Use when when deploying a multi-container application stack using docker-compose
Use when you have draft metabolic reconstructions in SBML or standard format for multiple organisms in a microbial community (e.
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 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 you have aligned ATAC-seq BAM files and want to discriminate between transcription factor binding sites that are actually occupied by protein versus sites with matching…
Use when when you have constructed a two-layer metabolite annotation network (knowledge-driven and data-driven) and need to propagate initial seed annotations (e.
Use when you have an unknown query spectrum suspected to carry a post-translational
Use when you have a set of gallery or example scripts that must run consistently across multiple backend implementations (e.g., matplotlib, Bokeh, Plotly), and you need to verify…
Use when you have a two-dimensional GC–MS or LC–MS dataset (m/z vs retention time) and need to identify discriminative analyte features without relying on conventional peak…
Use when you have a bacterium-phage infection study with normalized peak intensities from FT-ICR MS across multiple phage treatment groups (minimum 2–3 conditions such as HP1,…
Use when you have completed pathway analysis using multiple competing methods (e.g., PALS, ORA, GSEA) on a metabolomics peak intensity dataset and need to verify that ranking…
Use when you have loaded a raw or partially processed MsmsSpectrum object and need to reduce spectral noise before annotation, matching, or visualization.
Use when when you have imzML mass spectrometry imaging data files and need to convert raw ion image intensities into quantitative lipid abundance (pmol/mm²) using known internal…
Use when after LDA modeling has inferred a set of Mass2Motifs (in JSON format) from preprocessed MS/MS spectra and you need to annotate these motifs by retrieving matching entries…
Use when after consolidating aligned LC-MS peaks into a quantitative feature table (with m/z, retention time, and intensity values across all samples), and before proceeding to…
Use when you have a trained predictor (like BitterPredict) that accepts structured descriptors and want to understand feature importance without retraining.
Use when deploying the ipbhalle/metfragweb container and you need to supply custom MetFrag settings (ChemSpider tokens, proxy servers, local database connections) without…
Use when you have a set of small-molecule structures (SMILES, InChI, or SDF format) and need to predict their chromatographic retention times for a specific method, either to…
Use when you have a GNPS-generated classical or feature-based molecular network (in graphml or JSON format) and corresponding MS2LDA or chemical class assignment data, and you…
Use when you need to verify that a GitHub Actions workflow (such as dev_build_release.yml) successfully completes end-to-end, especially after code changes or to confirm that…
Use when you have transcript-level abundance, count, and length estimates (from salmon, Sailfish, or kallisto via tximport) and want to perform gene-level differential expression…
Use when after loading a feature table into memory when the table contains zero or missing values that represent true signal loss (not genuine absence), and you need to impute…
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 a collection of MS/MS spectra (in mzML or MGF format) from a proteomics experiment and need to group or retrieve spectra derived from the same peptide without…
Use when when you have a set of query chemicals (e.g., ethyl hexanoate, methyl salicylate, octanal, undecane) and need to evaluate them against reference compound categor — from…
Use when you have a peak-picked feature table (HDF5 format) from high-dimensional MS data (m/z, drift_time, retention_time, intensity) and need to identify and label isotopic…
Use when you have raw mass-spectrometry files (MGF, BIOM, mzXML, mzML) or feature abundance tables from external tools (MZmine2, peak detection software) and need to convert them…
Use when you have LC-MS metabolomics data in positive ionization mode and have already performed XCMS feature detection and RAMClustR clustering.
Use when you have a GTF annotation file and need to systematically extract all local alternative splicing event coordinates (not transcript isoforms) for downstream PSI…
Use when after parsing a MassQL query string into an abstract syntax tree or intermediate representation, before executing it against mass spectrometry data files (mzML, mzXML,…
Use when when exporting in-memory generated spectra as MSP-format spectral libraries, you must first map each spectrum record to required MSP fields (NAME, PRECURSORMZ, SPECTRUM)…
Use when you have a chromVARDeviations object with multiple annotation sets (such as JASPAR motifs and kmers) and need to determine which annotation pairs are redundant (high…
Use when you need to determine the complete set of validated instrument/vendor and acquisition mode combinations for a mass spectrometry analysis tool, when assessing whether your…
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 pre-trained TCN spectrum encoder, annotated MS/MS spectra paired with ground-truth molecular formulas, and you want to train only the formula ranking and…
Use when you have received a peak/feature table from an unknown or variable upstream peak-picking tool and need to ingest it into LipidMatch or a similar unified workflow.
Use when you have extracted MS/MS spectra for a given metabolomic feature across multiple replicates (e.g., after top-TIC filtering) and need to identify which fragments are…
Use when you have raw mass spectrometry intensity data from targeted analytes and a set of calibration standard measurements with known concentrations.
Use when you need to generate synthetic LC/GC-MS feature tables or raw mzML files with realistic peak complexity, ion multiplicities, and natural spectral variation—not just…
Use when building or auditing a multi-instrument MS data processing system that must route different chromatography modes (LC, GC), ion mobility, or imaging modalities (MALDI) to…
Use when you have applied two different clustering or dendrogram-flattening methods (e.g., constant-threshold vs.
Use when you have mass spectrometry spectral data loaded into a Pandas DataFrame with columns representing m/z (mass-to-charge ratio) and intensity values, and you need to…
Use when you observe jagged or noisy peak profiles in low-abundance ions after loading raw IM-MS data (Agilent MassHunter .
Use when you have acquired or generated multi-modal spectroscopic data (integrated NMR, HSQC, COSY, IR spectra) in the model's expected input format, a pre-trained…
Use when you have centroided LC-MS/MS spectral data (in MGF, mzXML, mzML, or mzData format) and want to identify known or predicted natural product structures present in your…
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 when deploying a complex bioinformatics pipeline (e.g., HiC-Pro) that depends on multiple external tools with version constraints (samtools ≥1.9, bowtie2, R packages,…
Use when you have normalized gene expression data (log-transformed, quantile-normalized) from a time-course or case-control experiment, a ranked gene statistic (e.g., mean…
Use when you need to containerize a C#-based Windows application (like AirdPro CLI) for Linux deployment, require Wine and .NET Framework 4.
Use when when comparing GNPS chemical annotations across two or more groups of samples (defined by ReDU sample-information categories such as sample type, extraction method, or…
Use when after parsing an imzML XML metadata file and loading the corresponding .ibd binary intensity data, when you need to isolate and visualize the spatial distribution of…
Use when you have an unknown compound's mass spectrum (m/z peaks and intensities) in positive or negative ion mode and need to identify candidate metabolites from a struc — from…
Use when when you have downloaded a released version of a structured dataset (e.g., LOTUS from Zenodo) and need to confirm it matches the documented headline statistics before…
Use when after quantifying the same read set with two versions of a mapping/quantification tool (e.g., C++ salmon 1.11.
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 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 a feature abundance table (rows=features, columns=samples)
Use when when a user has prepared a custom collection of metabolite sets (e.g., from spectral fragmentation clustering, literature curation, or domain-specific grouping) in CSV or…
Use when executing containerized conversion tools (e.g., AirdPro CLI) that must read vendor-format mass spectrometry raw files from the host filesystem and write converted output…
Use when you have a Thermo Fisher Scientific .raw file (e.g., Q Exactive HF, Orbitrap) and need to extract specific spectral scans, chromatographic traces, scan-level metadata, or…