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 you need to obtain source code or computational workflows from a published repository, particularly when the article explicitly provides a GitHub URL and documents that…
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 when deploying an R package from a non-CRAN repository (e.g., r-universe, Bioconductor, GitHub), or when verifying that a package build is reproducible and meets CRAN…
Use when when comparing experimental spectra to reference library spectra and fragment ion m/z values show systematic drift or measurement noise that could distort neutral loss…
Use when when you have a set of candidate LC gradients (parameter combinations) that you wish to evaluate with a Gaussian process model, or when you need to convert raw gradient…
Use when when you have a target compound (modified or unmodified) and need to obtain its experimental MS/MS spectrum and metadata to serve as a known reference for ModiFinder…
Use when when comparing two MS/MS spectra using modified cosine similarity and the precursor m/z values differ, indicating potential neutral losses, adduct variations, or analogs…
Use when when you have deposited or archived biosynfoni fingerprint vectors (such as from Zenodo 10.5281/zenodo.14822624) and need to ingest them into a Python workflow to compute…
Use when you have mass spectrometry data (m/z, retention time, intensity) loaded into a Pandas DataFrame and need to explore the full 3D structure of a peak map interactively,…
Use when you need to verify that visualization functions produce graphically correct output that matches previously validated baseline images.
Use when after fitting a Multi-Block PLS (MB-PLS) discriminant or regression model on multi-assay LC-MS intensity data (e.g., HPOS, LPOS, LNEG blocks), and you need to identify…
Use when you have raw MS2 spectra in common formats (mzML, mzXML, msp, MGF, JSON) from one or more metabolomics samples, and you need to prepare them for MS2 fingerprint — from…
Use when when you have coordinate-sorted BAM files from single-cell ATAC-seq experiments (e.g., 10X Genomics scATAC-seq) and need to generate a compressed fragment file for…
Use when when benchmarking or validating the scalability of single-cell algorithms that claim linear or sublinear space complexity, particularly when processing datasets with ≥10…
Use when when you have isolated, high-confidence reference chromatographic peaks (ground-truth) from reference LC-HRMS chromatograms that have been matched across multiple…
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 MS2 fragmentation spectra from multiple metabolomics samples and need to compare them in a retention time-agnostic manner, especially when samples are chemically…
Use when when setting up a new conda environment for a Python-based bioinformatics pipeline and you need to confirm that all declared dependencies (e.g., pysam >=0.15.4, bx-python…
Use when you have computed RAS (Reaction Activity Scores) from transcriptomics and GPR rules, RPS (Reaction Propensity Scores) from intracellular metabolomics via mass-action…
Use when you have a log2-normalized, zero-mean and unit-variance standardized intensity matrix of metabolite features (rows=metabolites, columns=samples) and need to compute a…
Use when you have PSI (percent-spliced-in) matrices calculated independently for two or more biological conditions, each with two or more replicate samples, and you want to…
Use when you have raw or processed arrival-time data from a traveling-wave ion mobility mass spectrometry (TWIM-MS) platform and need to convert it into standardized collision…
Use when you have an untargeted metabolomics feature table with m/z values, retention times, and intensity measurements, a metabolic network representation with compound — from…
Use when processing raw GC-MS data in NetCDF format where peaks have been detected but lack standardized retention indices.
Use when you have completed Hi-C map generation (producing .hic files from aligned reads) and need to detect and annotate topological features such as chromatin loops,…
Use when when you have deposited mass spectrometry imaging datasets for plant roots in CDF format paired with pre-computed Matlab workspaces, and you need to reproduce per-root…
Use when you have a feature list with assigned molecular formulas and m/z values from non-target HRMS analysis, and you need to identify and rank potential PFAS compounds among…
Use when after XCMS feature detection and alignment when you have a CSV-formatted
Use when when processing LC-MS data with multiple overlapping m/z scan windows and observing sawtooth-pattern distortions in EICs during tardisPeaks() execution.
Use when you have preprocessed 1H NMR spectral data (e.g., from plasma or biological samples acquired on a 600 MHz instrument) and need to identify the chemical composition of a…
Use when when you have a complete metabolomics abundance table (e.g., targeted LC/MS or untargeted GC/MS counts) and need to generate synthetic left-censored missingness for…
Use when when you have peripheral blood sample cohorts (plasma/serum) with multiple timestamps (e.
Use when you have a set of natural product molecules (or suspected natural products) in SMILES, InChI, or SDF format and need a chemical representation suitable for biosynthetic…
Use when when you have extracted MS2 spectra from DDA chromatographic peaks and need to identify the originating compound by comparing against reference MS2 spectra (e.g., from…
Use when importing raw or public mass spectrometry spectral data in formats such as MGF, MSP, or mzML that may contain incomplete metadata (e.g., missing instrument type,…
Use when you have preprocessed tandem mass spectrometry spectra converted into a bag-of-fragments representation (with fragments and neutral losses extracted and noise filtered)…
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 an unknown MS/MS spectrum (with ≥10 peaks, precursor m/z, and at least 5 fragment ions) and need to identify it by comparing against a curated spectral…
Use when when you have installed a Python package (e.g., via pip or conda) and need to confirm that the installation succeeded and all expected submodules can be imported.
Use when when you have: (1) a collection of molecules represented as molecular graphs (nodes=atoms, edges=bonds with chirality/order attributes); (2) structured metadata…
Use when you have raw GC-MS output files (vendor formats or netCDF) from a chromatography instrument and need to prepare them for automated peak deconvolution and spectral…
Use when you have executed batch searches of MS/MS spectra against multiple domain-specific MASST tools and need to synthesize results across domains (e.
Use when when you have preprocessed MS/MS spectral peak data (m/z and intensity pairs) and need to compute a complexity metric for individual spectra prior to similarity…
Use when you have executed multiple database search pipelines (Dereplicator, VarQuest, and/or Dereplicator+) on centroided LC-MS/MS spectra (in MGF, mzXML, mzML, or mzData format)…
Use when you have long-read RNA-seq samples quantified by oarfish (output as quant.gz files) and need to extract transcript-level or gene-level abundance, count, and length…
Use when you have millions of MS/MS spectra to cluster and have already constructed nearest neighbor indexes (partitioned Voronoi diagrams of spectrum vectors bucketed by…
Use when after performing LOWESS regression on landmark peak RT pairs between a sample and reference, you need to encode the learned RT transformation as a reusable,…
Use when when fitting a multi-block PLS discriminant model on multi-assay LC-MS metabolomics data and you need to determine the number of latent variables to retain without…
Use when after performing an ANOVA-style multi-group de_design() analysis on a LipidomicsExperiment object, when you need to determine whether a categorical sample variable (e.g.,…
Use when when importing mass spectrometry spectral data from public repositories or multi-source MGF/MSP files where metadata fields are inconsistent, missing, or non-standard;
Use when salmon quant is run with the --writeMappings/-z flag and you need to verify that all mapped reads appear in the SAM output file.
Use when you have a set of chemical compounds (with known retention times and intensities) loaded into a ViMMS IndependentMassSpectrometer and need to simulate a specific MS/MS…
Use when you have raw Hi-C FASTQ files from a public repository (NCBI SRA, GEO, or ENCODE-deposited accession) and need to reproduce or validate Hi-C map generation following the…
Use when when you have predicted BGC-spectrum IOKR scores or other pairwise linking scores, and need to rank genomic clusters (GCFs from BiG-SCAPE) against metabolomic clusters…
Use when you have a feature table from nontargeted LC-MS peak detection (containing m/z, retention time, and intensity values) and need to disambiguate whether detected features…
Use when when you have a collection of molecular structures (as InChI strings, SMILES, or RDKit Mol objects) and need to feed them into a pretrained or transfer-learning neural…
Use when when you have downloaded a curated structure-organism dataset (such as LOTUS) in TSV or CSV format with separate 2D and 3D structure-organism pair tables, and ne — from…
Use when you have multidimensional MS data converted to MZA HDF5 format (from Agilent .d, Bruker .d with ion mobility, Thermo .
Use when when deploying a complex bioinformatics pipeline (like HiC-Pro) across heterogeneous computing environments where required tools (bowtie2, samtools, R, Python) may be…