Use when you have replicate MS/MS spectra with labeled fragment recurrence frequencies and need to select an optimal frequency threshold (beyond the default 0.1) that maximizes…
Use when when you have resolved mzML or mzXML spectrum files and need to isolate signals for a target m/z value (e.g., 870.954) across all retention times or a specific scan.
Use when you have one or more mzML files (XML-based mass spectrometry data) and need to convert them into mzPeak format for downstream analysis, archival, or integration with…
Use when you have prepared metabolomics input files (feature quantification table, MS/MS spectra in MGF format, sample metadata) and are about to execute the TIMA taxonomically…
Use when you have raw gas or liquid chromatography–mass spectrometry data (in NetCDF or mzML format) and need to detect features, align them across samples by retention time and…
Use when you have single-cell RNA-seq count matrices or processed expression data and need to store them alongside cluster assignments (e.g., leiden cluster labels), cell…
Use when after running RAMClustR clustering on XCMS-detected LC-MS features in positive ionization mode, when you need to assign molecular weights to compound clusters and want to…
Use when you have a set of compounds (e.g., novel NPS analogues in an evaluation dataset) and need to classify them as structurally similar to or divergent from a reference set…
Use when after importing raw metabolomics data (e.g., from Metabolon, Nightingale, SomaLogic, or Olink platforms) into a Metaboprep object, but before quality control or…
Use when after ASE-ANI has filtered conformers to remove high-energy geometries, and you need to compute electronic properties required for CCS prediction.
Use when you have aligned and baseline-corrected GC-IMS data with detected and clustered peaks, and you want to extract peak intensities using a consistent integration window.
Use when when converting tabular data to JSON via the matrix directive, you need to exclude records that fail domain-specific validation (e.g., only retain records where a 'test'…
Use when after feature detection when you have a feature table with m/z, retention time, and intensity columns, and you need to group features into empirical compounds (putative…
Use when when processing raw CE-MS data and need to establish a baseline migration time scale before transforming to effective mobility.
Use when you have a trained predictor (like BitterPredict) that accepts structured descriptors and want to understand feature importance without retraining.
Use when after running retention-order prediction experiments on a test or held-out evaluation dataset.
Use when importing mass spectra from multiple open mass spectra libraries (OMSLs) or databases with heterogeneous metadata quality.
Use when when ingesting spectra from multiple open mass spectrometry libraries (OMSLs) in .mgf, .msp, .json, or .csv format and you observe mixed experimental protocols,…
Use when you have a pretrained model with documented performance on a bounded input domain (e.g., molecules ≤19 heavy atoms, sequences <1000 bp) and you need to establish whether…
Use when you have raw MS/MS peak lists and suspect electronic noise contamination—particularly
Use when when developing or validating a DNA methylation array analysis pipeline using ChAMP, you need an independent ground-truth dataset to confirm that DMR detection is working…
Use when when configuring a multi-well plate design (96-well, 384-well, or other format) in InjectionDesign for LC/GC-MS analysis and you need to specify whether analytical…
Use when you are evaluating a new or existing data analysis pipeline (e.g., MetaboDirect) and need to produce a transparent, evidence-based feature matrix showing which analyses…
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 running salmon quant with the --writeMappings/-z flag to produce SAM output, or when investigating discrepancies between the number of mapped reads reported in…
Use when after converting or downloading a pre-trained Keras model to HDF5 TensorFlow 2.3.0 format, particularly when integrating the model into a fixed-interface pipeline (e.g.,…
Use when you have a cooler file (.cool or .mcool) from a Hi-C or micro-C experiment and need to quantify the total number of sequencing reads assigned to each genomic bin to…
Use when when you have imported a raw GCxGC-MS chromatogram as a 2D-TIC (2D Total Intensity Chromatogram) object from a NetCDF file and observe steady or increasing baseline…
Use when immediately after loading a raw GC-MS CSV file and before executing the spreadOut() function. Use it when you have received peak table data from an instrument vendor (e.
Use when you have an isotope-corrected or raw MSI dataset stored in HDF5 format following Cardinal::HDF5 conventions, a user-provided internal standard definition (sample…
Use when you have matched multiomics data (genomics, epigenomics, transcriptomics,
Use when you have a preprocessed feature table (m/z, retention time, intensities) from LC-MS and need to group features into empirical compounds.
Use when when you have computed PCA coordinates from chemical annotation matrices (e.
Use when after implementing or modifying a cross-language integration layer that wraps Python mass spectrometry functions (e.g., spectral matching, peak detection, normalization…
Use when you have a mature Python package (e.g., Mummichog 2.x) that needs to be relocated to a new GitHub organization (e.
Use when you have peak-picked MS/MS data (e.g., from MZmine, XCMS, MS-DIAL, or Compound Discoverer) and need to identify lipid species present in your sample.
Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS)…
Use when you have completed parallel QUICK quantum calculations on multiple conformers filtered by ASE-ANI and need to extract electronic properties from the output logs and…
Use when after denoising MS/MS spectra at multiple frequency thresholds and matching each thresholded spectrum against a -matching reference spectrum.
Use when immediately after peak detection and feature table generation from LC-MS data, when you need to rank or filter features by confidence before annotation or statistical…
Use when you have XCMS-processed LC/MS peak data from dual-labeled (e.g., 13C) and unlabeled (12C) metabolomics samples and need to distinguish features genuinely enriched by…
Use when when a new file format specification has multiple language implementations and you need to validate that all implementations correctly interpret the specification.
Use when after batch correction has been applied to metabolomics data using pooled SQC samples, and you need to retrieve the corrected ratios (compound / internal standard) for…
Use when you have a pre-trained MS/MS spectral embedding model and need to validate that it achieves strong and consistent retrieval performance on curated spectral libraries that…
Use when you have tabular metabolomics data (tab-delimited or Sciex OS format) and need to apply a specialized R package's analysis pipeline—such as mzQuality—that requires…
Use when you have received raw CE-MS or LC-MS output files in vendor-specific formats from a mass spectrometry instrument and need to process them through an untargeted…
Use when after GNPS_GC molecular networking job completion, when you have retrieved raw network output files and need to extract, validate, and structure the network topology for…
Use when you have transcript-level abundance estimates and inferred counts from salmon/kallisto/Sailfish (with or without Gibbs/bootstrap replicates) that must be summarized to…
Use when when you have received raw MRM lipidomics export files in vendor-specific
Use when when setting up a new conda environment for a Python-based bioinformatics pipeline and you need to confirm that all declared dependencies (e.g., pysam >=0.15.4, bx-python…
Use when after mass tracks have been aligned across samples into a MassGrid structure and retention time calibration dictionaries (rt_cal_dict) have been computed for eac — from…
Use when immediately after parsing mzML files into (m/z, scan_number, intensity) tuples when you need to build mass tracks from raw MS1 spectra.
Use when you have split multi-assay LC-MS intensity data into training (90%) and test (10%) subsets with assay-specific column prefixes, and you need to fit a discriminant or…
Use when you have a collection of molecular structures (as SMILES or SDF files) and need to generate pre-computed CCS values for fast retrieval in downstream mass spectrometry…
Use when you have ATAC-seq BAM files aligned to a reference genome, a set of transcription factor motif locations (BED format), and you need to determine which motifs are actually…
Use when you have assembled genome FASTA sequences (from SPAdes, metaSPAdes, or antiSMASH output) and need to systematically identify precursor peptides corresponding to a target…
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 when you have a trained multitask model that accepts multiple input modalities (e.g., 1D NMR spectra in different nuclei or complementary analytical techniques) and you…
Use when after generating combined or alternative scores for a set of BGC-metabolite (GCF-MF) link candidates, you need to evaluate whether a scoring function preferentially ranks…
Use when you have a GC-MS dataset in CSV format with retention times, base peak m/z values, component areas, and compound names, and you need to identify whether specific query…