Use when when you have raw MS2 spectra (m/z and intensity pairs) and need to compute a Probability Product Kernel score or other fragmentation-based similarity metric against a…
Use when you have intracellular metabolomics abundance data (measured metabolite concentrations) from multiple biological replicates collected from two or more cell lines or…
Use when you have raw LC/MS data in mzML format and need to perform non-targeted
Use when you have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each genomic bin to…
Use when you have MS/MS fragmentation spectra (from Orbitrap or Q-TOF instruments) in MGF format with known precursor m/z, adduct type, and collision energy, and you need to…
Use when you need to systematically enumerate all possible lipid species within a defined analytical scope—specifically when you have specified one or more lipid classes (e.g.,…
Use when you have IM-MS lipidomics data with measured CCS values, samples spiked with U13C-labeled lipid internal standards (e.
Use when after installing a Python package (especially one with optional dependencies) to confirm that: (1) core modules are accessible and importable;
Use when when ingesting heterogeneous MS spectral data from multiple open-access libraries (OMS libraries) where metadata completeness and correctness are uncertain.
Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that exhibits isolated high-intensity noise artifacts or instrumental artifacts that appear as discrete,…
Use when when you need to verify a Python package installs successfully from a cloned or local repository, validate that all tests pass after installation, or prepare a…
Use when after mass track construction and before composite map building, when you need to align retention times across multiple LC-MS samples.
Use when you have a raw or preprocessed single-cell count matrix (from BAM-to-fragment or FASTQ-to-matrix pipelines) and need to apply matrix-free algorithms like tl.spectral,…
Use when you have a collection of molecular fingerprint vectors (such as biosynfoni count fingerprints) and need to measure structural similarity between all pairs of molecules.
Use when when preparing to create a release branch in a Maven-based multi-module
Use when after XCMS feature detection, grouping, and retention time correction when you have aligned features with consistent retention times and intensity patterns across samples.
Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically…
Use when after executing a MassQL query that returns a tabulated results DataFrame (e.g., MS1 or MS2 scan metadata, peak intensities, retention times), and you need to produce…
Use when you have a mass spectral library (EI or MS2 format) loaded into R via read_lib() and possess either MOL files (from Lib2NIST export) or an SDF file containing the…
Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
Use when when you have preprocessed MS/MS spectral data (normalized peak intensities and m/z values) and need to convert each spectrum into a learned molecular embedding — from…
Use when you have paired ChIP and control BED/BEDPE files and need to account for local sequencing bias before peak calling.
Use when after organism names have been cleaned and standardized (e.g., via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) but before final integration of organism, structure, and…
Use when when you have scored GCF-MF (gene cluster family–molecular family) links using two or more complementary scoring approaches (e.g., standardised strain correlation and…
Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that…
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 you have a set of small-molecule structures (SMILES, InChI, or SDF format) and need to predict their chromatographic retention times for a specific method, either to…
Use when you have a raw NV (NMRViewJ) binary file and need to confirm it is well-formed before parsing or processing.
Use when when you need to verify that a Java project's automated build pipeline (GitHub Actions workflow) executes without errors and generates distributable artifacts (e.g., .deb…
Use when after normalizing an MSI pixel array to TIC or an internal standard, when the raw pixel intensity distribution spans multiple orders of magnitude and produces images with…
Use when when implementing or reverse-engineering a custom binary file format (e.
Use when you have raw MS data files from one or more instrument vendors (Agilent, Bruker, Thermo Fisher, or mzML-formatted) and need to convert them to a vendor-agnostic…
Use when you have baseline-corrected and smoothed 2D-TIC chromatogram objects from individual GCxGC-MS samples that exhibit retention-time variations relative to a reference…
Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple…
Use when you need to compile and test a .NET-based metabolomics or bioinformatics
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 after nontargeted peak detection and segmentation has generated a feature table from raw LC-MS data (mzML or vendor format), apply quality assessment when you need to…
Use when after identifying statistically significant features within individual LC-MS assays (e.g., via MB-VIP and permutation testing), use this skill when you have multiple…
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 after a CNN model has generated predicted molecular embeddings from mass spectrometry data, use this skill to match those predictions against a curated reference — from…
Use when after correlation testing has validated putative parent–adduct ion pairs (e.g., via corrPairsMSI() on a massdiff object annotated with adductMatch results), use this…
Use when after running QC analysis on NMR or MS metabolomic data and obtaining per-feature CV values, use this skill to validate that the dataset meets FDA thresholds (CV < 0.30…
Use when you have MSMS spectra from two or more compounds and need to identify which are structurally related.
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 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 a Siamese neural network on MS/MS spectrum pairs, use this skill to quantify prediction performance on a disjoint test set (e.g., 3600+ spectra from 500…
Use when when you have paired mass spectra and molecular structure data and need to train a unified model for structure elucidation.
Use when when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes.
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 when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks.
Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints.
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 after merging methylation call files into a unified methylBase object (covering all samples at common base positions), apply this skill to assess whether biological…
Use when when you have detected m/z values from LC-IM-MS/MS that match a candidate CCS prediction database but require structural confirmation.
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 your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations.
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 centroided mzML files from LC-MS metabolomics and need to construct high-mass-resolution mass tracks for each sample before alignment.
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 computing a histogram of all pairwise mass differences from an MSI dataset, use this skill when you have observed mass difference peaks that may correspond to known…