Use when when you have trained multiple regression models (e.g., using different feature sets: descriptors-only, fingerprints-only, or combined) on the same training data and need…
Use when when you have processed LC-MS/MS spectral data in .mgf format with feature identifiers and need to compute a pairwise similarity matrix to support interactive exploration.
Use when you have a filtered FT-ICR MS peak list (m/z values and assigned molecular formulas per sample) and wish to reconstruct biochemical transformation networks ab initio to…
Use when your goal is to assess whether a pretrained NMR2Struct model trained on molecules ≤19 heavy atoms can generalize to larger, more complex molecules, or whether accuracy…
Use when after performing an ANOVA-style multi-group de_design() analysis on a LipidomicsExperiment object, when you need to determine whether a categorical sample variable (e.g.,…
Use when after theoretical spectra have been generated for lipid–adduct combinations with enumerated fragment masses and intensities, and you need to deploy them for downstream…
Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
Use when you have tandem MS/MS spectra annotated by at least two of GNPS (FBMN), ISDB-LOTUS (CFM-ID 4.0 spectral matching), and Sirius 6, and you need to rank features by…
Use when you have a trained neural network model and a labelled validation dataset (with high-quality and low-quality peak annotations), and you need to determine the optimal…
Use when after community-dependent gap-filling has proposed reactions to fill metabolic gaps in individual consensus reconstructions.
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 annotating matrix-related signals in MSI datasets where chemical formulas or spatial distributions alone are ambiguous, or when multiple ions share nominal m/z values…
Use when you have nuclear magnetic resonance (NMR) peak data (1H and 13C measurements) that you need to classify using a deployed SMART 3 model, and you want to submit peaks…
Use when you have untargeted metabolomics peak intensity data and spectral groupings (Molecular Families or Mass2Motifs) but lack confident chemical annotations or want to avoid…
Use when when preparing heterogeneous column-metadata inputs for a graph transformer model that operates on molecular graphs.
Use when you have 1D ¹H and/or ¹³C NMR spectra (as preprocessed numerical arrays or peak lists) from an unknown organic molecule with ≤19 heavy atoms, and you need to recover its…
Use when you have a coordinate-sorted BAM file from a single-cell ATAC-seq experiment (especially 10X Genomics platforms) and need to extract per-fragment information including…
Use when after applying biotransformation rules to generate candidate product structures from input molecules, when the same transformed structure can be produced via multiple…
Use when you have cloned a bioinformatics repository (e.g., FredHutch/SEACR) and need to confirm that its shell and R scripts are executable and will run successfully on your…
Use when you have proton (1H) and carbon-13 (13C) NMR peak measurements from a molecular sample and need to classify the molecule using the SMART 3 deep learning API.
Use when when you have trained a regression model on experimental retention times or similar continuous molecular property predictions and need to quantify its generalization…
Use when after normalization of a metabolomic feature matrix but before statistical testing, when you have both QC (technical replicate) and non-QC (study) samples and need to…
Use when you have translated or raw SMILES strings from a chemical structure curation pipeline and need to remove invalid chemical structures, resolve sanitization errors (e.
Use when you have paired ChIP and control BED/BEDPE files and need to account for local sequencing bias before peak calling.
Use when you have a collection of MS/MS spectra (≥2 spectra) and wish to identify fragmentation signatures common to subsets of those spectra.
Use when when you have a preprocessed sample chromatogram (smoothed and baseline-corrected) and a preprocessed reference chromatogram, and need to align them using 2D COW.
Use when you have Nightingale Health 1H-NMR metabolomics data (feature matrix with named metabolite columns) and need to compute predicted metabolic age for each sample, typically…
Use when you have trained predictive models (e.g., MiMeNet neural networks) on microbiome-metabolome paired data using k-fold cross-validation, held out test folds for each…
Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract…
Use when when you have known metabolite concentrations and their spin-system coupling constants (J-values) and need to generate synthetic ¹H NMR spectra for method validation,…
Use when your peak intensity matrix exhibits batch-to-batch variation (retention time drift, signal intensity fluctuation across injection sequences), you have QC samples injected…
Use when after training a transformer-encoder-based mass spectrometry embedding model (e.
Use when your metabolomics experiment includes samples acquired across multiple instrument runs, different preparation dates, or distinct sample cohorts.
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 you have applied two different clustering or dendrogram-flattening methods (e.g., constant-threshold vs.
Use when you have UPLC-HRMS data from ThermoFisher, Agilent, or other vendor instruments (converted via MSConvert if needed), organized as batch-processed files ready for…
Use when you have a metabolomics dataset and want to perform pathway enrichment analysis using ORA, but need to first understand its behavior, limitations, and correct application…
Use when when you have generated a set of predicted metabolite structures from BioTransformer's metabolism prediction engine and need to assign identity to observed compounds from…
Use when you have a normalized peak-abundance matrix from FT-ICR MS data (peaks as rows, samples as columns) and need to compare the number and diversity of detected molecular…
Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation…
Use when you have a tandem mass spectrum (MSMS) loaded via USI and wish to maximize the interpretability of observed peaks.
Use when you have a two-dimensional MS map (m/z vs retention time) from GC–MS or LC–MS data and need to discriminate analytes and identify marker features without false positives…
Use when when you have experimental MS/MS spectra and want to discover structurally similar compounds beyond exact spectral library matches—particularly useful for identifying…
Use when you have a raw LC–MS compound metadata file (xlsx or csv) with heterogeneous column names and column order, and you need to prepare it for targeted peak detection in…
Use when when you have obtained a raw Orbitrap mass spectrometry file and need to verify that the instrument was configured as claimed in the methods section or dataset…
Use when you need to generate synthetic LC/GC-MS feature tables or raw mzML files with realistic peak complexity, ion multiplicities, and natural spectral variation—not just…
Use when when you have raw IM-MS data from drift tube (DT) or SLIM instruments in Agilent MassHunter (.
Use when you need to create a synthetic chemical population for testing data-dependent acquisition (DDA) strategies in a simulation environment before committing to real mass…
Use when you have a curated training dataset of molecular structures with known CCS values, a target set of ≤10,000 molecules requiring CCS predictions, and need to apply a…
Use when you have custom lipid entries (e.g., synthetic lipids, rare natural variants, or isotopically labeled standards) not covered by LipidMatch's default in-silico library,…
Use when after mass track construction and before composite map building, when you need to align retention times across multiple LC-MS samples.
Use when you have IC-FTMS measurement records in JSON format with multiple samples per metabolite assignment and you need to verify that a matrix directive with…
Use when when you have constructed a two-layer metabolite annotation network (knowledge-driven and data-driven) and need to propagate initial seed annotations (e.
Use when you have a set of conformers that have already been filtered by ASE-ANI neural network potentials and need to extract quantum-mechanical electronic properties…
Use when you have a fitted alignment model (e.g., metabCombiner object with pre-aligned feature pair candidates and RT spline mapping) and known shared compound identities (ground…
Use when when you have deployed NP Classifier using Docker Compose and need to confirm that both the server and TensorFlow Serving containers are running and healthy before…
Use when after raw GC-MS CSV input has been parsed into separate matrices (Component.RT, Base.Peak.MZ, Compound.Name, Match.Factor, Component.Area) and you need to enrich…
Use when after XCMS feature detection, grouping, retention time correction, regrouping, and missing value filling on LC-MS or GC-MS data, when you have an aligned feature table…
Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
Use when after extracting raw MS/MS spectra from mzML files but before consensus spectrum generation, when you observe high-resolution fragment lists where nearby peaks (within a…