Use when you need to deploy a complex multi-language pipeline (e.g., HiC-Pro) that requires Python >3.7 libraries (pysam, bx-python, numpy, scipy), R packages (ggplot2,…
Use when when you have (1) transcriptomics data and a metabolic network model with GPR rules to compute RAS scores; (2) constraint-based model predictions (RPS from optGpSampler…
Use when you need to open an mzML file in pymzML and must automatically select the correct handler based on file extension (.mzML, .mzML.gz, .db) and—for gzip files—indexed vs.
Use when you have observed compounds (from LC-MS, GC-MS, or spectroscopy) and a set of predicted metabolite structures from BioTransformer, and need to assign identities to the…
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 when beginning ChIP-Seq analysis with single-end BED/SAM input and no prior knowledge of the library's fragment length.
Use when you have deconvolved GC-MS spectra (from overlapping chromatographic peaks) in MGF or mzTab format and want to group chemically related compounds, visualize their…
Use when you have MS/MS spectra matched to a reference library via both identity search (exact or high-similarity matches) and fuzzy/analog search (structurally related compounds…
Use when you have an unknown metabolite with unknown mass spectrum and need to prioritize structural candidates from databases (PubChem, HMDB) by their likelihood of being the…
Use when you need to persist and communicate the health status of multiple external web services queried during an annotation run.
Use when you have clustered single-cell RNA-seq data (via Leiden, Louvain, or equivalent) and a k-nearest neighbor graph computed in PCA space, and you want to abstract cell-level…
Use when when you have cloned a multi-framework .NET project (e.g., MsdialWorkbench
Use when after constructing a NetworkX graph object from structural clusters (via MamsiStructSearch), when you need to interactively explore feature relationships or publish a…
Use when you have pairs of augmented ion images from mass spectrometry imaging data and need to generate low-dimensional representation vectors that maximize similarity between…
Use when you have peak intensity vectors from LC/GC-MS experiments with corresponding QC (quality control) sample measurements, and you need to correct for batch…
Use when you have assembled genomic DNA sequences (contigs in FASTA format, not antiSMASH or BOA output) and corresponding LC-MS/MS data (in MGF, mzXML, mzML, or mzData format)…
Use when you have acquired full-scan mass spectrometry imaging data (e.g., from a mouse bladder or tissue section) with detected m/z features and want to assign chemical…
Use when you have deconvolved GC-MS spectra in GNPS_GC input-compatible format and want to construct a molecular network to identify relationships between unknown compounds and…
Use when you have raw GC-MS or LC-MS data in vendor format (NetCDF, .raw, .d) or generic mass lists, and you need to assign chemical identities to detected peaks.
Use when after feature table normalization and imputation are complete, immediately before MS1 and MS2 annotation.
Use when you have deconvoluted or processed MS/MS spectra from SWATH-MS data that need to be (1) ingested into tools requiring open formats (e.g., spectral library matching,…
Use when you have experimental retention times (RTs) for a small set of calibration molecules (≥10) measured on both a source chromatographic method and a target method, and you…
Use when you have individual MS/MS spectra or batch .mgf files from untargeted metabolomics experiments and need to search them against domain-specific reference libraries (e.
Use when a practitioner has pre-computed features from an external feature-finding procedure (e.g., vendor software, alternative open-source tools) and wishes to incorporate them…
Use when when training a fresh NeatMS CNN model from scratch on LCMS peak classification and you need to determine which optimizer (Adam vs.
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 raw or Seurat object-backed scRNA-seq expression matrix and need to: (1) stabilize variance across genes with SCTransform normalization, (2) extract feature…
Use when immediately after executing the MetaboAnalystR 4.0 unified LC-MS workflow (feature detection and quantification module) on raw mzML or netCDF data.
Use when you have raw GC-MS data with overlapped peaks in a specific retention time region and need to resolve the individual pure mass spectra of all components present in that…
Use when after scipy.signal.find_peaks has identified candidate peaks on a composite mass track segment, evaluate each peak to decide whether to retain it in the final feature…
Use when after computing all pairwise mass differences from a mass spectrometry imaging dataset, when you need to identify which mass differences correspond to real molecular…
Use when you have GC-MS data preprocessed into a structured spread format and need to confirm that a set of known or suspected compounds are correctly identified in your samples.
Use when after filtering LC-MS features by statistical significance (e.g., p-value < 0.01) and you wish to group features that represent the same metabolite at different — from…
Use when your gene expression matrix or pathway collection uses identifier formats incompatible with your enrichment analysis tool (e.g., gene symbols vs.
Use when you have untargeted metabolomics data with unknown or ambiguous molecular identities, anchor metabolites (known structures in SMILES or MOL format), and a curated…
Use when you have trained a DNN retention time predictor and need to rank candidate metabolites for an unknown compound: the DNN outputs both point estimates and uncertainty…
Use when when processing low-resolution GC-MS data in NetCDF format where you have already performed retention-index calibration and peak deconvolution, and you need to assign…
Use when when you have downloaded raw spectroscopic datasets from multiple sources (NMR, HSQC, COSY, IR files) and need to combine them into a single coherent training corpus…
Use when when you have a small-molecule structure (SMILES, MOL, or SDF format) and need to identify probable metabolites or degradation products in a specific biological — from…
Use when you have a pretrained deep learning model, a reserved test set with ground-truth annotations, and need to evaluate prediction quality or generate embeddings for…
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 you have cloned or loaded a deep-learning architecture extension (e.g., chemprop-IR) and need to verify that its feature extraction component can be instantiated and…
Use when you have generated consensus metabolic reconstructions for multiple members of a microbial community (e.
Use when you have detected and clustered unknown MS features from untargeted xenobiotic metabolomics data, computed fragmentation pattern similarity scores between features and…
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 you have extracted retention times from MS1 spectra for top signals in a single LC-MS/MS run and need to evaluate whether that gradient's separation performance is…
Use when after calling MsmsSpectrum.annotate_proforma() to assign fragment ions to a mass spectrum, verify that each annotated peak has the correct ion_type ('b' or 'y'), charge…
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 immediately after peak detection in the IDSL.IPA workflow, when you have a list of candidate peaks extracted from EIC data and need to remove noise-dominated signals…
Use when you have MS/MS spectra in MGF or similar format and a reference library of molecular structures (SMILES or SDF), and your goal is to retrieve the most likely structures…
Use when you have mass spectrometry imaging data in Cardinal format (versions 2.
Use when you have loaded raw NMR or MS metabolomic abundance data into a SummarizedExperiment object and need to assess feature reproducibility before downstream association…
Use when you have two co-registered LA-ICP-MS element channel images and need to quantify whether their spatial distributions are statistically correlated or independent.
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 after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
Use when you have generated or received bedGraph files from paired-end sequencing (via bedtools genomecov or similar) and need to verify they conform to UCSC bedGraph format…
Use when you have transcript-level quantification files (salmon quant.sf.gz, kallisto h5, or Sailfish output) and need to perform gene-level differential expression analy — from…
Use when after you have detected LC-MS features, grouped them into empirical compounds via isotope and adduct clustering (using khipu), and have accurate m/z and retention time…
Use when you have a query mass spectrum (or representative metabolite spectrum from public data) and need to identify it by searching against large spectral reference databases…
Use when when you have tandem mass spectra (mz/intensity pairs with precursor m/z) and need to train interpretable machine learning models—particularly decision trees or — from…