Use when you have loaded raw MS intensity tables into QuantyFey and observe or suspect intensity drift artifacts across your measurement sequence.
Use when when preparing SMILES strings as training targets for a sequence-to-sequence
Use when you have large spectral libraries (thousands to millions of spectra) and need to search query spectra against them for peptide identification with tolerance for…
Use when when you have a USI string (e.g., mzspec:GNPS:TASK-d93bdbb5cdda40e48975e6e18a45c3ce-f.mwang87/data/Yao_Streptomyces/roseosporus/0518_s_BuOH.
Use when after cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data.
Use when you have filtered peak counts from ATAC or DNase-seq data (with GC bias correction and sample/peak filtering applied) and want to annotate peaks by k-mer content rather…
Use when you have a compressed mzML file (mzML.gz or indexed gzip format) and need to extract a single spectrum or a small subset of spectra by their known numeric identifiers,…
Use when you have generated PSI matrices for alternative splicing events or transcripts across two or more biological conditions using SUPPA's psiPerEvent or psiPerIsoform…
Use when you have molecular structures (SMILES or SDF format) for which you need to predict retention time in liquid chromatography, especially when your target dataset contains…
Use when when you have preprocessed 1H NMR spectral data from flavor mixtures or similar compound identification tasks, and you need to identify which compounds are present.
Use when you have ATAC-seq BAM files and want to detect transcription factor footprints—characteristic depletion patterns of Tn5 insertions around protein-bound motif sites.
Use when a Shiny application or R package currently runs only on Windows and you need to enable deployment on Linux or macOS.
Use when you have centroided high-resolution Orbitrap or GC-CI-MS mzML files and a formulaTable of target compounds with known m/z, retention time, and molecular formula, and you…
Use when after computing InChIKey and neighbourhood scores for library match candidates, you need to write results to a persistent format (CSV, JSON, or database) for storage,…
Use when you have raw LC/MS data in mzML format and your analysis goal is to comprehensively detect and annotate all mass spectral features present, rather than measuring…
Use when you have LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and corresponding genomic sequence data (raw FASTA nucleotide sequences or genome mining tool…
Use when you have extracted MS1 and MS2 scans (in mzML/mzXML format) from raw chromatogram files and possess user-provided metadata (retention time, m/z, compound name, m — from…
Use when you have a Python webservice codebase (e.g., a Flask, Django, or FastAPI application) and need to document its HTTP API surface (endpoints, methods, parameters, schemas,…
Use when you are preparing to apply Probability Product Kernel–based scoring to MS2 spectra for genomic–metabolomic linking, and you need to establish a reference set of ion peaks…
Use when after anchor selection and RT mapping spline construction, when you have a fitted metabCombiner object with pre-aligned feature pair candidates and need to tune the…
Use when when beginning an untargeted LC-MS annotation workflow, before attempting to match experimental m/z peaks to metabolite identities.
Use when you have raw or preprocessed mass spectrometry feature matrices (e.g., from low mass resolution or sparse acquisition) and want to enhance signal quality and spatial…
Use when you are extending the MsBackend virtual class to create a new backend for storing MS spectra data and need to define the internal data structure.
Use when when comparing large numbers of MS/MS spectra against spectral libraries or in molecular networking, particularly when molecules differ by multiple structural…
Use when you have chemical entity records scattered across two or more public repositories (e.g., HMDB, ChEMBL, PubChem, KEGG) and need a single authoritative, deduplicated…
Use when when you have submitted the same MS/MS spectrum query to multiple domain-specific MASST tools and need to compare matches, combine ranked results, or generate…
Use when after instantiating a specXplore dashboard session layer with a loaded session data object from disk, before conducting visual exploration of LC-MS/MS spectral data.
Use when after ModiFinder has generated modification site probability scores for an unknown compound by comparing its MS/MS spectrum to a known analog, and you have access to the…
Use when you are implementing a new MsBackend subclass and need to store spectra metadata (sample names, retention times, precursor m/z, etc.) separately from peak data (m/z and…
Use when when a statistical method offers a parameter to trade computational cost for precision (e.
Use when when you have an unknown metabolite's predicted structural similarity scores (from a deep learning model such as DeepMASS) against all known metabolites in a reference…
Use when you have SMILES strings or 2D molecular structures of N-Me derived unsaturated sterol lipids (or other C=C-containing molecules) and need to generate 3D conformational…
Use when you have a mass spectral library in MSP format (e.g., from NIST, SWGDRUG, or other sources) exported alongside a folder of MOL files, and you need to populate the SMILES…
Use when immediately after loading a raw GC-MS CSV file and before executing the spreadOut() function. Use it when you have received peak table data from an instrument vendor (e.
Use when after constructing a metabCombiner object by grouping features from two metabData objects by m/z, and before proceeding to anchor selection, RT mapping, or alignment…
Use when when Rapid QC-MS receives vendor-format LC-MS acquisition files from instrument data folders and must prepare them for automated QC checks and MS-DIAL processing.
Use when after calculating differential methylation across samples using calculateDiffMeth(), when you need to separately enumerate and extract hyper-methylated (increased…
Use when after isotope correction when you have extracted intensity matrices from imzML or HDF5 MSI data and need to convert raw or isotope-corrected ion-image intensities into…
Use when when converting simulated or real LC/GC-MS spectral data (m/z–retention-time
Use when you have an untargeted metabolomics feature table (m/z and retention time columns) and a statistical test result (p-value) per feature, but lack confident metabolite…
Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train an interpretable model (e. — from HolobiomicsLab/asb-skill-collections
Use when you have TWIM-MS experimental data with assigned biomolecular class labels (e.g., peptides, lipids, carbohydrates) and arrival time measurements, and you need to compute…
Use when after creating a methylRawListDB object via methRead() with dbtype='tabix', or when loading pre-existing tabix-backed methylation files, to verify that bgzipped files are…
Use when after completing a multi-stage Docker build targeting a compiled runtime environment (e.g., airdpro:cli produced from a Wine + .NET Framework 4.8 + Ubuntu 22.
Use when you have a working base MPNN model (e.g., chemprop) and need to add task-specific feature processing layers (spectral, electronic, or domain features) to improve…
Use when your peak table includes features flagged in blank control samples (e.g., solvent blanks, media blanks) at relative abundance above a project-specific threshold.
Use when you have a feature table with candidate metabolite annotations (m/z, retention time, chemical identifiers) from MS/MS spectra or external tools (SIRIUS, GNPS), sample…
Use when you have a collection of molecular structures (with SMILES strings, InChI, or similar identifiers) and corresponding experimentally determined or reference CCS values,…
Use when after running do.findmain on a RAMClustR-clustered object to infer molecular weights and assign features to compound clusters, when you need to conduct structural…
Use when you have a published scientific article describing a computational method (e.g., natural products annotation, MS/MS data processing) and need to assess reproducibility…
Use when after XCMS feature detection, grouping, and retention time correction when you have aligned features with consistent retention times and intensity patterns across samples.
Use when you have a set of observed m/z values extracted from a Cardinal MSImagingExperiment object, raw LC-MS data, or similar high-throughput MS dataset, and you need to assign…
Use when after drift correction has been applied to your LC-MS peak table and you need to identify low-quality metabolic features that exhibit high internal spread (RSD, RSD*) or…
Use when a user uploads a JSON project file to the platform and you need to verify it matches the required format defined in app/public/schema.json before accepting it into the…
Use when when preparing metabolomics abundance tables with left-censored missingness (values below instrument detection limit or quantification limit) for imputation.
Use when you have RNA-seq read count data (from alignment tools, transcript quantification, or feature counting) organized in a count matrix with samples as columns and genes as…
Use when when you have IM-MS lipidomics data with measured CCS values from samples spiked with U13C labeled internal standards, and you need to assess systematic CCS bias or…
Use when you have mass spectrometry spectral data loaded into a Pandas DataFrame with columns representing m/z (mass-to-charge ratio) and intensity values, and you need to…
Use when when you have 1H-NMR metabolite measurements from Nightingale Health assayed on a new cohort and wish to compute risk scores (e.g., all-cause mortality, cardiovascular…
Use when when you have molecular input data available in two or more distinct formats (e.g., RDKit-extracted fingerprints AND torch_geometric Graph objects representing molecular…