Use when you have raw IMC (protein imaging) and SIMS (metabolite imaging) data from tissue regions that require spatial co-registration, single-cell-level intensity…
Use when when you have LC-MS/MS data in Mascot Generic Format (mgf) files and need to identify compounds against a curated custom database (e.g., prepared using CFM-id for a…
Use when after khipu has grouped LC-MS features into empirical compounds with inferred molecular formulas and adduct assignments.
Use when after loading centroided .mzML LC-MS data and creating a target list with compound ID, name, theoretical or measured m/z, expected RT (in minutes), and polarity…
Use when you have a trained NeatMS neural network model and labelled peak validation data, and need to select an operational classification threshold or understand how TPR and FPR…
Use when converting intermediate JSONized experimental metadata (extracted from tagged tabular data) to a target repository format (e.
Use when after executing forward inference on preprocessed mass spectrometry spectra with a deep learning model (e.g., PS²MS), when you have per-spectrum predictions with…
Use when you have two implementations of the same quantification method (or major versions) and observe a persistent disagreement in mapped-read counts, per-read alignment…
Use when when processing downloaded mass spectral libraries (particularly MoNA EI or MS2 libraries) where SMILES information exists but is embedded in unstructured Comment fields…
Use when you have a metabolite abundance table (rows=metabolites, columns=samples)
Use when you have transcript-level abundance and count estimates from salmon, sailfish, kallisto, or oarfish and need gene-level matrices for downstream differential analysis with…
Use when when annotating m/z features against a metabolite database (HMDB, Lipidmaps, etc.) and the sample preparation, ionization method, or polarity mode favors specific adduct…
Use when when you have MS/MS spectra (LC-MS or equivalent positive ionization mode data) that you intend to embed using Word2Vec or similar distributional semantic models, or when…
Use when after peak detection and feature extraction have produced a composite feature table with m/z, retention time, and intensity values for individual samples.
Use when when you need to deploy a Java web application packaged in a Tomcat Docker container to a specified HTTP endpoint, and must verify that the container starts successfully,…
Use when your IM-MS lipidomics samples have been spiked with fully labeled isotopic internal standards (e.
Use when when performing targeted quantification of known compounds in LC-MS data using TARDIS, especially when the instrument acquired data with multiple overlapping m/z scan…
Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type,…
Use when when you have downloaded a released version of a structured dataset (e.g., LOTUS from Zenodo) and need to confirm it matches the documented headline statistics before…
Use when you have run a peak-calling algorithm on sparse CUT&RUN bedGraph data and received a BED-format output file;
Use when you have executed batch searches across two or more domain-specific MASST tools and obtained separate output files (_microbe.json, _plant.json, _tissue.
Use when after preprocessing GCxGC-MS chromatograms (smoothing, baseline correction, peak alignment) when you need to uncover latent metabolite patterns that distinguish…
Use when after a GitHub Actions CI workflow has executed static analysis (e.g., via Sonarcloud) and generated a quality report.
Use when you need to serialize heterogeneous data (e.g., index integers and file offsets of different byte widths) into a compact binary format, or parse a binary file format…
Use when you have two or more independent scoring functions ranking the same set of candidate links (GCF-MF pairs, BGC-spectrum associations, etc.), and you want to determine…
Use when you have completed peak calling and cell annotation in ArchR and want to perform trajectory inference or visualization in STREAM.
Use when you need to validate that a repository's automated build, test, or publish pipeline is functioning correctly on a target branch (e.g., release branch); when you want to…
Use when when you have extracted concatenated MS/MS spectra for multiple features from replicate mzML files and need to verify that a TIC-based filtering step (e.g., top x% TIC…
Use when after peak detection and feature table generation when you have a collection of m/z, retention time, and intensity values and need to identify which features are related…
Use when you have a vendor mass spectrometry raw file (e.g., .raw format) that requires conversion to Aird format using AirdPro CLI, and you are running on macOS or Linux.
Use when when you have retrieved a large, heterogeneous collection of tandem MS files from ReDU or MassIVE and need to isolate a subset sharing specific sample characteristics (e.
Use when investigating how a specific pull request (e.g., PR #72 introducing MS2Query''s two-branch workflow split) modified the codebase architecture, control flow, or data…
Use when when you have just loaded the rawrr R package and need to confirm that the bundled .NET 8.0 assembly (rawrr.exe) is present and functional before performing any mass…
Use when after identifying a set of differentially accessible peaks (via tl.diff_test or equivalent), when you need to infer which transcription factors may regulate the observed…
Use when after executing a spatial analysis function (e.g., squidpy.gr.sepal) that modifies or augments a data object, verify that the expected output fields exist with correct…
Use when when implementing a new MsBackend subclass that stores only a subset of core spectra variables (e.
Use when when you have detected LC-MS/MS features (MS1 peaks with MS2 fragmentation spectra) from untargeted metabolomics experiments and seek to organize them into a chemical…
Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained…
Use when after combining multiple EI or MS2 mass spectral libraries and you have access to NIST RI reference files (ri.dat and USER.DBU) and need to assign experimental retention…
Use when you have unaligned MS2 spectra from multiple metabolomics samples (in mzML, mzXML, or MGF format) and need to compare them without relying on retention time or aligned…
Use when training a contrastive learning model on ion image data (mass spectrometry imaging) where augmented pairs of the same ion image must maximize similarity while different…
Use when after generating cross-spectrum negative examples via precursor m/z windowing and before training a rescore model (e.g., Siamese architecture in FIDDLE v2.0.0).
Use when you have raw GC-MS output from Agilent Unknowns Analysis (a .CSV with columns Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, File.
Use when you have raw imzML and ibd (ion binary data) files from spatial mass spectrometry imaging and need to convert them into a standardized AnnData representation where m/z…
Use when when you have run a spectral networking job on GNPS (e.g. ProteoSAFe-METABOLOMICS-SNETS-V2) and need to reuse the network output files locally with MetaMiner or another…
Use when when analyzing normalized DNA methylation beta matrices (450K or EPIC arrays) and you need to identify the true number of latent batch or technical factors present in the…
Use when when deploying Mass2SMILES inference on CPU-only hardware (e.g., when GPU/CUDA support is unavailable), you need to verify that the InferenceModel cpu_threads parameter…
Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) and need to verify the reported counts of unique entities (source databases, organi — from…
Use when after EIC candidate generation from LC/HRMS data (mzXML, mzML, or netCDF formats), when you need to localize discrete peaks within chromatographic profiles and assign…
Use when after feature extraction and quality control filtering (blank masking, sample dropping, normalization) have been applied, but before statistical analysis or machine…
Use when after standardizing link scores (strain correlation and IOKR) across all potential GCF-MF pairs in a metabologenomics dataset, perform significance testing to determine…
Use when when you have N-Me derivatized unsaturated sterol lipid structures (as SMILES or molecular formula) and need to predict MS/MS fragmentation patterns with…
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…
Use when when you have downloaded raw spectral datasets from multiple spectroscopic modalities (NMR, HSQC, COSY, IR) in their native or proprietary formats and need to convert…
Use when when predicting one data modality (e.g., metabolite abundances) from another (e.g., microbiome composition) and you need to distinguish genuine microbe–metabolite…
Use when when integrating two spatial omics modalities (ST and SM) measured on the same tissue sample but at different spatial resolutions or spot coordinates.
Use when when preparing MS/MS spectral data for training word-embedding models (Word2Vec, Skip-gram, CBOW) that will learn relationships between fragment ions and neutral losses.
Use when after building multiple Docker image variants (e.g., cli, dev, linux, windows) using multi-stage builds with --target flags, and you need to verify that each variant's…
Use when after metabolite annotation has been completed (level-1 confidence via spectral library matching in margheRita or equivalent), and you need to perform pathway enrichment…
Use when you have an enumerated list of lipid species (identified by class, fatty acid composition, and chain length) and need to generate theoretical precursor m/z values,…