Use when analyzing RNA-seq count data from a DESeq2 workflow where you have fitted negative binomial generalized linear models and need to extract final results.
Use when you have experimental fragment m/z peaklists from Q-Exactive orbitrap, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF UHPLC-HRMS/MS instruments (in CSV or mzML-derived table…
Use when you have high-resolution LC-MS data processed through both XCMS feature detection and RAMClustR clustering, and you need to verify the reliability of molecular weight…
Use when you have raw LC-MS/MS spectra from vendor instruments (mzML, mzXML, MGF, or MSP format) with variable peak quality and intensity distributions, and you plan to perform…
Use when you have antiSMASH v5.0.0 BGC predictions from a set of microbial genomes and you need to integrate those predictions with GNPS metabolomic data (MS2 spectra and…
Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity…
Use when when implementing or auditing a data replacement method (e.g., `mz<-`, `intensity<-`) in an MsBackend subclass that must enforce ordering or format constraints on peak…
Use when at the start of any DaDIA pipeline execution, or whenever you are preparing to run a complex multi-package R workflow on a new system or after updating package managers.
Use when you have a raw metabolite count data frame (e.g., c57_nos2KO_mouse_countDF)
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 have constructed a NetworkX graph with LC-MS features as nodes and need to annotate each node with metadata derived from the MamsiStructSearch output (assay source,…
Use when when you have a GC-MS dataset (CSV with columns: Component.RT, Component.Area, Base.Peak.MZ, File.Name, Compound.Name, Match.Factor) and a known set of target chemicals…
Use when you have loaded fragment data from single-cell ATAC-seq experiments into a backed AnnData object (with fragments stored in .obsm['fragment_paired'] or .
Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) — from HolobiomicsLab/asb-skill-collections
Use when when processing mass spectrometry spectral records from a database where critical fields (e.g., adduct annotation) are absent or null, and you have a secondary field…
Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions…
Use when when you have MS/MS spectra with assigned precursor formulas and need to annotate fragment peaks with their chemical subformulas, but want to avoid the computational…
Use when you have a set of metabolite structures (or their molecular descriptors) and need to construct training or target feature matrices for CCS prediction.
Use when you have computed eigenvector values from a prior eigs_cis calculation on a cooler Hi-C matrix and need to classify genomic regions into discrete A/B compartment…
Use when when processing untargeted LC-MS metabolomics data with XCMS and need to identify low-quality peak integrations that may introduce noise or bias into subsequent compound…
Use when during the LDA training phase when you need to decide whether the model has learned a stable representation of Mass2Motifs.
Use when you have NMR peak data (1H and 13C chemical shift values) that must be submitted to a remote DeepSAT SMART 3 classification API for structural prediction, and you need to…
Use when you have generated or received a mass spectrometry data file in a structured format (e.g., mzPeak, Parquet-based archive) and need to verify it conforms to the published…
Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating…
Use when when you have mass spectral libraries from multiple sources (NIST, MoNA, RIKEN, GNPS) in disparate formats (MSP, MGF, MOL folder structures) or with misaligned 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 you have multiple feature tables (CSV files) from different LC-MS analytical experiments, each containing mass, retention time, intensity, isotope, and adduct…
Use when when you have observed fragment peak m/z values from tandem mass spectra and need to assign chemical subformulae to them.
Use when you have a new or draft file format specification (e.g., mzPeak) with multiple independent language implementations, and you need to verify that all readers agree on the…
Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover con — from…
Use when you have a large compressed scientific data file (e.g., indexed gzip mzML) where you need to retrieve specific spectra, chapters, or records by integer ID without loading…
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 when adopting a mass spectrometry data processing tool (e.g., LipidMatch) and needing to verify whether your specific instrument platform (vendor + model) and acquisition…
Use when after extracting ion chromatograms and ion mobilograms from raw diaPASEF or DIA data within specified m/z, retention time, and ion mobility windows.
Use when when claiming that one mass spectrometry processing library achieves higher throughput than competitors, or when evaluating whether a new or optimized implementation…
Use when when you have a pre-trained model and need to report stable, generalizable performance on a fixed training set with multiple held-out test splits.
Use when when implementing new scoring components (inchikey score, neighbourhood
Use when you have a multi-cluster single-cell RNA-seq dataset with cell-type annotations and you want to test whether known biological pathways (e.g., KEGG or MSigDB gene sets)…
Use when after detecting local-maxima in LC-HRMS profile mode datasets and before training or inference with a CNN model for peak classification.
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 after loading centroided .mzML LC-MS data and defining a target list (compound ID, name, m/z, RT, polarity) when you need to: (1) automatically locate and integrate peaks…
Use when when you have paired spatial transcriptome and metabolome datasets with spot-based coordinates that need to be aligned for multi-modal integration.
Use when after completing outlier detection, batch correction, and quality metric calculation on a SummarizedExperiment object using mzQuality's doAnalysis function, and after…
Use when you have untargeted metabolomics data (MS/MS spectra) and need to annotate metabolites at scale.
Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist…
Use when when standard conversion directives (headers, collate, fields_to_headers, exclusion_headers, values_to_str, sort_by, test) cannot express the required transformation…
Use when you have constraint-based metabolic models with integrated multi-omics constraints (transcriptomics via Reaction Activity Scores, extracellular flux ratios via YSI…
Use when you have PSI matrices for two or more conditions with replicates per condition, and you need to determine which alternative splicing events show significant changes…
Use when you have imported raw mass spectrometry data in formats such as MGF, MSP, mzML, or mzXML and need to clean the spectral data prior to similarity comparisons, metadata…
Use when when you have sampled the feasible flux solution space of constraint-based metabolic models (via optGpSampler or equivalent uniform sampling) and need to normalize flux…
Use when you have raw RNA-seq count data (from HTSeq, featureCounts, Salmon, or similar quantification tools) organized in a count matrix with samples as columns and genes as…
Use when your metabolomics analysis pipeline requires CCS value prediction for ion-mobility mass spectrometry data, you have access to a curated training set of known metabolites…
Use when after batch correction of metabolomics QC samples using pooled study quality control (SQC) samples, when you have multiple candidate internal standards and need to…
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 you have normalized and aligned lipidomic and metabolomic spectral features from the Multi-ABLE method across multiple biological samples grouped by phenotype (e.
Use when you have raw MRM sample files from an LC-MS/MS instrument and need to programmatically identify and tabulate all precursor m/z and product m/z pairs for each MRM…
Use when after a trained CNN model has generated molecular embeddings for query spectra, and you need to retrieve the most likely candidate molecules from a reference database.
Use when ingesting mass spectrometry spectra from heterogeneous databases or libraries where adduct annotations may be incomplete, incorrectly formatted, or inconsistent with the…
Use when you have raw metabolomics mass spectrometry data in mzML or mzXML format and need to extract, align, and normalize metabolic features across multiple samples or…
Use when parsing, standardizing, or filtering MS spectra from mixed or heterogeneous databases where adduct assignment may be manually entered, auto-inferred, or missing.