Use when you have Thermo Fisher Orbitrap .raw files and need to locate and quantify specific peptide precursor ions (e.g., iRT calibrants, synthetic standards, or putative…
Use when when processing centroided .mzML LC–MS runs with a multi-polarity target list (i.e., some targets ionize in positive mode, others in negative mode, or both) and you need…
Use when when you have a parsed mass spectrum (precursor m/z, ionization mode, collision energy, and fragment peak list as m/z–intensity pairs) and need to obtain molecular…
Use when your input is a raw two-dimensional MS map (m/z vs retention time) derived from chromatography–mass spectrometry data with poor signal-to-noise characteristics, and you…
Use when when you have completed feature detection in MZmine3 or similar tools and produced a feature quantification table (rows = features, columns = samples with intensity…
Use when when you have a tandem mass spectrometry spectrum with a known or inferred peptide sequence that may contain post-translational modifications (phosphorylation,…
Use when after implementing or modifying a numerical compression codec (such as MSNumpressCoder for m/z and intensity arrays in mass-spectrometry workflows) to verify that…
Use when you have raw spectroscopic datasets from heterogeneous sources (multiple Zenodo repositories with different file formats and scales) that must be jointly normalized,…
Use when when you have a trained or untrained chemprop base model (graph convolution + readout layers) and need to extend it to predict infrared spectral properties rather than…
Use when when your DDA-mode LC-MS/MS data exhibits chimeric spectra patterns that differ systematically from the reference training set used in DNMS2Purifier, or when you wish to…
Use when after XCMS feature detection and alignment when you have a CSV-formatted
Use when when you need to extract both local spatial patterns and global long-range dependencies from sequential or spectral data (e.g., 1H NMR spectra), and neither CNNs nor…
Use when you have loaded an MsmsSpectrum object from a proteomics or metabolomics dataset and need to focus the analysis window on a specific m/z range relevant to your experiment…
Use when apply batch normalization after dense hidden layers (but not the final embedding layer) in a deep neural network trained on MS/MS spectral data, particularly when the…
Use when after drift correction and before imputation when you have LC-MS data with designated QC samples and you need to remove features with poor reproducibility across QC…
Use when you have a pre-generated .hic contact map file (from Juicer pipeline or external source) and need to systematically call chromatin loops, detect topologically associating…
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 processing raw MS/MS spectra (in MGF, mzML, mzXML, JSON, or MSP format) prior to MS2Query library matching or MS2Deepscore embedding calculation.
Use when after initializing and executing a forward pass through a dual-branch RT-Transformer model (combining fingerprint and molecular graph inputs) on a batch of molecular…
Use when your input is raw .idat files or a beta-valued matrix from Illumina HumanMethylation450 or EPIC arrays, and you need to remove unreliable probes (those with detection…
Use when you have GNPS-style MGF spectral files as input and need to run Mass2SMILES MS/MS-to-structure inference without installing TensorFlow, CUDA, or Python dependencies…
Use when you have a working base MPNN model (e.g., chemprop) and need to add task-specific feature processing layers (spectral, electronic, or domain features) to improve…
Use when when you have a USI string (e.g., 'mzspec:GNPS:TASK-abc123:scan:1943') and need to retrieve the underlying spectrum data from its native repository without knowing a…
Use when after extracting raw MS/MS spectra from mzML files for individual features (identified by precursor m/z and retention time) and you have multiple replicate spectra for…
Use when you have raw metabolomics data files in one or more of the supported formats (.raw from Thermo instruments, .d directories from Agilent, or mzXML open-format exports) and…
Use when when comparing two MS/MS spectra (query and reference) to quantify their spectral resemblance for compound identification or molecular networking, particularly when you…
Use when you have raw ATAC-seq BAM files and need to perform footprinting analysis to detect transcription factor binding through Tn5 insertion patterns.
Use when you have transcript abundance estimates from RNA-seq quantification tools (e.
Use when when building an extensible converter framework where new converter implementations (e.g., WebConverters or ComputeConverters for external chemical services) should be…
Use when you have draft metabolic reconstructions (in SBML or standard format) for multiple organisms sampled from the same microbial community and need to produce a single…
Use when you have 512-dimensional representation vectors output from ResNet18 encoders processing paired augmented ion images, and you need to prevent trivial solutions…
Use when when you have separate LC-MS peak tables for unlabeled (C12) and labeled (C13) isotope tracer experiments and need to identify which features correspond to the same…
Use when you have MS/MS spectra contaminated with chemical noise (spurious fragment ions that do not correspond to real chemical bonds or rearrangements), a known or predicted…
Use when you have raw mass spectrometry instrument output (mzML, vendor binary formats, or mzPeak archives) and need to load spectrum metadata, chromatogram data, or signal arrays…
Use when when you have deposited a collection of JSON project documents in a platform and need to verify that all conform to the published schema before public release or — from…
Use when after Casanovo has generated ranked peptide sequence predictions from MS/MS spectra and you need to persist, share, or integrate the results into a proteomics data…
Use when you have normalized or voom-transformed gene expression counts/intensities indexed by gene and sample, along with an experimental design matrix specifying condition,…
Use when you have raw MS intensity tables showing systematic drift during a measurement sequence (e.g., declining or variable ion counts across a run), particularly in targeted…
Use when after loading a raw MsmsSpectrum object from a tandem mass spectrometry
Use when you have a calibrated FT-ICR transient (ESI_NEG or similar ionization mode) and need to annotate each detected m/z peak with its most likely elemental composition.
Use when when you have antiSMASH-predicted BGCs and wish to link them to metabolomic data via structure prediction, but only BGCs with sufficient structural homology to…
Use when you have an untargeted metabolomics feature table (with m/z and retention time columns) and a metabolic network database with compound chemical formulas, and you want to…
Use when after EIC candidate generation and peak detection have been completed on LC/HRMS data, when you need to extract the retention time and intensity values at peak maxima for…
Use when immediately after loading raw methylation array data (.idat files or beta-valued matrix) from HumanMethylation450 (450k) or EPIC arrays when conducting primary quality…
Use when after importing raw LC-MS/MS data files into the SIRIUS Java framework, before constructing indexed spectrum objects or submitting data to CSI:FingerID, CANOPUS, or…
Use when you have a trained GNN model predicting CCS values from molecular graphs and need to understand which structural features (node and edge attributes) are most influential…
Use when you have 1D NMR spectra (¹H or ¹³C or both) for an unknown organic compound with ≤19 heavy atoms and need to rapidly predict its molecular formula and connectivity graph…
Use when you have transcript-level quantification output files (e.g., quant.sf from salmon, abundance.
Use when you have preprocessed individual GCxGC-MS chromatograms (each smoothed with Whittaker smoother, baseline-corrected with asymmetric least squares, and aligned against a…
Use when you have experimental RT measurements from a source chromatographic method and need to predict RTs for the same molecules on a target chromatographic method, but lack a…
Use when you have raw or peak-picked mass spectrometry data in HDF5 format that needs to be loaded into memory for downstream processing (feature alignment, isotope detection, CCS…
Use when you have access to a project README or repository documentation (Zenodo deposit, GitHub, or local clone) describing multiple domain-specific web applications, and you…
Use when you have MS imaging or LC-MS data with pre-annotated m/z values that include multiple isomer or metabolite names per m/z (stored as semicolon-delimited or multi-record…
Use when your LC-HRMS metabolomics analysis must run on a high-performance computing cluster (e.g., HiPerGator, SLURM-managed systems) that lacks Docker support or prefers…
Use when when implementing a custom MsBackend and the spectraData() method needs to return all core spectra variables (e.g., centroided, polarity, collisionEnergy) regardless of…
Use when you have a backed AnnData object populated with fragment coordinates (stored in .obsm['fragment_paired'] or .
Use when before constructing a DESeqDataSet from any count matrix (whether from tximport, HTSeq, featureCounts, or raw counts).
Use when after RDKit has generated a large set of 3D conformers for a molecule in SDF or XYZ format, and before submitting conformers to computationally expensive quantum-chemical…
Use when when you have a C++ library (such as OpenMS) with nanobind binding specifications in a designated bindings directory and need to create a Python module that exposes C++…
Use when you have nuclear magnetic resonance (NMR) peak data (1H and 13C measurements) that you need to classify using a deployed SMART 3 model, and you want to submit peaks…