Use when you have a Cardinal MSImagingExperiment object (e.g., from imzML or Analyze 7.5 files) and need to retrieve the complete set of m/z values and their intensities for…
Use when after quantifying the same read set with two versions of a mapping/quantification tool (e.g., C++ salmon 1.11.
Use when you have loaded a raw GCIMS dataset and need to isolate the region of interest in drift time (typically 5–16 ms for small organic molecules) to exclude low-drift-time…
Use when when you need to establish a reproducible inventory of compounds for LC-MS/MS simulation studies, particularly to determine how many unique molecular formulas fall within…
Use when you have extracted a large feature set of m/z values (hundreds to tens of thousands) from a Cardinal MSImagingExperiment object or similar MS dataset and need to assign…
Use when after sample alignment step in untargeted LC-MS workflows, particularly when processing multi-sample cohorts with QC samples interspersed throughout the sequence.
Use when you have transcript-level abundance estimates and inferred counts from salmon/kallisto/Sailfish (with or without Gibbs/bootstrap replicates) that must be summarized to…
Use when your raw TOF-MS data (Agilent MassHunter .d format) exhibits jagged, artifact-prone peaks in low-abundance ions that compromise peak quality assessment or when you need…
Use when you have mzML mass spectrometry files that need both compression and rapid random access by spectrum ID (e.g., direct retrieval of spectrum 2540 without sequential…
Use when your LC-MS peak table from MS-DIAL or similar software contains data from multiple ionization modes (positive and/or negative) and/or multiple chromatographic columns (e.
Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or…
Use when when you have raw mass spectrometry spectral data in JSON format from open mass spectra libraries (OMSLs) or other sources and need to validate structural completeness,…
Use when you have generated one or more MemoMatrix objects (MS2 fingerprint matrices from separate sample sets) and need to combine them for cross-cohort alignment, validate…
Use when a Shiny application or similar cross-platform tool is restricted to a single operating system (e.
Use when you have an experimental MS/MS spectrum (e.g., from MassBank or local data) and need to identify significant fragment ions above noise, assign occurrence scores to peaks,…
Use when you have a trained predictor (like BitterPredict) that accepts structured descriptors and want to understand feature importance without retraining.
Use when when deploying a complex bioinformatics pipeline (like HiC-Pro) across heterogeneous computing environments where required tools (bowtie2, samtools, R, Python) may be…
Use when you observe discrepancies in mapping rate or per-transcript quantification between two salmon implementations, or when the default chain-pruning thresholds…
Use when when you have IM-MS lipidomics data spiked with U13C labeled lipid internal standards (e.g., fully labeled yeast extract) and want to assess whether measured CCS values…
Use when you have developed a new machine learning model for predicting metabolomic profiles from microbiome data and need to quantify its performance improvement over existing…
Use when after running tardisPeaks() in screening mode or peak detection mode, when you need to visually confirm that target compounds are visible in the expected m/z and…
Use when you have a filtered peak list (CSV with m/z values and assigned molecular formulas) from FT-ICR MS and want to infer biochemical transformations occurring in microbial or…
Use when when you have pre-computed spectral embeddings (vectors) for both query spectra and a reference library, and you need to measure retrieval performance by ranking…
Use when xCMS has produced aligned LC-MS features but alignment quality is suspected to be poor—especially when analyzing hundreds of samples, data acquired over extended periods…
Use when after running annotateRC on LC–MS AIF data when you need to inspect whether a feature has multiple plausible annotations (e.g., isobaric lipids, isomers with the same…
Use when after running MetaboAnnotatoR's annotateRC function when you need to (1) verify that the top-ranked annotation for a feature is correct, (2) understand what alternative…
Use when you have tandem mass spectra data and need to predict a discrete molecular property (e.g., presence/absence of a sulfo group) while maintaining full interpretability of…
Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
Use when you have two or more feature tables in HDF5 format with detected features characterized by m/z, drift time, retention time, and intensity, and you need to match…
Use when after fitting a polynomial calibration model to tunemix reference data in DEIMoS, assess whether the model explains sufficient variance in the m/z–drift-time–CCS…
Use when you have a preprocessed LC-MS peak table exported from peak-picking software (e.g., MS-DIAL) in Excel format with three logical compartments: sample annotation (rows),…
Use when you have a normalized gene expression matrix (log2-quantile normalized, filtered to high-variance genes) and a collection of annotated gene sets (e.g., Reactome, MSigDB…
Use when when you have Thermo Fisher Scientific .raw files from an Orbitrap instrument and need to identify the m/z value and corresponding intensity of the most abundant ion in…
Use when after generating a Chemical Feature Tree from q2-qemistree (or any tree artifact) and before using it for alpha-diversity or beta-diversity phylogenetic analyses.
Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you…
Use when you have experimental MS/MS spectra from nontargeted metabolomics data and need to assign molecular identities or identify structurally related analogs.
Use when when implementing an igzip parser, decoder, or validator that must interpret the custom header format; when debugging igzip file corruption or encoding errors; or when…
Use when when you have aligned ChIP-Seq reads (BED or BEDPE format) and a corresponding control sample, and you need explicit control over peak-calling parameters—including…
Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.
Use when you have raw read count matrices from RNA-seq quantification (e.g., from featureCounts, HTSeq, Salmon, or kallisto) and need to prepare them for differential expression…
Use when your input is an AnnData object with expression matrix X as a sparse scipy matrix or Dask-backed array, and you need to apply preprocessing functions (normalization, PCA,…
Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo…
Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for eac — from…
Use when after drift correction and before imputation when you have LC-MS data with designated QC samples and you need to remove features with poor reproducibility across QC…
Use when after calculateDiffMeth() has been run on a methylBase object and you have a methylDiff object with q-values and methylation difference estimates.
Use when after initial retention-time-based feature grouping when you have groups of multiple features at similar m/z and retention time but need to determine which features…
Use when processing raw IM-MS data (Agilent MassHunter .d or UIMF format) that contains jagged, low-abundance ion peaks or when saturation repair has been applied and the…
Use when you have raw 1D NMR spectral data (urine, worm, or other biological samples) that needs to be converted into peak tables for metabolite identification and quantification.
Use when you have a Chemical Feature Tree artifact (phylogeny) output from q2-qemistree's make-hierarchy method and need to verify its structural validity, count nodes (leaves and…
Use when when your input includes molecular structures (SMILES, conformers) and you need to predict a continuous property (e.g., CCS, binding affinity, solubility) that depends on…
Use when after feature extraction (Asari) has produced a full feature table from mzML data, but before normalization and annotation.
Use when after elution peaks have been detected on composite mass tracks using local maxima and prominence detection, before reporting features in the final feature table — from…
Use when when comparing two or more MSMS spectra and you need to emphasize structural relationships revealed by neutral losses (mass differences between precursor and fragment…
Use when you have a normalized LC-MS/MS metabolite abundance matrix (e.g., from MS-DIAL preprocessing) with multiple samples across experimental groups (e.
Use when you have pre-processed MS/MS spectra and need to prepare them for word-embedding-based similarity methods (e.g., Spec2Vec).
Use when when preparing raw MS2 spectra (m/z and intensity pairs) for kernel-based scoring methods such as IOKR, especially when the training dataset is large and represents…
Use when xCMS alignment produces suspected misaligned feature groups across hundreds of samples or long acquisition runs (>1 week), particularly when global XCMS warping functions…
Use when you have computed raw strain correlation scores and IOKR scores for the same set of GCF–MF (gene cluster family–molecular feature) pairs, and you want to compare or…
Use when after running qc_summary() on a filtered mpactr object and aggregating ion counts by filter status category (passed/failed).
Use when when you have computed raw p-values for multiple independent statistical tests (e.g., Pearson correlation tests across all pairwise ion combinations in MSI data) and need…