Use when when reading mzPeak files or other Parquet-backed mass spectrometry archives where spectral m/z and intensity arrays are stored in columnar layouts (point or chunked…
Use when when you have pre-computed Word2vec spectrum embeddings and need to perform fast approximate nearest-neighbor retrieval from a library of millions of spectra (e.g., NIST…
Use when you have raw Hi-C FASTQ files from a high-throughput chromatin conformation capture experiment and need to generate a normalized contact matrix (.hic file) for downstream…
Use when when building a neural network to map between mass spectrometry spectra and molecular properties (e.g., fingerprints, SMILES, or fragment ions) where sequential or…
Use when after matrix annotation has been performed on mass spectrometry imaging (MSI) data when you need to identify and document ions whose m/z values overlap with or are…
Use when you have newly assayed 1H-NMR metabolomics data from Nightingale Health (CSV or TSV format) and need to apply one or more published metabolic risk scores (Deelen et al.
Use when you have an LC-MS peak-intensity matrix (rows = peaks with m/z and intensity; columns = samples) and need to assign KEGG compound identifiers to observed peaks.
Use when you have raw .idat files or beta-valued matrices from HumanMethylation450 (450k) arrays and need to remove low-quality probes, correct for technical artifacts (batch…
Use when when you need to construct a dual-branch neural network encoder that processes two augmented versions of the same input (e.g., ion images in COL or ISO mode) and must…
Use when you have Bruker NMR spectral files (raw instrumental output) and need to prepare them for automated metabolite identification and quantification.
Use when you have raw peak tables exported from a tandem mass spectrometry preprocessing tool (e.g. Progenesis, MS-DIAL, or Bruker Metaboscape) and need to integrate them with…
Use when you have genome FASTA or annotated genome files (antiSMASH .gbk, BOA .annotated.txt) and wish to discover ribosomally synthesized and post-translationally modified…
Use when immediately after loading raw single-cell gene expression count matrices (AnnData objects) and before identifying highly variable genes or performing dimensionality…
Use when when preprocessing a heterogeneous spectral library (e.g., GNPS public library) that contains spectra from multiple instrument types, and you need to partition data by a…
Use when when you have high-resolution tandem MS/MS spectra in mzML, mzXML, or MGF format and need to cluster or search millions of spectra efficiently.
Use when after feature detection but before statistical analysis, when your study includes blank samples (e.g., solvent or extraction blanks) and you want to remove features that…
Use when when preparing mass tracks for retention-time (RT) alignment across multiple LC-MS samples.
Use when your metabolomic dataset contains missing values (common in untargeted or targeted mass spectrometry data) and you need to perform PCA for outlier detection at multiple…
Use when performing untargeted metabolomics annotation (i.e., matching observed spectra to a compound database without a pre-defined target list) and you need to assign…
Use when you have observed compounds (from LC-MS/MS, GC-MS, NMR, or other analytical techniques) with unknown identity and you want to assign candidate metabolite structures by…
Use when after applying pycombat-based batch correction to multi-batch interpolated feature tables in LC-MS metabolomics workflows, when you need to verify that batch effects have…
Use when when you need to capture a snapshot of a research software project's health metrics from multiple CI/CD and repository services (Travis CI, Landscape.
Use when you have paired spatial transcriptome and metabolome datasets (both as h5ad files with .obsm['spatial'] coordinate matrices and .
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 spectrum or chromatogram data stored as XML strings (e.g., in a SQLite database indexed by spectrum ID) and need to access individual spectra by ID or iterate…
Use when when executing peak integration on preprocessed GC-IMS data (after alignment and baseline correction) and you need to decide whether to include or exclude peaks that…
Use when after preprocessing, imputation, and batch correction of LC-MS peak tables when you need to group redundant or related feature measurements (e.g., [M+H]+ and [M+Na]+…
Use when after MS-Dial peak picking and feature table construction, when you observe a high proportion of features with anomalous m/z decimal values that are inconsistent with…
Use when after applying mspcompiler pipeline transformation steps (e.g., reorganize_mona, assign_smiles, assign_ri, read_multilibs, separate_polarity, complete_mgf) to confirm the…
Use when you have paired microbiome and metabolomic abundance tables (samples × features) with relative abundance or raw count values, and you are preparing data for downstream…
Use when you have instantiated a learned component (embedding layer, encoder, or transformer submodule) from a published codebase and need to verify that its forward pass produces…
Use when when comparing mapped read counts between two RNA-seq quantification implementations (e.
Use when you need to validate that a software project''s release branch is stable and ready for distribution.
Use when when you have an aligned GCIMS dataset and need to configure the findPeaks function with CWT algorithm to detect peaks across retention time and drift time dimensions.
Use when you have a cooler file (.cool or .mcool) from a Hi-C experiment and need to generate a genome-wide track of per-bin sequencing depth to assess coverage uniformity,…
Use when you have a GNPS-generated classical or feature-based mass spectral molecular network (graphml or JSON format) and a corresponding MS2LDA experiment with Mass2Motif…
Use when you have raw tabular experimental metadata (mass spectrometry or NMR sample descriptions, sample-to-treatment mappings, instrument parameters, etc.) that needs to be…
Use when when beginning an LC-MS/MS metabolomics analysis pipeline and you have preprocessed xcms result objects (XcmsExperiment or legacy xcmsSet) that need to be loaded into…
Use when you have loaded a collection of molecular fingerprint vectors (such as biosynfoni fingerprints from a deposited dataset) and need to characterize their statistical and…
Use when you have aligned feature tables (CSV format) with corresponding MS2 spectra data (MGF or mzML files), and need to construct a sample-level vectorization matrix where each…
Use when after nontargeted peak detection has identified candidate peaks in LC-MS chromatograms, when you need to establish exact peak start/end retention times and extract…
Use when after executing the Juicer pipeline on raw Hi-C FASTQ files, to confirm that the pipeline has generated the expected .hic output artifact and that the contact matrix…
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 need to verify that a Python package (or similar installable software) passes its declared integration test suite as a prerequisite to trusting its reliability in…
Use when when processing untargeted LC-MS metabolomics data with XCMS and need to identify low-quality peak integrations that may introduce noise or bias into subsequent compound…
Use when when you have aligned ChIP-Seq reads (BED or BEDPE format) and a corresponding control sample, and you need explicit control over peak-calling parameters—including…
Use when when you need to prepare mass spectra and molecular structures for joint modeling in a BART or transformer-based sequence model, and you lack a unified representation…
Use when when exporting quantified ion images and pixel metadata from LipidQMap to HDF5 format for use in downstream Cardinal or other MSI analysis workflows.
Use when you have preprocessed MS/MS spectra with measured precursor m/z values but the ionization adduct type is unknown or ambiguous—particularly in metabolomics workflows where…
Use when you have natural product molecules (or compounds from natural product-like databases such as COCONUT or ZINC) in structural format (SMILES, InChI, or SDF file) and need a…
Use when when you have ranked gene statistics and gene set collections, and your analysis requires P-value discrimination below a fixed lower bound (e.g., distinguishing between…
Use when augmenting mass spectrometry ion images for contrastive learning, specifically when you need to simulate the natural Poisson noise that arises from photon-counting…
Use when you have aligned ATAC-seq BAM files, corrected Tn5 insertion bias and computed footprint scores (via TOBIAS ATACorrect and ScoreBigwig), a motif database in JASPAR or…
Use when you have uploaded a pre-analytical data table containing sample metadata, processing delay timestamps (pre- and post-centrifugation), and NMR metabolomic measure — from…
Use when when you have paired mass spectra and molecular structure data and need to train a model that can bidirectionally map between experimental spectra and chemical s — from…
Use when you have imported a raw GCxGC-MS chromatogram (NetCDF format folded into 2D-TIC) that exhibits chemical noise, instrumental artifacts, or baseline drift—conditions that…
Use when after peak detection and before any comparative analysis (e.g., diversity indices, ordination, or statistical testing) when working with direct injection FT-ICR MS data…
Use when analyzing CE-MS(/MS) data where electroosmotic flow fluctuations cause variable migration times for the same compounds across runs.
Use when you have parsed imzML XML metadata and loaded the corresponding .ibd binary intensity file, and need to extract specific ion images at one or more target m/z values.
Use when after loading a specXplore session data object file from the hard drive and instantiating a dashboard session layer with it, validate that the architecture layer has…