Use when after computing expected accessibility from filtered peak and sample counts, and before computing final deviation scores.
Use when after training a tandem mass spectrometry embedding model (such as MSBERT) on a reference spectral library (e.g., GNPS), apply this skill to confirm that the…
Use when you have one or more .msp spectral library files (NIST format) that need to be ingested for metadata curation, enrichment via web services, or export after…
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 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 you have obtained a Rust source repository (e.g., mzpeak_prototyping) and need to compile it into a working command-line converter tool or library.
Use when after running the annotateRC function on LC-MS All-ion fragmentation (AIF) features and obtaining a populated annotations object with ranked candidate matches, use this…
Use when after retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra.
Use when you have a feature list from LC-MS preprocessing (e.g., asari output) and have already identified all pairwise feature matches to isotope and adduct patterns.
Use when when you have a metabolite structure (SMILES or molecular graph) and need to predict its ionization behavior in a mass spectrometry experiment using a specific…
Use when you have raw mass spectrometry spectral data in common formats (MGF, MSP, mzML, mzXML, JSON) that requires standardized metadata cleaning, validation, and peak filtering…
Use when you have developed or adapted an analytical method (e.g., NPFimg for GC–MS marker identification) and need to demonstrate its reliability or improved performance over a…
Use when you have a set of ions detected in LC-MS data that are suspected to derive from the same neutral compound via different isotope and adduct patterns.
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 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 training or loading a pre-trained deep learning model that produces high-dimensional embeddings (e.g., 200-dimensional vectors from MS2DeepScore).
Use when after running TOBIAS ATACorrect to generate bias-corrected signal tracks from aligned ATAC-seq reads. Use this skill when you have corrected cutsite signal (as .
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 computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular…
Use when when you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before…
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 you need to deploy a containerized web application (such as MetFrag webapp on Tomcat) and make it accessible at a specific HTTP endpoint on the host machine.
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 after identifying differentially methylated bases (q-value < 0.01, methylation difference > 25%) using calculateDiffMeth(), use this skill to determine what fraction of…
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 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 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 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 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 when you have molecular input data (SMILES strings or graph representations) and need to predict molecular properties or spectra using graph neural networks.
Use when after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format.
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 organism name cleaning and standardization (via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) has produced a cleaned organism table…
Use when when you have raw SMILES strings collected from multiple external databases that require standardization and deduplication before integration into a unified chemical…
Use when you have MS/MS spectra with assigned precursor formulas and need to annotate the chemical composition of individual fragment peaks for metabolite structure elucidation or…
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 you need to containerize a C# application (e.g., AirdPro) that targets .NET Framework 4.8 and must run on Linux hosts via Docker, but the application was originally built…
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 running DESeq() on a DESeqDataSet and extracting results with results(dds), you have a results table with log₂ fold changes, p-values, and adjusted p-values (padj).
Use when after computing link scores (e.g., strain correlation, IOKR, or combined scores) across GCF-MF pairs, use this skill to assess whether scores achieve sufficient…
Use when when you have raw HPLC column specifications from RepoRT or similar metadata repositories and need to prepare them as input features for machine learning models.
Use when when a preprocessed metabolomic feature table (e.g., MS-Dial output) retains features and samples that passed filtering for missingness thresholds and m/z validity, but…
Use when after running formula inference on a benchmark dataset with known formula and adduct ground truth (e.g., NPLIB1, NIST20, or CASMI 2022).
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 when converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring.
Use when after fitting a Gaussian Process regression model to prior LC-MS gradient evaluations (where gradients are encoded as input and separation efficiency is output) — from…
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 when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection.
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 after generating ChIP pileup and local lambda (background) BEDGRAPH tracks with matched sequencing depth, use this skill to assign statistical significance scores to each…