Use when after running the msfeast_pipeline notebook to generate dashboard_data.json
Use when you have preprocessed tandem mass spectrometry spectra converted into a bag-of-fragments representation (with fragments and neutral losses extracted and noise filtered)…
Use when when setting up a ViMMS chemical sampling environment and you need to restrict the chemical search space to a specific m/z range (e.g., 100–1000) and MS level (e.g., MS1…
Use when when you have a metabolomics dataset loaded into a SummarizedExperiment
Use when when you have loaded aligned peak-alignment data from a molecular networking task and need to distinguish high-confidence, reproducible peak alignments from noise or…
Use when you have model predictions and ground-truth labels for a test set and need to assess how well the trained model generalizes to unseen data.
Use when you have two or more mass spectral libraries in different formats (NIST binary exports converted to MSP, MoNA downloads, RIKEN public databases, GNPS MGF, or batches of…
Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable,…
Use when when you have downloaded fragment records from separate experimental and predicted online databases and need to verify that each fragment can be traced back to a valid…
Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) — from HolobiomicsLab/asb-skill-collections
Use when you need to understand how a data-processing software system discriminates among multiple input types (LC, GC, IMS, MALDI) and selectively instantiates processing…
Use when you have completed pathway analysis using multiple competing methods (e.g., PALS, ORA, GSEA) on a metabolomics peak intensity dataset and need to verify that ranking…
Use when when you need to verify or retrieve package-internal metadata about compiled .NET assembly location and version before processing raw mass spectrometry files, or when…
Use when when you have MS/MS spectra with known chemical structures (InChIKeys or SMILES) and want to validate whether a novel or existing spectral similarity scoring method…
Use when you have IM-MS measurements of samples spiked with U13C-labeled internal standards (e.g., fully labeled yeast extract) and need to assess whether measured CCS values…
Use when when you have LC-MS/MS data collected in DDA mode and suspect that MS/MS spectra contain chimeric (multiply-charged or co-fragmented) ion signals that will degrade…
Use when when you have a USI (Universal Spectrum Identifier) string referencing a spectrum in a public metabolomics repository (GNPS Molecular Networking, GNPS Spectral Libraries,…
Use when when setting up imzML Writer for the first time on a new machine, or when raw vendor mass spectrometry file conversion fails with ''msconvert not found'' or Docker image…
Use when you have a raw peak-intensity matrix from untargeted LC-MS data (organized as rows=peaks, columns=samples) and need to generate initial candidate metabolite assignments.
Use when you have located a workflow definition file (YAML or JSON) from a versioned release and need to confirm that all mandatory workflow metadata fields (name, version,…
Use when after training a NeatMS CNN model on labeled MS1 peaks and generating predictions on a held-out test set, compute ROC-AUC to assess whether the model achieves the target…
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 you have filtered ATAC-seq or DNAse-seq peak counts (after GC bias correction, sample filtering, and peak filtering) and wish to measure how strongly each annotation…
Use when you have a collection of annotated MS/MS spectra with precursor m/z values and fragment peak lists, and you aim to train or apply a spectral similarity model (such as…
Use when you have a Spectra object in R and need to apply a specialized Python MS algorithm (e.
Use when when you have preprocessed MS/MS spectra (normalized intensities, filtered for quality, with top peaks retained) that have been encoded using a spectral representation…
Use when you have paired predicted and observed metabolite abundance vectors from a predictive model (e.
Use when you have evaluated a parametric denoising strategy (e.g., frequency-based
Use when after completing feature m/z grouping and pairwise alignment detection on two LC-MS datasets acquired under non-identical conditions.
Use when you have grouped unique 2D chemical structures by organism prevalence and need to confirm that the counts in each frequency bin (singleton, low-diversity,…
Use when you have transcript-level quantification files (quant.sf.gz or quant.gz) from salmon, sailfish, kallisto, or oarfish and need to aggregate them into gene-level or…
Use when analyzing GC-MS data containing overlapping chromatographic peaks—a common scenario in untargeted metabolomics and environmental screening where sample complexity or…
Use when when a tool claims to be 'scalable' or 'performance-conscious' but lacks published performance benchmarks, or when you need to confirm that runtime and memory scale…
Use when you have sparse, single-cell or bulk ATAC/DNAse-seq data from multiple cell types or conditions (e.g., GM vs H1 cell lines), pre-filtered and GC-bias-corrected, with…
Use when after constructing a background set for ORA in metabolomics: you have loaded an experimental detection list and a metabolomics pathway database, applied background-set…
Use when after deploying a TensorFlow-backed classification service, you need to verify that the model's input layer names ('input_2048' and 'input_4096') and output layer name…
Use when you have raw lipidomic and metabolomic data files generated by the Multi-ABLE method (high-pressure liquid chromatography–mass spectrometry output) and need to p — from…
Use when when you have generated or extracted a chemical mixture (via DatabaseFormulaSampler, ChemicalMixtureCreator, or ChemicalMixtureFromMZML) and need to establish a virtual…
Use when you have transcript-level quantification files (salmon quant.sf.gz, kallisto, or Sailfish output) and need to perform gene-level differential expression analysis — from…
Use when after LDA-based Mass2Motif discovery has generated a set of recurring fragmentation patterns (motifset_optimized.
Use when you have acquired raw mass spectrometry data from ThermoFisher, Agilent, or compatible vendors in their native formats (.raw, .d, or equivalent) and need to prepare it…
Use when when you need to extract both local spatial patterns and global long-range dependencies from sequential or spectral data (e.g., 1H NMR spectra), and neither CNNs nor…
Use when you have raw MS data files in vendor-native format (.raw, .d, .ms) from CE-MS or LC-MS instruments and need to process them through AriumMS or other open-source…
Use when after RDKit generates multiple 3D conformers from ionized molecular structures using distance-geometry embedding, before filtering with ASE-ANI or submitting to quantum…
Use when you have 512-dimensional representation vectors output from paired ResNet18 encoders processing augmented ion images, and you need to: (1) introduce an intermediate…
Use when you are parsing mass spectrometry spectral library files in MSP format and need to guarantee that all spectrum records are either successfully integrated into the final…
Use when when you have simulated DDA (data-dependent acquisition) scans from a ViMMS Environment and need to (1) quantify how well the simulated acquisition matched real or…
Use when you have paired spectrum-compound reference data and need to simultaneously retrieve candidate compounds rapidly (bi-encoder) while also refining relevance scores through…
Use when you are repeatedly querying or iterating over multidimensional MS data stored in MZA HDF5 format (retention time, drift time, m/z dimensions) and profiling shows that…
Use when when you have generated spectral embeddings for a query set and a reference spectral library, computed pairwise cosine similarity scores between them, and need to…
Use when you need to containerize a C#-based Windows application (like AirdPro CLI) for Linux deployment, require Wine and .NET Framework 4.
Use when when you have a validated ReDU sample-information metadata file (gnps_metadata.
Use when you have cloned a scientific Python project (e.g., scverse/scanpy) and need to verify that your local development environment matches the CI specification before…
Use when after executing memo_from_unaligned or memo_from_aligned functions to generate a MemoMatrix object from MS2 spectra or aligned feature tables.
Use when after running inference on a trained structure prediction model with one or more input modalities (1H NMR, 13C NMR, or combined), you have generated predicted molecular…
Use when you need to set up a local copy of a scientific software project (e.g., Scanpy) to run its test suite, modify source code, or prepare a feature or bugfix contribution.
Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple…
Use when you have raw MS imaging data in imzML (continuous or processed) or Analyze 7.5 format and need to load it into R for spectral processing, normalization, peak-picking, or…
Use when when working with raw or filtered MsmsSpectrum objects where peak intensities span a wide dynamic range and need to be normalized for downstream spectrum comparison,…
Use when you have a GNPS-generated molecular network (either classical or feature-based) and corresponding MS2LDA experiment output containing Mass2Motif-to-spectrum assignments,…