Use when you have labeled training data (e.g., pqm_development with 500 peaks and 89 samples) and need to select which of multiple classification algorithms (e.g., AdaBoost,…
Use when when you have a generic constraint-based metabolic model, cell-line-specific
Use when you have preprocessed 1H NMR spectral data with an unknown or ambiguous peak (e.g., at a specific chemical shift δ), and you need to determine its chemical identity.
Use when when you have millions of high-dimensional objects (e.g., MS/MS spectra converted to feature-hashed vectors) and need to compute pairwise similarities or retrieve nearest…
Use when you have constructed or received a SummarizedExperiment object (or similar S4 class) containing MS feature tables, counts matrices, or sample-level metadata, and need to…
Use when you have LC-MS/MS data preprocessed with MZmine2 into an MGF file (containing MS1 and MS2 spectra) and a feature table (peak areas per sample), and you want to relate MS1…
Use when preprocessing raw Agilent MassHunter (.d) or UIMF IM-MS data files that exhibit signal saturation—ion intensity clipping caused by detector or amplifier limits—which…
Use when you have extended a metabolite identification tool (such as Met-ID) to support a new derivatizing matrix beyond the default (e.
Use when you have raw molecular structures in SMILES or SDF format and need to prepare them as input for BitterPredict.m or similar descriptor-based classifiers.
Use when you have loaded a raw or partially processed MsmsSpectrum object and need to reduce spectral noise before annotation, matching, or visualization.
Use when when you have a resolved spectrum file in mzML or mzXML format and need to identify where MS2 (tandem mass spectrometry) scans occur within an LC-MS run, particularly to…
Use when you have raw MS2 spectra files (mzML, mgf, msp, mzxml) that may contain multiple MS2 spectra per feature and require reduction or standardization before library matching.
Use when after running annotateRC() on LC-MS AIF features, when you need to validate whether a feature's rank-1 annotation is reliable or when you suspect that structurally…
Use when you need to reverse-engineer or document the architecture of a multi-component research software system where design information is embedded in repository structure,…
Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a…
Use when you have paired-end Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited) and need to produce standardized .hic binary contact maps that conform…
Use when you have a cooler-format Hi-C contact matrix and need to establish a genome-wide baseline contact frequency by genomic distance.
Use when your workflow fetches data from multiple external web services (e.g., CIR, CTS, PubChem, IDSM, BridgeDb) asynchronously and you need to track which services are…
Use when when you have a spatial molecular dataset (e.g., Visium, MERFISH) with categorical cell-type or feature annotations and want to test whether specific categories are…
Use when you have a metabolite intensity matrix (samples × metabolites) with assigned annotations (peak IDs mapped to KEGG or ChEBI compound IDs), a metabolic pathway database,…
Use when when you have intermediate JSON data that must be selectively transformed or enriched according to declarative conversion rules—for example, when extracting experimental…
Use when you have paired scATAC-seq and scRNA-seq data from the same cells (multiome experiment) and want to perform integrated analysis that leverages both chromatin…
Use when when you need to simulate LC-MS/MS data for fragmentation strategy development and do not have (or wish to augment) real experimental chromatograms.
Use when after mark_nas() has replaced non-NA missing-value codes (e.g., 0, 1) with R's NA in the exprs matrix of a MetaboSet object, and you need to decide whether to apply…
Use when when compiling EI or MS/MS spectral libraries from multiple gigabyte-scale sources (e.
Use when when you have trained a regression model on experimental retention times or similar continuous molecular property predictions and need to quantify its generalization…
Use when you have a curated relational dataset (structure-organism pairs) and need to quantify how structures distribute across a categorical variable (e.g., organism prevalence).
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 you are preparing to apply Probability Product Kernel–based scoring to MS2 spectra for genomic–metabolomic linking, and you need to establish a reference set of ion peaks…
Use when after a mass spectrum has been matched against a reference m/z file (e.g., SRFA.ref) and a sufficient number of calibration points (≥5) have been identified within a…
Use when you need to confirm that a documented web service URL is live and reachable before attempting to submit analysis jobs, download results, or integrate the service into an…
Use when you have a small training dataset for molecular property prediction (e.g., <500 samples from PredRet or MoNA databases) and a pre-trained GNN model is available that was…
Use when when you need to evaluate GNN performance on collision cross section prediction using the enveda/ccs-prediction repository, either by loading an existing pre-trained…
Use when you have an untargeted metabolomics dataset with a two-layer network topology already constructed (one layer representing biochemical knowledge/pathways, the other…
Use when immediately after loading raw .idat files or beta-value matrices from HumanMethylation450 or EPIC arrays when you need to exclude probes that fail quality control.
Use when processing raw IM-MS data (UIMF or Agilent MassHunter .d format) that exhibits jagged peaks in low-abundance ions, isolated high-intensity noise spikes, or saturated…
Use when you have sampled feasible flux distributions from multiple constraint-based
Use when after a GitHub Actions CI workflow has executed static analysis (e.g., via Sonarcloud) and generated a quality report.
Use when you have raw NMR metabolomics measurements paired with pre-analytical metadata (e.g., processing delay times, sample type designations [plasma vs.
Use when you have downloaded a GNPS archive from either GNPS1 (https://gnps.ucsd.edu) — from HolobiomicsLab/asb-skill-collections
Use when you have raw LC-MS/MS data in mzML or mzXML format and need to isolate specific MS1/MS2 scan pairs for a targeted compound list or for building a local spectral library.
Use when after identifying putative BGC-encoded precursor peptides from a genome assembly via MetaMiner's BGC identifier, when preparing a RiPP structure database for downstream…
Use when you have LC-HRMS profile-mode data with detected local maxima (from gradient-descent peak finding) and need to prepare them as input for a convolutional neural network…
Use when you have a new or modified LC-MS data processing tool and need to determine whether it can handle production-scale sample cohorts (50–100+ samples) on modest hardware…
Use when working with natural product molecules where conventional synthetic-molecule
Use when when you have a collection of N-Me derived unsaturated sterol lipid identifiers or structures and need to generate predicted collision cross section (CCS) values for…
Use when after constructing MetaboSet objects from Excel-formatted LC-MS peak tables and before drift correction or quality flagging.
Use when you have a large single-cell count matrix (≥10 million cells) in CSR format and need to verify whether the matrix-free spectral embedding in SnapATAC2 achieves its…
Use when you have LC-IM-MS/MS raw data from sterol-containing tissue samples and need to assign detected peaks to specific structural isomers (e.g., distinct double bond positions…
Use when you have paired cdf files (raw mass spectrometry imaging data) and Matlab workspace (.mat) files for the same root sample, and you need to reproduce published linear-axis…
Use when you have an observed m/z value from spatially-resolved mass spectrometry imaging and need to assign one or more plausible molecular formulae with confidence metrics.
Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1,…
Use when you have TWIM-MS experimental data with assigned biomolecular class labels (e.g., peptides, lipids, carbohydrates) and arrival time measurements, and you need to compute…
Use when you have constraint-based metabolic models with integrated transcriptomics (gene expression), intracellular metabolomics (substrate concentrations), and extracellular…
Use when you have time-resolved DBDI-MS data (intensity matrix with m/z features as rows and scan timepoints as columns) from direct injection analysis where chromatographic…
Use when after peak detection has been completed on individual LC-MS samples and you have a collection of detected peaks with m/z, retention time, and intensity values from each…
Use when when processing LC-MS mass tracks (EICs) and you need to identify genuine chromatographic peaks rather than noise artifacts.
Use when your annotation pipeline depends on multiple external web converters and you need to diagnose why annotation jobs are failing, slow, or incomplete.
Use when working with raw FT-ICR transient data (e.g., ESI_NEG_SRFA.d format) prior to noise thresholding and mass-domain calibration.
Use when you have selected statistically significant features from multi-assay untargeted LC-MS metabolomics data and need to group them by structural relationships defined by…