Use when you have a methylDiff object containing differentially methylated bases or regions from bisulfite sequencing, gene annotation in BED or similar format (RefSeq, Ensembl),…
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 when you need to verify that a GitHub Actions workflow (such as dev_build_release.
Use when when you have trained predictive models (e.g., neural networks) on paired microbiome-metabolome data and need to identify which metabolites are genuinely well-predicted…
Use when when implementing or validating a lossy numeric codec for mass-spectrometry
Use when when processing MS spectral data from multiple open mass spectra libraries (OMSLs) in mixed formats (MSP, MGF, JSON, CSV), especially when source data exhibits missing…
Use when when you have completed DESeq2 differential expression analysis on RNA-seq count data and obtained p-values for each gene, use IHW if you want to improve power to detect…
Use when you have co-registered IMC (protein imaging mass cytometry) and SIMS (secondary ion mass spectrometry for metabolites) data from the same tissue regions, cell…
Use when when setting up a bioinformatics pipeline (particularly Hi-C data processing) that depends on multiple external binaries with version constraints, and you need to…
Use when after blank masking and sample dropping, when you have a feature table with intensity values that exhibit systematic variation across sample collection batches or…
Use when when importing mass spectrometry spectral data from public repositories or multi-source MGF/MSP files where metadata fields are inconsistent, missing, or non-standard;
Use when you have a shallow decision tree trained on ChemEcho feature vectors (peak or neutral loss formulas) and need to deploy it as an executable query against tandem mass…
Use when you have created a GNPS molecular network (either classical or feature-based) and have computed MS2LDA motif assignments (probability and overlap scores) for the same…
Use when you have nuclear magnetic resonance (NMR) peak data (proton 1H and carbon-13 13C measurements) that you need to classify using a deployed deep learning model, and you…
Use when after collecting observed separation efficiency scores at sampled gradient conditions and you need to propose the next gradient to evaluate.
Use when when you have access to a peer-reviewed manuscript with an accompanying
Use when after implementing or modifying the scoring module that computes average InChIKey scores and neighbourhood scores for candidate matches, or when integrating new scoring…
Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed…
Use when you have a preprocessed LC-MS feature table (m/z, retention time, intensity columns) and need to identify which features belong together as isotopes or adducts of the…
Use when you have isolated TIC peak regions and need to extract ion chromatograms
Use when when you have variable-length MS/MS peak lists (m/z and intensity arrays) that must be fed into a transformer-based model for spectra analysis, and you need…
Use when you have raw LC-MS/MS data in MRM acquisition mode and need to systematically identify and catalog all precursor m/z and corresponding product m/z values for each…
Use when when working with large single-cell ATAC-seq or multi-omics datasets where in-memory storage is infeasible (>1M cells), and you need to iteratively add or modify count…
Use when after RAMClustR clustering and do.findmain molecular weight inference are complete, when you need to submit the same inferred spectra to multiple third-party annotation…
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 an untargeted metabolomics feature table (m/z values, retention times, p-values from statistical testing) and need to infer which metabolic pathways are active…
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 after matching mass-to-charge ratios to a KEGG database and obtaining multiple candidate metabolites per feature, but before filtering quasi-molecular adducts.
Use when when you have computed pairwise distances between MS2 fingerprint vectors from multiple metabolomics samples and need to visualize sample similarity relationships in low…
Use when when you need to establish a working installation of a Python package in a fresh or isolated environment, particularly when the package is available through multiple…
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 a pre-trained MS/MS spectral embedding model evaluated on one or more source datasets (GNPS, MoNA, MTBLS1572) and need to verify that it performs well on…
Use when you have extracted MS1 and MS2 scans in mzML/mzXML format from raw chromatogram files and a structured metadata file (containing retention time, m/z, compound name,…
Use when when you have access to the MAGMa source code and need to understand or audit how in silico metabolite candidates are enumerated from parent structures.
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 tandem mass spectra for compounds with known binary or categorical molecular properties (e.
Use when after installing ENPKG or any component of the workflow via conda/pip dependency manifests and before executing workflow scripts.
Use when when you have processed LC-MS data through XCMS alignment but suspect misaligned features due to retention-time drift over long acquisition periods (>1 week) or large…
Use when you have trained a shallow decision tree on ChemEcho feature vectors (representing unique peak or neutral loss formulas from tandem MS spectra) and need to deploy the…
Use when when you have a tandem mass spectrum (MSMS) with known peptide sequence and wish to assess whether enabling neutral loss annotation (e.g., NH3: −17.026549, H2O:…
Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the…
Use when when comparing two preprocessed MS/MS spectra for compound identification
Use when you have a collection of molecular structures intended for CypReact-based
Use when after mass-difference network generation has matched pairwise peak mass differences to a reference biochemical transformation key with mass error ≤1 ppm, and you need to…
Use when when you have raw LC-HRMS profile-mode data (rt × mz intensity matrices) and need to detect chromatographic peaks using gradient-descent or local-maxima algorithms.
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 after loading fragment counts into a SummarizedExperiment object (e.g., via getCounts) but before motif matching or deviation computation.
Use when you have a GNPS mass spectral molecular network (in graphml or cytoscape format) and want to enrich its nodes with chemical class information derived from GNPS public…
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 when you have extracted peak tables from multiple independent LC/HRMS analysis batches (each with retention time and m/z values) and need to align peaks across batches to…
Use when when annotating .msp mass spectrometry files with chemical structure metadata and you need fast, offline molecular transformations (SMILES↔InChI, canonical SMILES…
Use when when comparing two MS/MS spectra where the precursor m/z values differ (indicating potential mass modifications, adducts, or related compounds), and you want to detect…
Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a…
Use when when you have cloned a Python package repository and need to prepare a working environment for development, debugging, or contribution.
Use when you have prototyped a novel data-dependent acquisition strategy that uses dynamic exclusion with intensity or ROI weighting, and you need to quantitatively compare its…
Use when when installing HiC-Pro on a shared HPC cluster or multi-node computing environment where job submission must be routed through a scheduler rather than running locally.
Use when after mass track construction for individual samples, when you need to establish consensus m/z values across a cohort of LC-MS samples to build a unified feature table.
Use when when you have mzPeak files (Parquet-based archives in uncompressed ZIP containers) or other PyArrow-compatible columnar formats containing mass spectrometry spectra, and…
Use when after successfully matching at least 5 reference m/z points (from a .ref file) to spectrum peaks within a PPM error window (starting at ±1.0 ppm and widened iteratively…
Use when when you have a containerized scientific tool available on Docker Hub (e.