Use when immediately after loading metabolomics measurements into a SummarizedExperiment
Use when you have a new fragmentation acquisition strategy (e.g., a weighted exclusion variant, alternative TopN ranking, or dynamic isolation window rule) that you wish to…
Use when you have raw RNA-seq read counts and a set of normalization factors (e.g., TMM-computed library size scales from edgeR's calcNormFactors), and you plan to fit a linear…
Use when you have collected MS/MS spectra from a microbial sample (pure culture, environmental isolate, or mixed community) and need to assign chemical identities to observed m/z…
Use when you have raw MS intensity data paired with known-concentration calibration standard measurements, and you need to convert intensities to absolute or relative…
Use when when you have ionized adduct structures (SMILES or MOL format) from a prior ionization-state determination step and need to create multiple low-energy 3D conformations…
Use when when reproducing or auditing FIDDLE's formula prediction pipeline, or when implementing the TCN encoder in your own codebase and need to confirm that the precursor m/z…
Use when you have chemical annotations (GNPS spectral library matches) assigned to MS/MS samples and a validated ReDU sample-information template (TSV) with categorical metadata…
Use when when you have generated a scan index from rawrr::readIndex() on a Thermo .
Use when when you have raw mass spectrometry imaging data (full m/z profiles with intensity arrays) and want to classify spatial regions (e.
Use when you need to verify that a GitHub Actions workflow (such as a development build release pipeline) has completed successfully, capture its build artifacts (installers,…
Use when after running a 1D peak detection function (e.g., mzapy.peaks.find_peaks_1d_localmax
Use when when comparing two or more MSMS spectra using intensity-weighted similarity measures (cosine similarity, modified cosine, or neutral loss similarity), and the spectra…
Use when you have a time-series of repeated QCpool (pooled quality control) injections measured at regular intervals during one or more LC-MS/MS sequences, exported from Sciex…
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 when you have generated a feature abundance matrix from mzrtsim() peak list simulation with known sample-level attributes (condition assignments, batch labels, sample…
Use when you have a normalized count matrix (from Salmon or similar quantification
Use when you have paired GCF and MF datasets with strain membership information and need to rank candidate GCF–MF links to identify which biosynthetic gene clusters likely produce…
Use when you have normalized peak-abundance matrices with sample metadata containing categorical treatment variables (e.
Use when apply SSC when you have preprocessed and normalized MS imaging data (e.g., after TIC normalization and peak processing) and need to discover spatially distinct metabolite…
Use when after peak detection when you have a table of detected peaks with m/z values and need to improve mass accuracy for downstream annotation.
Use when you have a connected subnetwork of feature ions that have been validated as belonging to the same empirical compound (khipu instance), with isotope and adduct edges…
Use when you have computed a histogram of pairwise mass differences from MS peaks and want to determine which observed mass differences correspond to known chemical species such…
Use when when you have validated link annotations from multiple independent datasets (≥2), individual scoring functions with per-dataset enrichment p-values, and you want to test…
Use when when setting up a new computational environment for tandem MS/MS spectrum clustering or other proteomics analysis, and you need to install a tool (like falcon) that…
Use when immediately after extracting ion chromatograms (EICs) by binning mass spectral data across the full m/z range from raw LC/HRMS files (mzML, mzXML, or netCDF format).
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 when evaluating a trained spectral embedding model on publicly available datasets (GNPS, MoNA, MTBLS1572, MassBank, or MassSpecGym) and you need to report averaged…
Use when after generating ranked predictions of chemical formulas or subformulas for MS/MS spectra (from a neural network model like MIST-CF's formula transformer), compare…
Use when when preparing to read Thermo Fisher Scientific .raw files using rawrr functions (readFileHeader, readSpectrum, readChromatogram, readIndex), or when retrieving cached…
Use when when comparing mapped read counts between two RNA-seq quantification implementations (e.
Use when when cataloging a suite of related bioinformatics tools or web applications (particularly in domains like metabolomics, microbiology, or systems biology) and you need to…
Use when you have two or more feature tables in HDF5 format with detected peaks characterized across multiple dimensions (mz, drift_time, retention_time, intensity) and need to…
Use when when preparing to run Over-representation Analysis (ORA) on metabolomics pathway data, after you have loaded both a metabolomics pathway database (e.g., KEGG, MetExplore)…
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 processing paired augmented versions of the same input (e.g., two augmented ion images in COL or ISO mode) and you need to learn meaningful low-dimensional…
Use when you have a pre-trained GNN CCS prediction model and need to assess its predictive performance and cross-dataset generalizability.
Use when you have received a JSON response from the CSI:FingerID web service endpoint after submitting a fragmentation tree or tandem mass spectrum query, and you need to extract…
Use when you have draft metabolic reconstructions (in SBML or equivalent format) for multiple organisms sampled from a single ecological community (e.
Use when you have: (1) a trained IOKR model mapping from spectrum kernels to molecular fingerprints, (2) MS2 spectra from your sample, (3) a set of candidate BGCs with known or…
Use when after successfully constructing a nearest neighbor index from hashed spectrum feature vectors and before performing density-based clustering or similarity searches.
Use when when a user submits one or more MS/MS spectra and has declared or implied a domain context (microbial, plant, tissue, microbiome, food, or metadata aggregation), and the…
Use when when you have manually labeled LC-MS peaks as 'High quality' or 'Low quality' using NeatMS's annotation tool and need to create training/validation/test batches.
Use when you have access to both raw data (deposited in a repository like Zenodo) and analysis scripts (in a GitHub repository), and you need to confirm that the published…
Use when you have a feature list with m/z values from HRMS data and need to identify homologous PFAS series to prioritize suspect screening.
Use when when you have generated separate MemoMatrix objects from independent sample sets (e.g., sample set A and sample set B) and need to align and combine their MS2 fingerprint…
Use when after calling squidpy.gr.spatial_neighbors or any graph-building operation that outputs sparse matrices to adata.
Use when you have acquired untargeted MS data with orthogonal separations (LC, ion mobility) and/or data-independent acquisition (DIA) from Thermo, Agilent, or Bruker instruments,…
Use when you have raw read count matrices from RNA-seq quantification (e.g., from featureCounts, HTSeq, Salmon, or kallisto) and need to prepare them for differential expression…
Use when you have transcript-level quantification output files (quant.sf, quant.gz) from salmon, kallisto, sailfish, or oarfish and need to produce gene-level count matrices,…
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 after running the ENCODE Hi-C uniform processing pipeline or Juicer on FASTQ input data and generating a .hic output file.
Use when when comparing raw link scores (strain correlation or IOKR) across different GCF-MF or BGC-spectrum pairs and you need to distinguish true positive links from background…
Use when you have draft metabolic reconstructions in SBML or standard format for multiple organisms in a microbial community (e.
Use when implementing or validating a new MsBackend class that stores m/z and intensity values, or when assigning peak data to an existing backend.
Use when you have an aligned feature table from untargeted LC-MS with missing intensity values (NA or zero entries) for features that are present in some samples but fell below…
Use when when you need to quantify and compare the effect of multiple filtering thresholds (e.g., Match.Factor ≥65, ≥80, ≥90) on the size of a retained compound set.
Use when an ASB skill proved wrong, stale, missing or wasteful in practice — its steps failed, no skill covered the task, the leaves existed but nothing composed them, or the tool…
Use when you have a GNPS GraphML molecular network and need to isolate cohesive subsets of spectra (components) before analyzing which fragmentation patterns explain them.
Use when you have extracted and intensity-normalized fragment ion masses and neutral loss values from MS/MS spectra and need to prepare them for unsupervised topic modeling to…