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 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 when preparing raw HPLC column parameter arrays for featurization into feature vectors for retention time prediction models.
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 converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring.
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 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 receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline.
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 after converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format.
Use when when you have a query MS/MS spectrum (m/z and intensity pairs) and need to find potential structural analogues or exact matches in a large spectral library.
Use when you have raw mzML files from an FTICR-MS or other direct-injection MS instrument and need to identify discrete chromatographic peaks across the m/z and retention-time…
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 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 mass spectrometry spectral data in common formats (MGF, MSP, mzML, mzXML, JSON) that requires standardized metadata cleaning, validation, and peak filtering…
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 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 mass spectrometry data stored in mzPeak format (ZIP archive containing Parquet files) and need to read spectrum metadata, chromatogram metadata, and signal…
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 use this skill after performing Tn5 bias correction and footprint scoring on ATAC-seq BAM files when you need to inspect the spatial distribution of Tn5 insertions around…
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 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 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 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 LC-MS feature detection, alignment, and quantification are complete and you have a feature table with m/z and retention time attributes.
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 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 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 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 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 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 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 after organism name cleaning and standardization (via 1_cleaningOriginal.R and 4_cleaningTaxonomy.R) has produced a cleaned organism table…
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 training or loading a pre-trained deep learning model that produces high-dimensional embeddings (e.g., 200-dimensional vectors from MS2DeepScore).
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 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 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 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 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 an ArchR project with clustered single-cell ATAC-seq cells and want to reconstruct developmental or cellular transition trajectories.
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 after biclustering a normalized microbe-metabolite feature attribution score matrix into distinct functional modules, use this skill to summarize pairwise module…
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 you have multiple metabolomic studies with aggregate summary statistics (p-values, fold-change estimates) and need to perform meta-analysis while harmonizing compound…
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 training a FlavorFormer model end-to-end with weighted loss on 1H NMR spectra and compound labels, apply this skill to a held-out test set to measure compound…
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…
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 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 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 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 MS2LDA has inferred a motifset and you need to visualize and export the relationships between discovered Mass2Motifs for post-processing exploration, comparative…
Use when use this skill after khipu has assigned observed ions to grid positions (isotope and adduct combinations).
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 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 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 a parsed mwTab file (MS or NMR experimental data) must be assessed for conformance to its corresponding JSON schema specification.
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 virtual chemical mixture (MS1 peaks) and need to prototype a new DDA acquisition strategy before testing on real instrumentation.