Use when when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods.
Use when after running MetaMiner's Dereplicator stage to identify some RiPPs via direct database matching against a constructed structure database, apply this skill to enlarge the…
Use when after applying two or more LC-MS alignment algorithms (such as XCMS and ncGTW) to the same dataset, use this skill to determine which produces warping functions.
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 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 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 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 after retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra.
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 running DESeq() on a DESeqDataSet and obtaining initial results via results(), use this skill when you need to (1) extract base results tables for specific…
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 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 you have raw LC-HRMS metabolomics data in mzML or ABF format that needs to be processed through a reproducible pipeline.
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 after identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular…
Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification.
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 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 you have Thermo Orbitrap .raw files and need to extract specific spectral features (base-peak m/z, intensity values, chromatographic traces, scan-level metadata) for…
Use when when working with raw LC-HRMS profile-mode data containing noisy chromatographic signals, apply this skill before peak detection.
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 when you have MS/MS spectra from GNPS or other libraries and need to apply a pre-trained FIDDLE model (TCN formula predictor or Siamese rescore architecture) without…
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 after computing expected accessibility from filtered peak and sample counts, and before computing final deviation scores.
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 when you have raw SMILES strings collected from multiple external databases that require standardization and deduplication before integration into a unified chemical…
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 you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters.
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 you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites.
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 when you have mass spectrometry data stored in a database or non-mzML file format and need to integrate it into the pymzML pipeline without converting to mzML.
Use when after applying one or more mpactr filters (filter_mispicked_ions, filter_group, filter_cv, filter_insource_ions) to an mpactr object, use this skill when you nee — from…
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 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 computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular…
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 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 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 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 after concatenating replicate MS/MS spectra for each precursor feature (m/z and retention time), use this skill when you have multiple replicate scans per feature and…
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 when you have an observed m/z value from mass spectrometry imaging and need to annotate it with a ranked list of candidate chemical formulae.
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 after curating and integrating structure-organism pairs from multiple source databases, and before publishing or using the dataset for computational research.
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 after applying a filter function (filter_mispicked_ions(), filter_group(), filter_cv(), filter_insource_ions()) to an mpactr object, use this skill to inspect and…
Use when use this skill after building a Docker image that installs Wine and .NET Framework 4.8 on a Ubuntu 22.04 base, but before running production conversion tasks or batch…