Use when you have a trained NeatMS neural network model (.h5 format) and need to assess its classification performance at a specific decision threshold (e.g., 0.01) to de — from…
Use when you have co-registered IMC (protein imaging mass cytometry) and SIMS (secondary ion mass spectrometry for metabolites) data from the same tissue regions, cell…
Use when you have intensity measurements (peak features, protein intensities, or gene expression values) with compound or gene annotations (KEGG IDs, ChEBI IDs, UniProt IDs, or…
Use when when annotating large-scale untargeted metabolomics datasets where reference library coverage is incomplete and you need to infer metabolite identities for unannotated…
Use when when ingesting spectra from multiple open mass spectrometry libraries (OMSLs) in .mgf, .msp, .json, or .csv format and you observe mixed experimental protocols,…
Use when you have a pretrained TCN spectrum encoder from formula prediction and need to train a rescoring model that ranks formula candidates by confidence.
Use when when performing transcript- or gene-level differential expression analysis and your quantification tool (Salmon, Sailfish, or kallisto) has produced Gibbs sample or…
Use when after simulating and convolving individual metabolite multiplets with realistic lineshapes (Lorentzian or Gaussian) and combining them into a single time-domain FID array.
Use when when you have log-transformed metabolite abundance data from multiple batches (e.
Use when after applying a quantitative analysis function (e.g., cooltools.insulation, contact frequency calculations) to Hi-C cooler files or other genomic datasets, validate that…
Use when you have completed one or more LC-MS gradient runs, extracted separation efficiency metrics from the resulting MS1 and MS2 spectra, and need to incorporate those real…
Use when after calling squidpy.gr.spatial_neighbors or any graph-building operation that outputs sparse matrices to adata.
Use when you have MS/MS spectra with fragment frequency annotations (from consensus spectrum generation) and need to decide which fragments to retain versus remove.
Use when when processing raw CE-MS data and need to establish a baseline migration time scale before transforming to effective mobility.
Use when when you have raw LC-HRMS metabolomics data in .mzML or .abf format and need to perform untargeted feature detection with chromatographic alignment across multiple…
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 when performing m/z domain calibration on FT-ICR or high-resolution MS data and the initial calibration attempt finds fewer than 5 reference m/z matches within the…
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 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 when you have deposited a collection of JSON project documents in a platform and need to verify that all conform to the published schema before public release or — from…
Use when you have identified one or more proton NMR spectral regions-of-interest
Use when when a project README or documentation embeds badge endpoints that report real-time status (e.g., Travis CI build, Landscape.
Use when when you have a retention-time dataset (e.g., SMRT or Eawag_XBridgeC18_364)
Use when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzXML, mzML, or mzData format) and genomic data from a target organism, and you want to identify RiPPs by…
Use when you have extracted latent low-dimensional peak features from imaging mass spectrometry (IMS) data using a graph-attention autoencoder and need to identify a ranked subset…
Use when after you have (1) corrected ATAC-seq BAM files for Tn5 insertion bias using ATACorrect, (2) computed per-base footprint scores using ScoreBigwig, (3) obtained a motif…
Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each…
Use when you have imaging mass spectrometry data from spatial metabolomics experiments and need to reduce the high-dimensional peak space to a ranked set of marker ions for…
Use when when you need to validate that a .NET assembly (such as ThermoFisher.CommonCore.RawFileReader) is correctly installed and accessible before attempting data reading…
Use when analyzing raw 2D MS data (m/z vs. retention time maps) where conventional peak picking introduces unacceptable error rates, particularly in untargeted metabolomics or…
Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers…
Use when you have preprocessed, normalized beta-value matrices from EPIC or 450k methylation arrays with at least two sample groups (case/control, treatment/untreated, or similar…
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 a tagged tabular file (Excel or CSV) with columns marked using export tag syntax (e.g., #study.id, #subject.id, #.
Use when after completing a virtual LC-MS/MS acquisition simulation using ViMMS (e.g., after calling env.
Use when you have raw or annotated MS/MS spectra (in MGF, mzML, or mzXML format) destined for de novo peptide sequencing with Casanovo.
Use when after filtering a peak table to remove mispicked ions, group contaminants, and low-replicability features, you have a curated feature list with m/z, retention time, and…
Use when after harmonizing MS/MS spectra and metadata fields (compound identifiers, adduct annotations, collision energies, instrument types) to a common schema, and before…
Use when you need to transfer retention time predictions from one chromatographic method to another, but have access to only a small number (≥10) of molecules with known retention…
Use when you have an existing mass spectrometry data file in a vendor or standard format (mzML, NetCDF, etc.) and need to convert it to mzPeak format for downstream analysis,…
Use when when you have extracted multiple spectral attributes (e.g., base-peak m/z, intensity, retention time, scan index) from individual MS scans via accessor functions and need…
Use when you have CE-MS raw data (mzML or netCDF format) containing a target compound of known m/z ratio and you need to resolve it as a distinct peak on the effective mobility…
Use when after extracting raw MS/MS spectra from mzML files when you observe high fragment counts per spectrum (e.g., 98 fragments) and want to reduce noise from instrument…
Use when when building a graph-based molecular property prediction model that must process both molecular structures (as heterogeneous graphs) and tabular metadata…
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 after mass tracks have been aligned across samples into a MassGrid structure (m/z-aligned, same mass-to-charge ratio) and retention time calibration dictionaries — from…
Use when when setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all…
Use when you have mass spectrometry MS/MS spectral data in GNPS-style MGF format and need to feed it into the Mass2SMILES deep learning model for structure and functional group…
Use when you have parsed metabolite identities with known spin-system coupling constants (J-values) and chemical shifts, and need to generate the theoretical multiplet patterns…
Use when you have simulated or experimental mzML data from two or more fragmentation controllers (e.
Use when you have centroided MS2 spectra from data-dependent LC- or GC-HRMS measurements and need to rapidly prioritize potential PFAS features within a larger feature set.
Use when working with raw or minimally processed MS/MS spectra from repositories
Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal…
Use when you have vendor-independent centroided mzML files from LC- or GC-HRMS data acquired in data-dependent acquisition (ddMS2) mode and need to extract detected features with…
Use when you have mass spectrometry feature data stored in HDF5 format (.h5 files) and need to load specific dimensional columns (m/z, drift time, retention time, intensity) for…
Use when evaluating whether a published computational method can be independently executed: (1) source code is claimed to be available but repository structure, build…
Use when you have Thermo Orbitrap .raw files and need to access raw spectral data (individual MS1 or MS2 scans, base-peak values, chromatogram traces, retention times, or…
Use when after extracting tabular data into intermediate JSON representation (via tagging), or after manual JSON editing, and before converting to a target format (e.g., mwTab for…
Use when your input is a tabular file (CSV or Excel) with column headers annotated using MESSES tagging syntax (#<table_name>.id for record identifiers and #.
Use when when xcms has produced misaligned feature groups and you need to extract raw LC-MS profiles from source files into a structured format acceptable by ncGTW's realignment…