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 you have per-sample metabolite abundance data and a metabolite-to-pathway
Use when you have LC-MS normalized intracellular metabolite abundance data from multiple cell lines (or samples) and need to compute reaction-level propensity scores that account…
Use when after instantiating a transformer encoder module for mass spectrometry data processing (e.g., in IDSL_MINT), before training on large MS/MS datasets or running inference…
Use when after you have identified statistically significant LC-MS features and run MamsiStructSearch to generate structural clusters (isotopologue groups, adduct groups,…
Use when when you have processed scATAC-seq data (peak calling complete, cell-barcode matrix generated) and need to register it into ArchR for downstream multiome analysis…
Use when you have a Thermo Fisher Orbitrap .raw file and need to recover the intensity profile of a specific m/z value or peptide across the LC separation dimension…
Use when after generating a peak table from XCMS peakTable() output in an untargeted LC-MS metabolomics workflow, if your experimental design includes quality control (QC) samples…
Use when when preparing raw MS/MS spectra for input to a Siamese neural network trained to predict structural similarity scores (Tanimoto).
Use when after you have accumulated experimental MS data from ≥2 LC gradient trials, extracted separation efficiency metrics (retention time spacing) from each trial, and encoded…
Use when you have downloaded LC-MS spectral peak data (DOI 10.25345/C5FD2F or equivalent) and need to build a supervised deep neural network classifier to distinguish peak classes…
Use when after submitting a POST request to the /api/smart3/search endpoint with peak data as a JSON payload, you receive an HTTP response and need to extract classification…
Use when when you have run differential methylation analysis in methylKit and need to validate whether overdispersion correction (overdispersion='MN') produces appropriately…
Use when you have SWATH-MS data (mzML or vendor binary format) where precursor isolation windows intentionally capture multiple co-eluting compounds, resulting in multiplexed…
Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint…
Use when immediately after parsing and validating raw LC-MS/MS data files (mzML, mzXML, or vendor formats) when you need to prepare spectral data for fragmentation tree…
Use when you have extracted a chemical mixture from a real mzML acquisition (e.g., Beer1pos), simulated the same chemicals through ViMMS using a chosen controller (e.
Use when you have untargeted metabolomics data (e.g., LC-MS/MS spectra) and need to organize compounds by structural relatedness to enable structure discovery for unknown…
Use when when building Word2Vec or embedding-based spectral similarity models where you need to capture fragmentation patterns beyond individual peak positions.
Use when when ingesting mass spectral libraries (EI or MS2) where SMILES information is embedded in the Comment field rather than in a dedicated SMILES metadata field—particularly…
Use when when you need to verify that a software package (such as MassQL) passes its periodic integration test suite as indicated by CI workflow badges in the project…
Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified…
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 when applying a series of mpactr filter functions (filter_mispicked_ions,
Use when after normalizing a metabolomic feature matrix when you have both non-QC (study) samples and QC (quality-control) replicates in the same experiment.
Use when you have generated a lipid spectral library (lipid identities, adducts, m/z values, fragmentation patterns) and your downstream analysis requires DDA acquisition on an…
Use when you have detected and clustered unknown MS features from untargeted xenobiotic metabolomics data, computed fragmentation pattern similarity scores between features and…
Use when after implementing a neural network component that will feed into a downstream architecture (e.g., a transformer).
Use when when annotating .msp files with metadata from multiple external web services and you need to monitor which services are slow or unreliable.
Use when processing tandem MS/MS libraries in mgf format (such as GNPS) that lack a Molecular Formula (MF) field but contain valid SMILES strings.
Use when you have raw MS2 spectral data (MGF, mzML, or msp format) and need to generate a sample-level fingerprint for comparison across metabolomics samples, especially when…
Use when after converting or filtering objects (e.g., transformation products to suspect lists, feature groups through componentization) and before passing them to downstream…
Use when apply CLR transformation when you have microbiome or metabolomic count data that sums to a constant across samples (relative abundance or compositional data) and intend…
Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with…
Use when when you have discovered Mass2Motifs from MS2LDA topic modeling and need to automatically annotate them by finding the most structurally similar known spectra in a…
Use when you have MGF or native MS/MS arrays (mz_array, intensity_array, precursor_mz, adduct) and want to predict the most likely molecular formula.
Use when you have raw or processed MS spectrum data (mz/intensity pairs) from direct-injection MS (DI-MS), ASAP-MS, or other ambient ionization instruments (AI-MS, LDI-MS — from…
Use when you have peak intensity data from metabolomics experiments with annotated metabolites assigned to known groupings (KEGG pathways, Reactome, GNPS Molecular Families, or…
Use when when training a deep neural network on mass spectrometry spectral data where overfitting is a risk (especially with data augmentation applied), and when you need both…
Use when designing multi-batch LC/GC-MS experiments where samples belong to multiple groups or conditions and you need to ensure that each injection plate receives a balanced…
Use when after identifying statistically significant LC-MS features (e.g. via MB-VIP permutation testing) when you need to consolidate redundant measurements of the same…
Use when you have raw IM-MS data (Agilent MassHunter .d or UIMF format) and need to exclude early or late chromatographic regions—e.g., to skip dead volume, exclude blank runs,…
Use when you have raw mass spectrometry spectra (in MGF, mzML, or similar formats) that must undergo standardized preprocessing before library matching, similarity searching, or…
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 after LDA modeling has produced an inferred motifset (JSON format) containing Mass2Motifs with fragment and neutral-loss patterns.
Use when after mass track extraction and alignment across samples, when you have a MassGrid structure (m/z-aligned mass tracks) and corresponding retention time calibration…
Use when you have generated hypothetical links (e.g., GCF–MF pairs) and computed multiple independent scoring functions on them (e.g., strain co-occurrence, IOKR structural…
Use when you need to verify that a GitHub Actions workflow (such as 'dev_build_release.
Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS…
Use when you have a peak table matrix with NA values that need to be imputed using cluster statistics, or when a GCIMSDataset object requires filtering by retention time (0–1100…
Use when when you have a set of candidate molecular formulae for a measured m/z value and need to rank them by how closely their theoretical m/z matches the observed value.
Use when augmenting mass spectrometry ion images in ISO mode (isotope ions from the same molecule) and you need to simulate intensity-dependent data loss that reflects real…
Use when you have modified the Scanpy codebase (e.g., added a feature or bugfix) and need to confirm that all unit and integration tests pass before submitting a pull request, or…
Use when when you have CE-MS data with migration times that vary between runs due to electroosmotic flow drift, but you possess a reliable internal standard with a known effective…
Use when when you have a real mzML file from an untargeted metabolomics LC-MS/MS experiment and need to extract the chemical features it contains—either to simulate a…
Use when you have raw mass spectrometry data (vendor formats, mzML, or existing mzPeak files) and need to: (1) convert to mzPeak format for long-term storage and interoperability…
Use when when XCMS or other DTW-based aligners have produced misaligned LC-MS feature groups across hundreds of samples or long acquisition periods (>1 week), particularly when…
Use when your mass spectrometry DataFrame contains m/z, retention time (or mobility), and intensity columns, and you need to generate an interactive HTML figure for exploration,…
Use when you have collected liquid chromatography (LC) spectra and retention time labels for your in-house molecular database, and you want to leverage a pretrained GNN-RT model…
Use when you have (LC-)IM-MS lipidomics data from samples spiked with U13C-labeled yeast extract, measured CCS values for both labeled and unlabeled lipids, and need to quantify…