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 computing pairwise similarity scores between query molecular embeddings and a reference database, apply this skill when you need to distinguish high-confidence…
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 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 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 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 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 when deploying a Nextflow workflow across multiple execution environments (local machines, HPC clusters) where tool versions, dependencies, or OS configurations may…
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 after curating and integrating structure-organism pairs from multiple source databases, and before publishing or using the dataset for computational research.
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 retrieving a molecular network file (GraphML or JSON format) from GNPS_GC following submission of deconvolved GC-MS spectra.
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 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 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 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 LC-MS peak intensity data with mass-to-charge ratios and need to match them to known metabolites.
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 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 converting peak-picker output (from MZmine, XCMS, MS-DIAL, or Compound Discoverer) into LipidMatch-compatible format.
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 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 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 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 raw SMILES strings collected from multiple external databases that require standardization and deduplication before integration into a unified chemical…
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 computing pairwise similarity scores across a collection of preprocessed mass spectra using matchms similarity measures (Cosine-related, molecular…
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 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 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 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 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 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 when preparing raw HPLC column parameter arrays for featurization into feature vectors for retention time prediction models.
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 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 when you need to generate synthetic metabolomics feature tables with quantified batch effects for validating batch-correction methods.
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 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 training or loading a pre-trained deep learning model that produces high-dimensional embeddings (e.g., 200-dimensional vectors from MS2DeepScore).
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 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 converting pre-processed MS/MS spectra into fixed-length vector representations using Word2Vec embeddings for Spec2Vec similarity scoring.
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 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 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 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 after computing expected accessibility from filtered peak and sample counts, and before computing final deviation scores.
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 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 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 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 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 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 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 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 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…
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 when receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline.