Use when after peak detection in GC-IMS preprocessing, when you need to assess whether detected peaks from multiple samples align to the same chemical entities (clusters) using…
Use when you have raw metabolomics data in mzML or mzXML format and need to extract ion features, align them across samples, and produce a normalized feature table for downstream…
Use when when you have imported MSI data (imzML or vendor format) loaded into the napari plugin environment and need to organize raw spectral m/z and intensity arrays prior to…
Use when when preparing to run Over-representation Analysis (ORA) on metabolomics pathway data, after you have loaded both a metabolomics pathway database (e.g., KEGG, MetExplore)…
Use when you need to validate that Docker image builds for multiple deployment variants (e.g., cli, dev, linux, windows) meet documented compressed size ranges, or when you must…
Use when when you have received Sciex Multiquant TXT export files from a completed metabolomics or lipidomics analytical run and need to verify that QC pool samples were injected…
Use when after generating mzPeak files from prototype implementations (Rust, Python, R, or .NET) or after format conversion, and before integrating files into a mass spectrometry…
Use when you have an mzML file (e.g. Manuels_customs_ids.mzML) with non-standard
Use when when migrating spectral library data from file-based formats (JSON, CSV, binary) into a persistent store and need to support fast filtered queries on metadata and…
Use when when preparing paired MS/MS spectra for training or validation of a siamese neural network model, and you have chemical structure annotations (InChI, SMILES, or InChIKey)…
Use when you have extracted and intensity-normalized fragment ion masses and neutral loss values from MS/MS spectra and need to prepare them for unsupervised topic modeling to…
Use when you have variable-length lists of MS/MS peaks (m/z and intensity pairs) that need to be encoded into a fixed-dimensional representation compatible with transformer…
Use when you have raw MS data in vendor formats (Agilent .d, Thermo .raw, Bruker .
Use when you have received a conda/pip requirements file (e.g., jestr_requirements.txt)
Use when you have raw MS2 spectra (m/z and intensity pairs) that you want to match against a large training dataset of annotated library spectra (e.g., GNPS), and you need to…
Use when you have a Sphinx-based documentation project with multiple gallery scripts (e.
Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream…
Use when you have a flat table of structure-organism pairs or entity records and need to summarize their distribution across categorical bins (e.g., organism counts binned by…
Use when you have negative-mode MS/MS spectra with annotated molecular formulas and negative adducts (from repositories like MassIVE or MetaboLights), and your current formula…
Use when after fitting a linear model to expression data using limma's lmFit function on a design matrix encoding experimental groups, inspect the resulting MArrayLM object to…
Use when after generating ranked predictions of chemical formulas or subformulas for MS/MS spectra (from a neural network model like MIST-CF's formula transformer), compare…
Use when you have a trained baseline GNN model with established hyperparameters (dropout rate, learning rate, epochs, optimizer settings) and want to evaluate whether alternative…
Use when you have raw GC-MS data (aroma, breath, or other volatile analyte samples) in NetCDF or vendor-native format and need to identify multivariate chemo-/biomarker features…
Use when you have high-throughput replicate measurements (e.g., mass spectrometry metabolomics) on biological replicates and need to identify which sample pairs exhibit…
Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) — from HolobiomicsLab/asb-skill-collections
Use when when you have acquired ion mobility–mass spectrometry data (drift time and m/z dimensions) and need to convert observed drift times into calibrated CCS values.
Use when you have raw LC-MS fractional abundances (FAM) data from isotope labeling experiments and need to obtain true mass distribution vectors (MDV) that represent only the…
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 you have transcript abundance estimates from RNA-seq quantification tools (e.
Use when you have raw CE-MS or LC-MS instrument files (stored as OnDiskMSnExp objects or similar Bioconductor containers) and need to extract quantitative features (migration…
Use when when you have a list of chemically known compounds and need to validate that an MS processing pipeline (e.g., mzExacto) correctly retrieves their characteristic m/z,…
Use when after initial peak detection on composite mass tracks via local maxima and smoothing, when you have unfiltered peak lists (JSON or structured format) containing…
Use when you have a large mzML file or text corpus (e.g., Moby Dick, proteomics run) stored in compressed or database format and need to retrieve specific spectra or chapters by…
Use when when you have a resolved mzML or mzXML spectrum file and need to visualize or analyze the temporal intensity profile of a specific analyte (defined by its m/z value).
Use when after peak detection and feature alignment in a metabolomic LC–MS/MS or GC–MS workflow, when you have a feature table (rows=metabolic features, columns=samples) split…
Use when when you have isolated, high-confidence reference chromatographic peaks (ground-truth) from reference LC-HRMS chromatograms that have been matched across multiple…
Use when when evaluating a regression or similarity prediction model and you need to understand whether prediction error is uniform across the outcome space or concentrated in…
Use when you have experimental peaklist data (CSV or mzML-derived tables) from UHPLC-HRMS/MS instruments (Q-Exactive, Agilent/Bruker/SCIEX Q-TOF) with fragment m/z values and want…
Use when you have a GTF-formatted genome annotation file and need to generate alternative splicing events (exon skipping, intron retention, alternative splice sites, mutually…
Use when when you have thousands to millions of high-resolution tandem MS/MS spectra (in mzML, mzXML, or MGF format) that need to be clustered or compared, and exhaustive pairwise…
Use when after converting a decision tree path into a MassQL query string, before deployment to production mass spectrometry workflows.
Use when when deploying a metabolomics processing tool (such as asari) and needing to predict resource requirements or validate claimed scalability on laptop-class hardware (≤16…
Use when you have tandem mass spectra with precursor m/z and observed fragment peak m/z values (as mz/intensity pairs), and you need to construct interpretable feature vectors…
Use when after training a neural network or regression model to predict metabolomic profiles from microbiome data.
Use when when building a scientific visualization library that must support multiple plotting backends and needs to avoid backend-specific code duplication.
Use when a Python library exposes functionality that depends on external packages (like sqlalchemy, pandas, or lxml) that are not required for core operations.
Use when you have extracted parallel feature streams from a CNN backbone (local spectral patterns) and a Transformer backbone (global dependencies) in 1H NMR spectra, and you need…
Use when after chromatographic peak detection and feature detection in LC-MS preprocessing, when you have a set of detected features (m/z, retention time, intensity) and need to…
Use when when you have a set of MS/MS spectra with ground-truth structural similarity labels (Tanimoto scores computed from molecular fingerprints) and need to choose a decision…
Use when your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration,…
Use when you have aligned MS/MS feature tables (e.g., from MSDial ver. 4.80) representing unknown metabolites suspected to be Phase I/II transformation products of xenobiotics,…
Use when you need to query or extract data from Thermo Fisher Scientific .raw files or other proprietary binary formats accessible only through a compiled external executable…
Use when when comparing the robustness of multiple pathway ranking methods (e.g., PLAGE, ORA, GSEA) on metabolomics or other omics data, and you need to establish which method is…
Use when you have a derivatizing matrix (e.g., TAHS or other publicly documented reagent) with known composition and ionization behavior that you want to use in Met-ID for…
Use when building or auditing a multi-instrument MS data processing system that must route different chromatography modes (LC, GC), ion mobility, or imaging modalities (MALDI) to…
Use when you have generated or received mzPeak files from a Rust, Python, R, or other implementation and need to verify they comply with the published HUPO-PSI specification…
Use when you have a processed single-cell expression matrix (AnnData object) with pre-computed cluster assignments (e.g., leiden or louvain clusters in adata.obs) and want to…
Use when when you have constructed a MassGrid (m/z-aligned mass tracks across multiple samples) and need to retrieve all sample-specific mass tracks for a given m/z value in order…
Use when you have received chemical annotations from GNPS spectral library matching and need to (1) assess annotation confidence and validity for downstream analysis, (2)…
Use when you have fitted a linear model to gene expression data (microarray, RNA-seq, qPCR, or proteomics) across multiple samples and need to compute gene-level test statistics.