral data (individual MS1 or MS2 scans, base-peak values, chromatogram traces, retention times, or…
Use when you have multiple replicate MS/MS spectra for the same metabolic feature (e.g., 66 top-TIC spectra for feature 1982) and need to identify robust peaks by merging nearby…
Use when you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer…
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 raw IM-MS data in UIMF or Agilent MassHunter .d format acquired from a multiplexed (interleaved) ion mobility experiment, and you need to recover indivi — from…
Use when you have paired tandem MS spectra and either (1) molecular fingerprints
Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
Use when you have a raw feature table (TSV/CSV) derived from LC-MS peak detection (e.
Use when releasing a new version of a Python package to public repositories, when verifying that distribution pipelines are functioning after code changes, or when troubleshooting…
Use when when you have a query mass spectrum and a set of candidate molecular structures (as SMILES or 2D/3D coordinates), and you need to prepare them for cross-view similarity…
Use when you have preprocessed 1D ¹H and/or ¹³C NMR spectra from an unknown organic compound with ≤19 heavy atoms, and you need to recover its molecular structure (both formula…
Use when when processing mass spectrometry imaging (MSI) data in positive ion mode where both [M+H]+ and [M+Na]+ adducts are present for the same lipid species, and you observe…
Use when you have paired microbiome-metabolome (or similar multivariate) datasets and want to quantify whether training on a superset of features (e.g., both annotated and…