Use when when deploying a new Python package in a reproducible analysis environment or continuous integration pipeline, and you need to confirm that all required core modules…
Use when when quantifying or mapping RNA-seq reads with salmon quant using the --writeMappings (-z) flag, or in any streaming output scenario where record count discrepancies…
Use when you are preparing to run Hi-C data normalization or read alignment filtering steps that depend on Python modules (iced, pysam, numpy, scipy) and you need to ensure…
Use when when you have centroided .mzML LC–MS runs and a target list (compound ID, theoretical m/z, expected RT, polarity) but are uncertain whether your m/z and RT windows are…
Use when when generating synthetic LC/GC-MS .mzML files from MoNA or HMDB spectral records where you need to compute absolute ground-truth maximum intensity (sim_ins) for each…
Use when when you have a collection of mzML.gz files from a multidimensional MS instrument (e.
Use when you have multiple mass spectral library files in different formats (MSP, MGF, MOL folders) from sources like NIST, MoNA, RIKEN, or GNPS, and need to produce a single…
Use when after creating a fresh conda environment from a pinned dependency specification (environment.yml or requirements.txt) and installing packages via conda and/or pip.
Use when after running qiime qemistree make-hierarchy and obtaining a tree artifact (qemistree.
Use when when you have tandem mass spectrometry data (LC-MS/MS in MGF, mzML, mzXML, or mzData format) paired with either genome sequences or precursor peptide predictions, and you…
Use when you have measured CCS values from (LC-)IM-MS samples spiked with U¹³C labeled internal standards (e.
Use when after data merging and cleanup (blank removal) and before univariate or multivariate statistical analysis, when your merged feature table (samples as columns, metabolite…
Use when when you have pre-processed MS/MS spectra and a pre-trained Word2Vec model, and need to compute fast, scalable similarity scores for library matching or molecular…
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 you have two peak-picked, conventionally aligned untargeted LC-MS metabolomics datasets (metabData objects) acquired under different conditions and need to ident — from…
Use when after extracting NMR spectra and designating replicate QC samples (typically 10 samples run throughout the study), calculate CV for each metabolite feature to assess…
Use when a deep learning model for molecular structure prediction (e.g., NMR2Struct) has been trained and evaluated on a limited molecular size range (e.
Use when when you have limited real GC-MS overlapped peak data but need thousands of labeled examples to train a deep learning model for mass spectral deconvolution.
Use when after invoking pp.make_fragment_file to convert a coordinate-sorted BAM file (e.g., from 10X ATAC or standard alignment) into a compressed fragment file.
Use when you have preprocessed metabolite intensity data (log2-transformed, zero-mean unit-variance standardized) mapped to compound annotations, and you need to derive activity…
Use when you have raw IM-MS data in UIMF or Agilent MassHunter .d format acquired using multiplexed (compressed) ion mobility pulse sequences, and you need to recover con — from…
Use when after training multi-layer perceptron neural networks via cross-validation
Use when after peaks have been detected in aligned GCIMS samples using findPeaks with CWT parameters and peaks have been clustered across samples, and you need to integrate peak…
Use when after training contrastive embeddings that unify MS/MS spectra and molecular structures into a shared embedding space.
Use when when you have a pre-cleaned spectral library (e.g., GNPS, MoNA, or MTBLS1572) with an existing training/test boundary established by prior work (e.g., MSBERT), and you…
Use when when you have a metabolomics abundance table with missing values and need to decide which imputation method to apply, or when designing a simulation to evaluate…
Use when after running spectral networking on tandem MS data and obtaining a network graph, when you need to assess which spectra cluster together, determine cluster…
Use when you have peak data from MSI experiments (stored as .zip peak matrix files) where matrix ions (e.g., silver adducts in AgLDI-MSI) dominate the spectrum and obscure analyte…
Use when you have developed or adapted a peak detection method for chromatography–mass
Use when you have transcript quantification output (TPM or raw counts) from a pseudo-aligner (Salmon or kallisto) and an ioe/ioi event definition file from SUPPA2's generateEvents…
Use when after completing an Environment simulation run with save_eval flag enabled, when you need to preserve the EvaluationData object containing scan provenance, chemical…
Use when after a transformer-based de novo sequencing model (such as Casanovo) generates candidate peptide sequences from MS/MS spectra, before exporting results or using them in…
Use when you have assembled microbial genomes (nucleotide FASTA files) and want to identify biosynthetic potential and group related BGCs for downstream linking with metabolomic…
Use when after molecular formula assignment and peak filtering are complete, when you have a filtered peak list (m/z values and molecular formulas) and want to discover…
Use when you have GC–MS or LC–MS data represented as a two-dimensional map with m/z values on one axis and retention time on the other, and you need to identify analyte signals…
Use when you have uploaded a delimited data file (CSV, TSV, or semicolon-separated)
Use when you have raw HPLC column metadata containing categorical fields (e.g., column manufacturer 'Waters', USP type 'L1', solvent identities 'H2O'/'MeOH'/'ACN') that must be…
Use when before invoking any Python module in a multi-step Hi-C processing pipeline, or when a dependency has been freshly installed or reinstalled.
Use when you have vendor-independent centroided mzML files from LC- or GC-HRMS data acquired in data-dependent acquisition (ddMS2) mode and need to extract detected features with…
Use when when you have high-resolution tandem mass spectrometry (MS2) data in .ms2 format and need to identify and annotate lipid A structures at scale.
Use when you have extracted mass tracks (EICs) from individual samples at 0.001 amu m/z resolution and need to align them into a composite mass grid for feature detection.
Use when when preparing XCMS peak tables for quality classification and you observe that the default RSD threshold (0.3 or 30%) is either too permissive (retaining noisy EICs) or…
Use when when you have a repository containing hundreds or thousands of structured records (e.g., MassBank records in standardized format) that must be validated for correctness…
Use when after computing a sparse pairwise distance matrix from nearest neighbor indexes of MS/MS spectra (in mzML, mzXML, or MGF format), and you need to assign each spectrum to…
Use when you have a metabolite intensity matrix (samples × metabolites) with assigned annotations (peak IDs mapped to KEGG or ChEBI compound IDs), a metabolic pathway database,…
Use when when you have source code access to a webservice component (such as the MAGMa joblauncher) and need to enumerate all exposed HTTP endpoints, their methods (GET, POST,…
Use when you have raw MS/MS feature data with m/z, retention time, and fragmentation spectra from an untargeted metabolomics experiment, and you need to annotate reaction-derived…
Use when when analyzing high-resolution mass spectrometry data from natural-abundance
Use when you have raw untargeted LC/MS data in open mzML or mzXML format and need to extract a quantified feature matrix (m/z and retention time coordinates with sample…
Use when you have a published computational pipeline with deposited code and validation data, and you need to verify that the pipeline can be executed end-to-end to reproduce…
Use when after generating a Chemical Feature Tree artifact (Phylogeny[Rooted]) from q2-qemistree's make-hierarchy method, or when importing a tree from external sources, to…
Use when when you have molecular structures encoded as SMILES strings and need to incorporate them into a multi-modal language model (such as BART) that also processes mass…
Use when when you need to inventory a collection of related web applications or tools distributed across multiple repositories, discover their live deployment URLs, trace their…
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 converting JSON metadata and you need to populate a target field by selecting or iterating over records only when they satisfy a logical test condition (e.g., 'include…
Use when you have identified a package available in the Bioconda channel (indicated by a conda version badge or Bioconda recipe URL) and need to verify that installation succeeds…
Use when you have two or more complementary scoring functions (e.g., strain correlation and IOKR scores) that you wish to combine, and you need to determine which combination…
Use when after computing gene set enrichment scores (e.g., via GESECA on reverse PCA feature loadings) on a single-cell or bulk dataset with an existing dimensionality reduction…
Use when after building a SummarizedExperiment object containing LC-MS peak areas and internal standard assignments, when you need to identify study samples with anomalous…
Use when after individual mass tracks (EICs) have been extracted from each sample''s mzML file and you need to create a unified, cross-sample m/z reference structure.