Use when when you have completed spectral data preprocessing in Jupyter notebooks and generated a specXplore session data object saved to disk, use this skill to restore that…
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 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 MSMS spectra from two or more compounds and need to identify which are structurally related.
Use when after clustering single-cell ATAC-seq data (e.g., via Leiden clustering on spectral embeddings), use this skill to identify peaks within each cluster.
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 when comparing a query MS/MS spectrum (e.g., from an unknown metabolite) against a library spectrum to establish correspondence between peaks.
Use when you have raw LCMS data in mzML format and a feature table (CSV) from a peak detection pipeline (e.g., MZmine) and need to prepare these inputs for NeatMS preprocessing,…
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 when you have generated in silico annotations (from GNPS ISDB, SIRIUS, or timaR) and need to distinguish true matches from false positives by enforcing a mass accuracy…
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 when you have a raw GNPS or other spectral library dataset with inconsistent or incomplete instrument annotations, and you need to verify or reproduce reported dataset…
Use when you have a list of detected masses (m/z peaks) from MALDI-MS imaging data and want to systematically search for adduct relationships.
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 when you have raw LC/MS data in mzML format and need to execute the LAGF non-targeted screening pipeline.
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 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 preparing raw HPLC column parameter arrays for featurization into feature vectors for retention time prediction models.
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 deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may…
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 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 when you have paired mass spectra and molecular structure data and need to train a unified model for structure elucidation.
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 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 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 your project JSON document contains genome identifiers but lacks organism name or taxonomic annotations.
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 when a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification.
Use when after MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative…
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 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 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 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…
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 after merging methylation calls across all samples using unite() to create a methylBase object, apply this skill to characterize whether replicate samples cluster…
Use when before launching the DaDIA pipeline or any multi-package R workflow that has strict version constraints.
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 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 discovering Mass2Motifs via LDA on preprocessed MS/MS spectra, use this skill to assign putative substructure annotations by matching each motif's fragmentation…
Use when when you have calculated molecular descriptors from validated chemical structures and need to prepare them for BitterPredict.m classification.
Use when when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods.
Use when when you have a trained MS/MS spectral embedding model and need to measure compound identification accuracy on a held-out test set, but want to mitigate sensitivity to a…
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 you have computed a sparse pairwise distance matrix from nearest neighbor indexes and need to group spectra into clusters.
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 use this skill after khipu has assigned observed ions to grid positions (isotope and adduct combinations).
Use when after computing pairwise similarity scores between query molecular embeddings and a reference database, apply this skill when you need to distinguish high-confidence…
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 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 you have an ArchR project with clustered single-cell ATAC-seq cells and want to reconstruct developmental or cellular transition trajectories.
Use when you have compiled a multi-source EI library (NIST, RIKEN, MoNA, SWGDRUG) into a single msp object and want to enrich it with experimental retention index metadata.
Use when after fitting and optimizing a MB-PLS model on training data, apply this skill to the held-out test set (typically 10% of the original sample) to obtain unbiased…
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 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 you have raw LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites.
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 use this skill during pipeline installation or initialization when you need to locate required external binaries (e.g., bowtie2, samtools, R, Python) but the user has not…
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 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.