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 a research software project is decomposed into distinct subproject components (e.
Use when you have model predictions and ground-truth labels for a test set and need to assess how well the trained model generalizes to unseen data.
Use when you have cloned a bioinformatics repository (e.g., FredHutch/SEACR) and need to confirm that its shell and R scripts are executable and will run successfully on your…
Use when you have raw GC-MS output in CSV format (with Component.RT, Base.Peak.MZ, Component.Area, Compound.Name, Match.Factor, and File.Name columns) and need to systematically…
Use when you have RNA-seq read counts (FPKM or similar) for multiple cell lines or biological samples, a genome-scale metabolic model with GPR associations, and you need to…
Use when you need to enable optional modules in Pyteomics that depend on external libraries not bundled with the core package—such as h5py and hdf5plugin for mzMLb format access,…
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 you have a query mass spectrum (or representative metabolite spectrum from public data) and need to identify it by searching against large spectral reference databases…
Use when you have cross-validated, filtered metabolomic NMR or MS data in a SummarizedExperiment container and need to prepare it for metabolome-wide association studies (MWAS)…
Use when you have deployed a microservice (e.g., TensorFlow Serving, REST API) and need to verify that specific endpoints (e.g., /model/metadata, /classify) return responses with…
Use when when you have loaded a cooler file containing Hi-C contact matrices and need to quantify how contact probability decays with genomic distance within a single chromosome.
Use when when exporting quantified MSI data as HDF5 containers following the Cardinal::HDF5 layout convention, and you need to establish bidirectional indexing between intensity…
Use when you have tandem MS/MS spectra annotated by at least two of GNPS (FBMN), ISDB-LOTUS (CFM-ID 4.0 spectral matching), and Sirius 6, and you need to rank features by…
Use when when you have extracted low-resolution mass spectra from individual chromatographic peaks in GC-MS data and need to match them against a spectral library (e.g.,…
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 your research involves searching MS/MS spectra against multiple curated taxonomic or domain-specific databases (microbial, plant, tissue, microbiome, or food origin) and…
Use when when you have paired MS2 spectra and BGCs with structural candidates (e.g., from MIBiG homology), and you want to rank which BGC likely produces which spectrum using a…
Use when training a contrastive learning model on ion image data (mass spectrometry imaging) where augmented pairs of the same ion image must maximize similarity while different…
Use when when you have a Thermo Scientific .raw file from an Orbitrap instrument (e.
Use when after RAMClustR clustering and do.findmain molecular weight inference have been completed on XCMS-detected metabolomics features.
Use when you have a GNPS mass spectral molecular network and wish to annotate its nodes with both chemical class assignments (from GNPS public library matches) and MS2LDA-derived…
Use when training a deeply regularized deep neural network on a large molecular feature dataset (e.
Use when implementing replacement methods ($<-, [<-, spectraData<-, mz<-, intensity<-, peaksData<-) for a writable MsBackend subclass, or when modifying peak data in an existing…
Use when you have high-dimensional replicate experiment data (metabolomics, proteomics, or genomics) with multiple biological or technical replicates per sample, and you need to…
Use when when importing raw mass spectrometry data from instrument vendors or public repositories in one format (e.g., mzML, mzXML) and needing to export it in another format (e.
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 when you have installed or updated a DNA methylation analysis tool (e.g., ChAMP) and need to verify that it produces documented expected outputs on a reference simulation…
Use when when implementing or modifying a numerical compression/decompression component (e.g., Numpress for mass-spectrometry m/z and intensity arrays) and you need to verify that…
Use when when raw spectral data exists in one mass spectrometry file format but downstream analysis requires a different format; when integrating spectra from multiple sources or…
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 need to reverse-engineer or formally document the computational steps within a closed or under-documented scientific software module—particularly when the…
Use when when you need to assess whether a given ATAC-seq clustering method (or variant) is competitive on your data or when evaluating which published method to adopt.
Use when when you have validated SMILES strings or canonical molecule objects from RDKit and need to convert them into the fixed-size numerical tensor format expected by a deep…
Use when after LDA inference has produced a trained motifset (motifset.json or motifset_optimized.json) with Mass2Motif probability distributions over fragments and neutral losses.
Use when when you have a preprocessed sample chromatogram (smoothed and baseline-corrected) and a preprocessed reference chromatogram, and need to align them using 2D COW.
Use when you have millions of MS/MS spectra in mzML, mzXML, or MGF format that have been converted to low-dimensional vectors via feature hashing, and you need to identify which…
Use when you have a trained shallow decision tree on ChemEcho feature vectors (sparse, high-dimensional representations of tandem mass spectra peaks and neutral losses) and need…
Use when after feature detection and alignment (XCMS or equivalent), when you have a CSV feature table with m/z and retention time columns and need to group features derived from…
Use when after generating a q-value bedgraph track from ChIP-Seq pileup versus local lambda comparison, and you need to identify statistically significant narrow peaks with…
Use when when you have a GNPS molecular network (classical or feature-based) and corresponding MS2LDA experiment results, and you want to annotate network nodes with discovered…
Use when after making code modifications (bug fixes, new features, or refactoring) to the MS2Query codebase, or when contributing changes via pull request.
Use when you have (1) genomic data from a Streptomyces or other RiPP-producing organism in raw FASTA format or annotated GenBank format, (2) high-resolution LC-MS/MS spectra in…
Use when you have raw or processed LC-MS/MS data from DDA mode acquisitions and need to extract, annotate, and structure MS/MS spectra with purity labels (or quality indicators)…
Use when when preparing MS/MS spectral data for training word-embedding models (Word2Vec, Skip-gram, CBOW) that will learn relationships between fragment ions and neutral losses.
Use when you have a SMILES input file of small organic molecules and need to predict their collision cross sections or other molecular properties via quantum mechanics.
Use when you have extracted parallel feature streams from a CNN backbone (local spectral patterns) and a Transformer backbone (global dependencies) in 1H NMR spectra, and you need…
Use when you have multiple tandem MS/MS libraries in different formats (msp, mgf) from different providers (NIST, RIKEN, MoNA, GNPS) with incomplete or inconsistent structural…
Use when after downloading an mzML file from a remote repository (e.g., MetaboLights, MassIVE, GNPS) via USI resolution, before attempting to parse it into a spectrum container or…
Use when you have raw LC-MS/MS spectral data in vendor formats or unvalidated .mgf files before feeding them into the specXplore importing pipeline.
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 suspect XCMS grouping contains misaligned features due to suboptimal parameter settings or insufficient samples.
Use when you have MS/MS spectra with unknown precursor m/z values and need to assign the most likely chemical formula and adduct type (e.g., [M+H]+, [M+Na]+, [M+K]+) in a de novo…
Use when working with GCIMS datasets where retention time spans a wide range (e.g., 0–1500 s) but your analytes of interest are confined to a narrower window (e.g., 0–1100 s).
Use when when annotating observed mass spectrometry peaks against theoretical fragment ions (b, y, or other ion types) using ProForma 2.0 peptidoforms, compute the m/z deviation…
Use when when you have paired NMR metabolite measurements and corresponding processing metadata (pre-centrifugation delay, post-centrifugation delay, sample type, cohort) for a…
Use when you have an unknown mass spectrometry spectrum (acquired experimentally
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 when you need to quantify and compare the filtering efficacy of mutually exclusive noise-threshold methods on the same input mass spectrum, or when validating that a…
Use when you have MS/MS spectra with fragment frequency annotations (from consensus spectrum generation) and need to decide which fragments to retain versus remove.