Use when you have extracted ion chromatogram (EIC) candidate data from untargeted LC/HRMS files (mzXML, mzML, or netCDF format) and need to identify genuine peaks within each EIC.
Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for…
Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak…
Use when after loading an MS-DIAL feature table when you need to separate features into two disjoint groups: one meeting a quantitative threshold (e.g., m/z decimal values outside…
Use when you have a pre-trained Keras model and need to deploy it via a Docker-based TensorFlow Serving API (e.g., for molecular classification via SMILES), but the model's layer…
Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1…
Use when you have extracted a centroided MS/MS spectrum from a Thermo Orbitrap raw file (via rawrr::readSpectrum or equivalent) and need to verify that the observed y-ion…
Use when when ingesting or updating MassBank records in plain-text or structured format, and you need to verify that metadata fields (accession, name, formula, mass, spectrum…
Use when you have extracted parallel feature streams from a CNN backbone (local spectral patterns) and a Transformer backbone (global dependencies) in 1H NMR spectra, and you need…
Use when you have a methylBase object containing aligned methylation calls across multiple samples and need to verify whether samples cluster by expected experimental condition…
Use when after BGC detection and clustering (producing GCFs) and metabolomics profiling (producing MFs with MS/MS spectra), when you have paired genomic and metabolomic data from…
Use when when you have a trained GNN model for molecular property prediction (e.g., collision cross section) and need to identify which graph structural features—atomic…
Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association…
Use when when you have peak area tables (unlabeled C12 and labeled C13) from LC-MS metabolomics with sample metadata indicating case and control groups, and you need to…
Use when you have multiple CDF files containing mass spectrometry imaging data (spectra, m/z arrays, and spatial coordinates) that need to be ingested into MATLAB for the DIMPLE…
Use when you have a collection of preprocessed tandem mass spectra (binned into 10,000 equally-sized m/z bins, intensities square-root transformed, top 1,000 peaks retained), a…
Use when when you have replicate MS/MS spectra for the same feature (precursor m/z and retention time) and need to distinguish genuine fragment ions from noise.
Use when when processing a metabolomics feature table through multiple sequential transformations (e.g., imputation, normalization, batch correction, annotation) and you need to…
Use when after quantifying ion images in LipidQMap and before exporting to HDF5 format, when you need to organize per-feature metadata (lipid ID, class, adduct, m/z, internal…
Use when after data merging and cleanup (blank removal) and before univariate or multivariate statistical analysis, when your merged feature table (samples as columns, metabolite…
Use when you have a collection of tandem mass spectrometry spectra in mzML or similar format and need to prepare them for LDA-based motif discovery.
Use when you have loaded a collection of molecular fingerprint vectors (e.g., from biosynfoni fingerprints deposited in Zenodo) and need to assess their statistical properties…
Use when when you need to assess whether retention times measured on a given LC-MS run follow the expected linear relationship defined by iRT peptide standards (e.g., Pierce or…
Use when you have raw or minimally processed tandem MS spectra (in mzML, mgf, or other standard formats) and need to prepare them for spectral matching, library searching, or…
Use when after completing feature annotation with the annotateRC function on LC–MS All-ion fragmentation (AIF) datasets, when you need to persist ranked metabolite candidates,…
Use when when identifying landmark peaks for retention time alignment in multi-sample LC-MS metabolomics workflows.
Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.
Use when you have a trained baseline GNN model with established hyperparameters (dropout rate, learning rate, epochs, optimizer settings) and want to evaluate whether alternative…
Use when you have raw or normalized single-cell RNA-seq expression data stored in an AnnData object (`.h5ad` format) and your analysis goal is to infer developmental or…
Use when you have two or more CSV feature tables from separate metabolomic experiments (each containing mass, retention time, intensity, isotope, and adduct columns), and you need…
Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
Use when you have one or more MS/MS query spectra (in mzML, mgf, msp, mzxml, json, or pickled matchms format) and a pre-built spectral library stored in SQLite with precomputed…
Use when when you need to assess whether a given ATAC-seq clustering method (or variant) is competitive on your data or when evaluating which published method to adopt.
Use when after acquiring MS/MS spectral data from untargeted metabolomics experiments and having candidate transformed structures from biotransformation rule application.
Use when you have raw FASTQ sequencing reads (single-end or paired-end) and a reference transcriptome FASTA file, and you need to determine which transcript(s) each read aligns to…
Use when when deploying a multi-component research application (e.g., MAGMa's four subproject services) as containerized microservices that need to communicate…
Use when you have preprocessed mass spectrometry spectra (tokenized m/z and intensity pairs or feature matrices) and a trained deep learning model checkpoint, and you need to…
Use when you have a collection of tandem MS/MS samples (stored in MassIVE) with GNPS spectral library annotations (m/z, retention time, compound identity), and you want to explore…
Use when you are evaluating or selecting FT-ICR MS software for a specific metabolomics workflow and need to assess which tools support your required analytical dimensions (e.g.,…
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 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 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 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 when processing imzML/ibd Imaging Mass Spectrometry datasets and you need to extract ion density maps for specific analytes or isotopes.
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 curating and integrating structure-organism pairs from multiple source databases, and before publishing or using the dataset for computational research.
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 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 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 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 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 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 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 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 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 receiving raw MS data files of unknown or mixed acquisition modalities and needing to route each to its corresponding analysis pipeline.
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 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 identifying candidate parent–adduct mass-difference pairs (via massdiff, histogram binning, and adductMatch), apply this skill to discriminate true molecular…
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…