Use when when you need to validate that a Python package (or update to it) is accessible to end users through official distribution channels, or when you are preparing a release…
Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for eac — from…
Use when after extracting raw MS/MS spectra from mzML files for individual features (identified by precursor m/z and retention time) and you have multiple replicate spectra for…
Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
Use when when you have LC-MS/MS data in Mascot Generic Format (mgf) files and need to identify compounds against a curated custom database (e.g., prepared using CFM-id for a…
Use when you have a USI string referencing a spectrum in an online public repository (PRIDE, MassIVE, etc.) and need to load its raw spectral data without downloading the entire…
Use when you have raw Bruker NMR spectral files (from a Bruker instrument) in a directory and need to prepare them for automated metabolite identification and quantification using…
Use when after RDKit has generated multiple conformations for a molecule in an SDF or XYZ format, and you need to reduce the conformational ensemble to a tractable size (by…
Use when when you have SMILES strings or molecular formulae for N-Me derivatized unsaturated sterol lipids and need to generate theoretical MS/MS spectra (predicted fragment m/z…
Use when you have a spatial omics dataset (AnnData object with coordinate columns like 'x', 'y', 'z') and an associated tissue image file (e.g., TIFF, PNG, or HE-stained…
Use when you have integrated, normalized lipidomic and metabolomic feature tables from the Multi-ABLE method or similar concurrent multiomics workflows, with matched sample…
Use when training neural networks on MS/MS spectra (or similar scientific data) where you need to preserve model states that improve validation performance.
Use when when you have synthesized or assembled mass spectrometry spectral data (m/z values, intensities, retention times) and need to encode it as a portable, standard mzML file…
Use when your input is a single-cell gene expression matrix too large to fit in RAM, or you are working in a resource-constrained environment (e.g., shared compute cluster, laptop…
Use when you have transcript-level abundance and count estimates from salmon, sailfish, kallisto, or oarfish and need gene-level matrices for downstream differential analysis with…
Use when apply fillPeaks after retention time alignment (whether XCMS or ncGTW) when feature matrices contain missing peaks across samples due to alignment gaps or detection…
Use when after a transformer-based de novo sequencing model (such as Casanovo) generates candidate peptide sequences from MS/MS spectra, before exporting results or using them in…
Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you wish to group features that represent the same metabolite at different — from…
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 constructing a peak properties dictionary via csv_to_peak_properties
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 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 when you have a collection of N-Me derivatized unsaturated sterol structures from tissue samples or standards that must be fed into MS/MS fragmentation prediction or…
Use when when you have a webservice codebase (Python, Java, etc.) with HTTP route definitions, parameter handling, and serialization logic, and you need to generate an OpenAPI 3.
Use when preparing mass spectrum input tensors for transformer encoder layers in IDSL_MINT.
Use when you have cloned or loaded a deep-learning architecture extension (e.g., chemprop-IR) and need to verify that its feature extraction component can be instantiated and…
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 you have a set of chemical structures (as SMILES strings or convertible to SMILES) and need to submit them programmatically to the NP Classifier /classify endpoint for…
Use when you have raw or processed TWIM-MS data with arrival time and m/z values for multiple features, but lack prior structural identification (e.g., from spectral libraries or…
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 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 when you have peak area tables (unlabeled C12 and labeled C13) from LC-MS metabolomics with sample metadata indicating case and control groups, and you need to…
Use when you have an experimental mass spectrum (or a set of spectra from LC-MS/MS data) and need to identify the underlying metabolite(s) by comparing against known reference…
Use when you have received a conda/pip requirements file (e.g., jestr_requirements.txt)
Use when when you have received raw MRM lipidomics export files in vendor-specific
Use when you need to validate that a repository's automated build, test, or publish pipeline is functioning correctly on a target branch (e.g., release branch); when you want to…
Use when you have consensus metabolic reconstructions for all members of a microbial or plant community (e.
Use when when building a comprehensive lipid fragment ion library covering all chain composition and positional isomer variants (e.g., 168.6 million entries).
Use when you have raw ChIP-Seq and control BED files with potential PCR duplicates or unequal sequencing depths.
Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability…
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 after computing activity scores for a collection of metabolite sets (pathways, GNPS Molecular Families, or MS2LDA Mass2Motifs) from intensity and annotation data.
Use when you have fingerprint or spectrum data that requires compound-class annotation but prefer not to run SIRIUS locally, or need to integrate predictions into an automated…
Use when you have raw LC-MS data in mzML or equivalent binary format from a public repository (MetaboLights, MassIVE) or instrument vendor output, and need to ingest it into…
Use when converting raw MS/MS spectra from library files (e.g., .msp format) into structured library entries, or when annotating experimental LC–MS features against fragment…
Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
Use when when you have a spatial molecular dataset (e.g., Visium, MERFISH) with categorical cell-type or feature annotations and want to test whether specific categories are…
Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's…
Use when you have a working base MPNN model (e.g., chemprop) and need to add task-specific feature processing layers (spectral, electronic, or domain features) to improve…
Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed…
Use when after matching mass-to-charge ratios to a compound database (e.g., KEGG) and assigning adduct/fragment types, when you have an annotated feature table with retention…
Use when you have independent LC-MS assays (e.g., positive and negative ionization modes, different lipid profiling assays, or different chromatographic methods) analyzed on the…
Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties…
Use when when you have aligned peak data from molecular networking (with m/z, intensity, retention time, and alignment quality metrics across multiple spectra) and need to…
Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra…
Use when after LCMS feature alignment (e.g., Eclipse output) when you have a feature table with retention times and intensity profiles across multiple injections, and you need to…
Use when you have GC–MS data from human breath samples and need to identify marker metabolites for disease diagnosis, phenotyping, or biomarker discovery without a predefined…
Use when you have a collection of N scripts (e.g., 19 gallery examples) that must run on multiple backends or configurations, and you need to produce a reproducible benchmark…
Use when you have trained a neural network or regression model on one paired microbiome-metabolome dataset and wish to test whether it can predict metabolite abundances in an…
Use when when you have metabolomics results from multiple studies reporting compound identifiers, p-values, fold-changes, and study sizes (N), and you need to prepare them for…