Use when you have transcript-level quantification files (quant.sf, kallisto abundance.h5, or RSEM output) from one or more RNA-seq samples and need to construct a count matrix for…
Use when you have run mass detection and chromatogram building independently on each LC-MS/MS sample and produced per-sample feature lists with m/z, retention time, and intensity…
Use when when you have generated or extracted a chemical mixture (via DatabaseFormulaSampler, ChemicalMixtureCreator, or ChemicalMixtureFromMZML) and need to establish a virtual…
Use when when you have access to a research repository or README documenting a machine learning implementation (e.g., Keras/TensorFlow-based deep learning model) and need to…
Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among…
Use when you have paired tandem MS/MS spectra with known molecular fingerprints,
Use when comparing mapping outputs from two different salmon versions or implementations (e.g., C++ 1.12.0 vs.
Use when when you need to locate and extract quantitative retention time and intensity data for known peptide standards (e.g., iRT peptides) from a Thermo .raw file to validate…
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 you have Nightingale Health 1H-NMR metabolomics measurements for a new cohort and wish to compute one or more established metabolic risk scores (mortality, MetaboAge,…
Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.
Use when you have detected multiple LC-MS features (m/z peaks) across a chromatogram and need to distinguish true chemical relationships (isotopes differing by 1.003 Da, adducts…
Use when you have aligned ATAC-seq BAM files and want to discriminate between transcription factor binding sites that are actually occupied by protein versus sites with matching…
Use when when you have XCMS-preprocessed LC-MS metabolomics data with a peak table and an accompanying covariate/metadata file that contains a 'SampleType' column, and you plan to…
Use when when you have peak-abundance .csv files and assigned molecular formula data from FT-ICR MS preprocessing, and you need to verify that a published pipeline's runtime…
Use when you have transcript-level quantification (TPM or counts from Salmon/kallisto) and need to quantify the inclusion level of specific alternative splicing events (exon…
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 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 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 when you have raw mass spectrometry data from diverse instrument vendors (Thermo, Sciex, etc.) and need to harmonize and standardize spectrum-level metadata—including…
Use when when running Mass2SMILES inference on a TensorFlow-CPU build (e.g., delser292/mass2smiles:final container) and you need to optimize inference speed by controlling CPU…
Use when you have a set of differentially accessible peaks (output from differential accessibility testing, e.g., tl.
Use when when you need to verify that a GitHub Actions workflow (such as dev_build_release.
Use when you have aligned single-cell ATAC-seq data as BAM files or fragment files (TSV format with genomic coordinates) and need to prepare it for spectral embedding, clustering,…
Use when when executing a multi-converter annotation workflow on mass spectra metadata (.
Use when you have a repository of structured records (e.g., mass spectrometry data, metadata, or domain-specific formats) and need to enforce validation rules systematically…
Use when after completing Cardinal-based preprocessing (feature summarization, TIC normalization, peak processing, spatial segmentation, and SSC annotation), use this conversion…
Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation…
Use when you have cloned a Python project (e.g., scverse/scanpy) that includes a hatch.toml configuration file and need to set up a consistent development or testing environment.
Use when when you have mzML spectrum XML already parsed (either from a file, a database query, or an in-memory representation) and need to construct Spectrum or Chromatogram…
Use when after calling squidpy.gr.spatial_neighbors on an AnnData object containing spatial coordinates in obsm.
Use when after loading and preprocessing raw scATAC-seq data into an ArchR project object when you need to compute low-dimensional embeddings for clustering, UMAP/tSNE…
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…
Use when after community-dependent gap-filling has proposed reactions to fill metabolic gaps in individual consensus reconstructions.
Use when when you have a calibrated FT-ICR mass spectrum (e.g., ESI-NEG mode) and need to decide between rapid single-assignment (first_hit=True) and exhaustive multi-assignment…
Use when you have raw LC-MS spectral peak data (in the format provided by DOI 10.25345/C5FD2F) and need to build a classifier that can distinguish valid peaks from false positives…
Use when you have a set of anchor feature pairs (m/z and retention time values) from two disparately-acquired LC-MS datasets and need to fit a smooth, nonlinear RT correction…
Use when when you have raw count matrices from paired microbiome (16S rRNA or metagenomic) and metabolomic (LC-MS/MS) profiling data that will be used to train or apply a…
Use when when building a Graph Transformer model for continuous property prediction on molecules with associated experimental or instrumental metadata (e.g., retention time…
Use when you have already assigned samples to batches (inter-batch balance is fixed) and need to shuffle injection order within each batch to decorrelate sample properties from…
Use when you have loaded a Bruker Solarix transient file (.d format with .ser or .fid content) and need to generate a processed mass spectrum for peak picking and molecular…
Use when after composite map peak detection has generated a full unfiltered peak list with SNR values computed for each candidate peak.
Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered…
Use when after XCMS feature detection and retention time correction, when you need to group features derived from the same compound.
Use when you have generated or curated a lipid spectral library (with precursor m/z, adduct information, charge states, retention times, and fragmentation patterns) and need to…
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 when processing open mass spectrometry library (OMSL) data that may contain duplicate spectral records (e.
Use when your metadata table contains compound names but lacks structure information (SMILES, InChI, molecular formula, or PubChem CID).
Use when after applying cluster-based filtering with quasi-molecular adducts and frequency thresholds on candidate metabolites from KEGG matching.
Use when you have measured intracellular metabolite abundances (LC-MS or similar) across multiple cell lines or conditions and a stoichiometric metabolic model (with…
Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure…
Use when when you have a large MsBackend object and need to (1) select a contiguous or non-contiguous range of spectra for focused analysis, or (2) combine spectra from multiple…
Use when after deploying a TensorFlow Serving container (especially within a Dockerized stack like NP-Classifier), before running classification or inference pipelines, to confirm…
Use when you have two or more independently processed MemoMatrix objects (each generated from a separate sample set) and your analysis goal requires direct comparison of MS2…
Use when you have created a GNPS molecular network (classical or feature-based workflow) and separately run an MS2LDA experiment on the corresponding MGF file, and you want to…
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 you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak…
Use when when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to identify and annotate lipid A structures at scale.
Use when when calling filter functions (e.g., filter_mispicked_ions(), filter_group(), filter_cv()) on R6-based metabolomics data objects in the mpactr package and you need to…
Use when you have extracted retention times from top MS1 features across an LC-MS run and need a single, comparable metric to evaluate how effectively a gradient spreads compounds…