Use when after loading an MSP spectral library file into memory using mssearchr's MSP parser, when you need to verify that each spectrum record contains complete and valid…
Use when after installing a package in development mode (e.g., via `pip install -e .[dev]`) to verify the package functions as intended, or before submitting pull requests to…
Use when you have a multi-cluster single-cell RNA-seq dataset with cell-type annotations and you want to test whether known biological pathways (e.g., KEGG or MSigDB gene sets)…
Use when you have raw or normalized microarray expression matrices stored in public repositories (GEO accessions) along with sample metadata, and you need to load both into R as…
Use when after recursive annotation propagation has assigned metabolite labels to previously unannotated nodes in a two-layer metabolomic network, and before reporting final…
Use when after EIC candidate generation and peak detection have been completed on LC/HRMS data, when you need to extract the retention time and intensity values at peak maxima for…
Use when you have a trained multitask model checkpoint and preprocessed spectral inputs (1D NMR spectra, 1H-only, 13C-only, or combined 1H+13C), and you need to generate…
Use when after training a GNN model on molecular structures with continuous targets (e.g., CCS values), when you need to understand which node-level (atom) or edge-level (bond)…
Use when after running an Environment simulation in ViMMS that has generated MS1 and/or MS/MS scans from a virtual mass spectrometer and controller pair.
Use when when you have mass spectrometry data stored in mzPeak format (ZIP archive containing Parquet files) and need to read spectrum metadata, chromatogram metadata, and signal…
Use when after a TCN-based formula prediction model has generated initial formula candidates from MS/MS spectra, apply this skill to rescore and refine those candidates when you…
Use when you have a cooler-format Hi-C contact matrix and need to identify TAD boundaries and insulation strength along the genome.
Use when you have an LC-MS peak-intensity matrix with observed m/z values (from negative or positive mode ionization) and need to map each peak to candidate neutral masses in…
Use when use this skill after XCMS feature detection and alignment on non-targeted LC-MS or GC-MS metabolomics data, when you have aligned features with quantitative profiles…
Use when you have a query electron ionization (EI) mass spectrum in msp format and wish to identify it by matching against a reference spectral library.
Use when after applying a sequence of mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an LC-MS/MS peak table in Progenesis or MS-DIAL…
Use when after loading a metadata file but before merging it with positive and negative mode m/z peaklists. Apply this skill when you have a candidate metadata table (e.
Use when when you have SMILES structures of small organic molecules and need to predict CCS values for metabolite annotation in untargeted mass spectrometry workflows.
Use when use this skill after khipu has assigned observed ions to grid positions (isotope and adduct combinations).
Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints.
Use when after generating a scan index from a Thermo Fisher Orbitrap raw file using readIndex(), apply this skill when your analysis goal requires working exclusively with MS1…
Use when after installing a package via conda or pip from a distribution channel (e.g., Bioconda, PyPI), run this skill to confirm the installation succeeded and that critical…
Use when when you have NMR peak assignments (1H and 13C chemical shift values) and need to submit them to the /api/smart3/search endpoint for automated structure classification.
Use when you have a gene expression matrix (RNA-seq counts, microarray intensities, or normalized expression values) and need to perform gene set enrichment analysis on preranked…
Use when you have completed peak picking with two or more competing tools (e.g., IDSL.IPA, MZmine 2, xcms, MS-DIAL) on the same LC/HRMS dataset(s) and need to quantify which…
Use when after LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes.
Use when you have processed the same GC–MS dataset (m/z vs retention time) through two independent signal acquisition pipelines and need to compute and compare their detection…
Use when when you need to confirm that a documented web service endpoint is deployed and accessible before using it for analysis, or when troubleshooting tool availability in a…
Use when when a user uploads a JSON project document to the Pairing Omics Data Platform, before accepting it into the repository or indexing it for search.
Use when when you have molecular structures (SMILES or graph formats) and need to predict a physicochemical or spectral property (e.g., infrared spectra) using a graph neural…
Use when after running fgsea() on a preranked gene list and obtaining a results table with raw pval, padj, ES, NES, and size columns, use this skill to: (1) subset results to top…
Use when after initial retention-time-based feature grouping (e.g., using SimilarRtimeParam with a 20-second window), apply this skill when you need to split large feature groups…
Use when after creating a GNPS mass spectral molecular network and running an MS2LDA experiment, use this skill when you want to identify and visualize which substructural motifs…
Use when when you need to verify that a GitHub Actions workflow (such as a development build or release pipeline) executes without fatal errors and produces expected artifacts.
Use when you have a virtual chemical mixture (MS1 peaks) and need to prototype a new DDA acquisition strategy before testing on real instrumentation.
Use when after molecular formula assignment has been performed on calibrated m/z values. Apply this skill when you need to quantify the accuracy of formula-to-peak matching,…
Use when when you have paired mass spectra and molecular structure data and need to train a unified model for structure elucidation.
Use when use this skill after training or fine-tuning a chemical formula transformer model on annotated tandem MS/MS spectra, when you need to measure whether the model's ranked…
Use when you have tandem mass spectra (MS/MS) with unknown precursor formulas and need to rank chemical formula candidates conditioned on observed fragment m/z values and…
Use when your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations.
Use when when you have raw LC/MS data in mzML format and need to execute the LAGF non-targeted screening pipeline.
Use when when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks.
Use when after annotating ion pairs with known adducts (using adductMatch or diffGetPeaks), use this skill to filter suspected adduct pairs by testing if their pixel-level…
Use when when you have computed similarity scores (e.g., MS2DeepScore, Spec2Vec, modified Cosine) between pairs of spectra or compounds and want to compare their ability to…
Use when you have MSMS spectra from two or more compounds and need to identify which are structurally related.
Use when you have a large, mixed-instrument GNPS spectral dataset and need to create an instrument-specific training set for FIDDLE or similar deep learning models.
Use when after parsing a centroid mzML file into (m/z, scan_number, intensity) tuples, when you need to organize sparse MS1 data for efficient peak detection and cross-sample…
Use when after training or loading a NeatMS neural network model, apply this skill when you have a labelled validation dataset and need to determine the optimal probability…
Use when when a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification.
Use when after invoking the DEIMoS CLI with a configuration file and allowing the Snakemake workflow to execute, use this skill to confirm successful completion of all workflow…
Use when when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection.
Use when after biclustering a normalized microbe-metabolite feature attribution score matrix into distinct functional modules, use this skill to summarize pairwise module…
Use when when you have raw MS/MS spectral data in the form of intensity arrays indexed by m/z values and need to feed them into the Spec2Mol encoder neural network.
Use when your input is an mzPeak archive (ZIP of Parquet files) and you need to recover spectrum signal data (m/z values and intensities) for downstream analysis, visualization,…
Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification.
Use when after extracting retention times from top MS1 features detected in an LC-MS run, and when you need to evaluate whether a given gradient time range (e.g., 0–30 minutes) is…
Use when after running DESeq2 differential expression analysis and extracting results with raw log fold changes, apply this skill when you observe high variance in effect size…
Use when after organism name cleaning and standardization (via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) has produced a cleaned organism table…
Use when when you have loaded MSI peak data with associated m/z values and need to disambiguate matrix ions from analyte ions.
Use when when you have molecular input data (SMILES strings or graph representations) and need to predict molecular properties or spectra using graph neural networks.