Use when when you have paired genomics (antiSMASH-detected BGCs with MIBiG homology assignments) and metabolomics data (MS2 spectra from GNPS), and you need to score BGC-spectrum…
Use when you have completed msFeaST pipeline preprocessing and generated a JSON output file (dashboard_data.
Use when when you have a GNPS molecular network (graphml or cytoscape format) and wish to annotate it with chemical class labels or MS2LDA-derived mass2motifs to highlight shared…
Use when after SMILES standardization when you have a table of translated SMILES strings (e.g., interim/tables/1_translated/structure/smiles.tsv.
Use when you are designing a new backend or data container that must integrate seamlessly with an existing Spectra-based workflow. You have identified a virtual parent class (e.
Use when you have aligned feature tables (CSV format) with corresponding MS2 spectra data (MGF or mzML files), and need to construct a sample-level vectorization matrix where each…
Use when after generating theoretical spin multiplets for individual metabolites via first-order or density-matrix NMR simulation, but before combining spectra or applying Fourier…
Use when you have an unknown compound's mass spectrum (m/z peaks and intensities in . — from HolobiomicsLab/asb-skill-collections
Use when you have a spatial transcriptomics dataset (AnnData object) with cell/spot coordinates and an associated tissue microscopy image file, and you need to compute…
Use when when you have real LC-MS/MS data (mzML format) from an untargeted metabolomics experiment and want to test how variations in TopN DDA parameters affect which precursor…
Use when you have trained two or more regression models (e.g., original vs. alternative GNN architectures) on the same training set and need to evaluate which generalizes better…
Use when immediately after loading raw MS/MS spectra from .mgf, .msp, or .mzML files, before generating the bag-of-fragments corpus or extracting neutral losses.
Use when you have raw Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited accession) and need to reproduce or validate Hi-C map generation following the…
Use when you have a set of small-molecule compounds (e.g., from MS/MS library matching or database annotation) that require retention time validation or ranking to resolve…
Use when when you have raw MS2 spectra (m/z and intensity pairs) and a curated reference peak list from a large training dataset (e.
Use when when you have extracted and concatenated MS/MS spectra from multiple replicates for a set of metabolomic features (stored in a preprocessed list), and need to apply…
Use when after training or loading a NeatMS neural network model, before applying it to filter false positive MS1 peaks in a new dataset.
Use when you have SMILES strings or molecular structure files (e.g., from a synthetic drug database) and need to feed them into a deep learning model like PS2MS, NEIMS, or DeepEI…
Use when you have mass spectrometry data stored in a SQLite database indexed by spectrum ID and need to retrieve specific spectra by ID (random access via __getitem__) or iterate…
Use when you have a new chromatographic dataset with molecular structures (as InChI or SMILES) and experimentally measured retention times, and you want to predict retention times…
Use when you have Nightingale Health 1H-NMR metabolomics measurements for a new cohort and wish to compute one or more established metabolic risk scores (mortality, MetaboAge,…
Use when after denoising MS/MS spectra at multiple frequency thresholds and matching each thresholded spectrum against a -matching reference spectrum.
Use when immediately after chromatographic peak detection (findChromPeaks) when you have detected peaks across multiple samples and need to identify which peaks represent the same…
Use when releasing a new version of a Python package, validating packaging infrastructure changes, or confirming that distribution channels (PyPI, Bioconda) remain functional…
Use when you have UPLC-HRMS data (ThermoFisher, Agilent, or MSConvert-compatible
Use when you have a preprocessed feature table (m/z, retention time, intensities) from LC-MS and need to group features into empirical compounds.
Use when after network partitioning, when you have identified connected subnetworks of features matched by isotope or adduct patterns and need to sanitize and categorize the…
Use when you have a feature table containing raw ion mobility arrival time measurements paired with experimentally assigned biomolecular class labels (e.g., lipid, protein,…
Use when starting from raw LC-MS spectral files (mzML or mzXML format) in a global metabolomics study and you need to produce a complete, validated feature table with m/z,…
Use when running targeted peak detection on LC-MS data acquired with multiple overlapping m/z scan windows and observing distorted or periodically discontinuous peak profiles in…
Use when after computing a scoring function over all possible genomic-metabolomic candidate pairs (e.g., all 2966 MIBiG-GNPS BGC-spectrum pairs), when you have a subset of known…
Use when after peak picking and sample alignment have produced an aligned feature table with m/z and retention time coordinates.
Use when you have completed DESeq differential expression analysis on a DESeqDataSet and obtained raw results with p-values across all genes.
Use when when constructing a sample list from an Excel template for LC/GC-MS analysis, you must classify each QC sample by type before proceeding to plate layout and randomization…
Use when when your metabolomic network contains multiple edge types (Biochemical,
Use when you have multiple MS/MS spectra (replicates) for a single metabolic feature (same m/z and RT window) and need to identify which fragments are reproducibly detected across…
Use when when you have normalized peak intensity matrices from FT-ICR MS data or other high-resolution metabolomics experiments and need to visualize sample relationships and…
Use when you have a binary file (e.g., NV format) with a known fixed-size header block (e.
Use when after peak detection in GC-IMS preprocessing, when you need to group peaks across multiple samples and must decide whether euclidean distance is appropriate for your…
Use when after feature detection and peak alignment have produced a feature table with zero or missing values across samples.
Use when when validating a new or reimplemented quantification tool against a reference implementation on the same dataset and index, or when investigating whether changes to seed…
Use when when you have prediction scores (softmax probabilities, uncertainties) from a trained deep learning model evaluated on a heterogeneous dataset and you need to determine…
Use when designing multi-batch LC/GC-MS experiments where you need to control for batch effects (e.g., instrument drift, reagent lot variation) and have identified both a balance…
Use when after raw lipidomic and metabolomic data files have been generated by the Multi-ABLE method and loaded into the R environment, but before performing multivariate…
Use when when you have a Python package repository on GitHub and need to automatically verify that pull requests and commits pass unit tests and meet code quality standards before…
Use when you have paired scATAC-seq peak matrices and scRNA-seq gene expression matrices from the same cells (multiome data) and need to perform joint clustering, visualization,…
Use when when you have sampled the feasible flux solution space of constraint-based metabolic models (via optGpSampler or equivalent uniform sampling) and need to normalize flux…
Use when you have millions of MS/MS spectra represented as low-dimensional vectors (via feature hashing) and need to compute pairwise distances only between similar spectra rather…
Use when after generating probability predictions for potential modification sites (via ModiFinder.
Use when after generating or filtering transformation products using generateTPs() or filter(), when you need to annotate MS/MS spectra using MetFrag and require a database of…
Use when when you have generated embeddings for query and reference MS/MS spectra, computed a cosine similarity matrix between them, and need to evaluate how often the correct…
Use when when you have raw mass spectrometry imaging data (full m/z profiles with intensity arrays) and want to classify spatial regions (e.
Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .
Use when when you have raw LC-MS/MS data files in mzML, mzXML, or vendor-specific formats and need to load them into a Java-based mass spectrometry analysis framework for…
Use when you have draft metabolic reconstructions in SBML or standard format for multiple organisms in a microbial community (e.
Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of…
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 after feature detection and quality control have produced a feature table in TSV format from Asari or equivalent preprocessing.
Use when after differential peak analysis (tl.diff_test) has identified peaks that differ in accessibility across cell types or conditions.
Use when when you have a feature abundance table (rows=features, columns=samples)