Data & Analytics

holobiomicslab Skill

Use when you have a .msp format MS/MS spectrum library (e.g., from MassBank or similar public databases) and need to convert it into individual CSV entries indexed by positive or negative ionisation mode for use as a custom fragment library in MetaboAnnotatoR annotation pipelines.

holobiomicslab Skill

Use when you have completed a BiG-SLiCE v2 clustering run and need to extract the pre-calculated BGC and GCF cluster assignments in TSV format for postprocessing, integration with SQL pipelines, or sharing with collaborators who require flat tabular output rather than the SQLite database or.

holobiomicslab Skill

Use when you have extracted MS1 or MS2 peak lists and scan headers from Thermo Fisher RAW files using MetaXtract and need to load them into pandas, NumPy, or external analysis tools.

holobiomicslab Skill

Use when you have a CSV or table-format spectral peak list (with chemical shift, intensity, and metadata columns) destined for NMRformer or similar peak-to-metabolite assignment models, and you need to exclude low-quality peaks that would otherwise harm prediction accuracy.

holobiomicslab Skill

Use when you have a raw peak table (CSV format, from any of 12 supported LC-MS software tools or standardized format) and a separate label file that assigns each sample to an experimental class (e.

holobiomicslab Skill

Use when you have completed a BiG-SLiCE v2 clustering analysis and need to convert the internal SQLite3 database results into human-readable, tabular TSV files for import into spreadsheet applications, statistical tools, or custom analysis pipelines that do not support SQLite3 directly.

holobiomicslab Skill

Use when after parsing and validating a .csv file containing comma-separated SMILES strings, and before formatting the molecule list for CypReact input.

holobiomicslab Skill

Use when you have MSI intensity data exported from MSiReader or SCiLS software as a plain-text CSV file (with peaks as columns and pixels/spots as rows), and you need to import it into R to perform pairwise mass difference calculations and adduct identification.

holobiomicslab Skill

Use when you have raw LC-MS data files (mzML, netCDF, or raw vendor formats) from multiple samples and need to extract, align, and quantify chromatographic features across the cohort.

holobiomicslab Skill

Use when when you have a .csv file intended as input to CypReact containing SMILES strings and need to verify it meets the required comma-separated format specification and that each SMILES string is syntactically valid before processing molecules through CYP isoform testing.

holobiomicslab Skill

Use when you have raw or processed HRMS/MS data from Q-Exactive, Agilent Q-TOF, Bruker Q-TOF, or SCIEX Q-TOF instruments in formats such as mzML, CSV peaklists, or vendor-specific formats, and you need to extract experimental fragment m/z values and their intensities for comparison against.

holobiomicslab Skill

Use when your MZmine MGF and CSV input files contain mixed or ambiguous ionization modes, or when your experimental design specifies separate negative (NEG) and positive (POS) ionization mode acquisitions that must be processed independently before merging.

holobiomicslab Skill

Use when you have raw mzML files and corresponding feature tables (CSV format, mzmine-formatted) from untargeted LCMS experiments, and you need to convert them into uniformly-shaped peak matrices (2 × 120 per peak: margin + signal regions) as input for neural network classification of MS1 peak.

holobiomicslab Skill

Use when when you have raw mzML files and a corresponding feature table (CSV format, e.g., from mzmine) and need to generate peak matrices with fixed dimensions (e.g., 2 × 120) that encode margin vs. peak signal regions for training a neural network classifier to filter false positive LCMS peaks.

holobiomicslab Skill

Use when after converting a CSV file of molecule definitions into a peak properties dictionary using csv_to_peak_properties, or after loading a serialized peak properties dictionary from pickle/JSON storage, before passing it to SMITER simulation functions (e.g., smiter.synthetic_mzml.write_mzml).

holobiomicslab Skill

Use when you have a CSV or table-formatted input spectral peak list (chemical shifts, intensities, metadata) destined for NMRformer metabolite identification, and you observe or suspect that the list contains noisy peaks or peaks with chemical shifts that do not match known reference standards.

holobiomicslab Skill

Use when when you have authored a custom .csv lipid library and need to confirm it adheres to LipidMatch's documented schema before placing it in the designated library directory and running the library integration/loading step.

holobiomicslab Skill

Use when when you have an Excel file downloaded from InjectionDesign's template or conforming to its schema, and you need to extract sample identifiers, classification dimensions (up to three), and QC type labels (Blank QC, Solvent QC, Pooled QC, Long-Term Reference QC, or custom) into a structured.

holobiomicslab Skill

Use when when you have quantitative lipidomics data (either from Skyline CSV export or numerical matrix format) with sample annotations and a biological grouping variable (e.

holobiomicslab Skill

Use when you have raw .msp spectral library files (e.g., from MassBank or custom sources) and need to convert them into a structured CSV library format for use in metabolite annotation.

holobiomicslab Skill

Use when you have a raw peak-picked untargeted LC-MS dataframe with columns containing mass-to-charge (m/z), retention time (rt), feature identifiers, adduct annotations, and sample measurements in non-standard column names or mixed column sets.

holobiomicslab Skill

Use when after completing a BiG-SLiCE clustering analysis and needing to access the pre-calculated BGC and GCF cluster assignments in tabular format for spreadsheet analysis, statistical testing, or integration with other bioinformatics pipelines.

holobiomicslab Skill

Use when you have CSV files containing fold-change estimates and statistical p-values from a differential expression analysis (e.

holobiomicslab Skill

Use when when you have LC-MS peak table data in Excel format (e.g., from MS-DIAL peak picking) with separate compartments for sample information, feature properties, and intensity values, and you need to construct a structured R object that enforces consistency between sample metadata (e.

holobiomicslab Skill

Use when you have loaded mzPeak spectrum or chromatogram metadata and signal data into PyArrow Table structures (via the Python mzPeak reader or equivalent) and need to persist them to disk in Parquet format for downstream analysis, interoperability with other languages (R, .

holobiomicslab Skill

Use when you have a workflow.csv file co-located with sequence.csv in a session directory, and you need to initialize a reproducible, ordered chain of processing steps (e.

holobiomicslab Skill

Use when you have raw MRM lipidomics export files in vendor-specific formats (e.g., TSV or CSV from a mass spectrometry instrument) and need to convert them into a standardized tabular format before performing lipid identification, statistical analysis, or visualization.

holobiomicslab Skill

Use when you have molecular structures in raw or unstructured form and need to submit them to CypReact or similar command-line chemistry tools that accept CSV input.

holobiomicslab Skill

Use when you have a CSV file containing molecule definitions (chemical formula, m/z, intensity, retention time, or other peak properties) and need to prepare it for SMITER's simulation workflow.

holobiomicslab Skill

Use when you have raw MS data in a supported instrument format (Agilent .d, Thermo .raw, Bruker .d, mzML) and a predefined list of molecular targets (CSV with m/z and/or retention time) that you need to quantify.

holobiomicslab Skill

Use when when you have an Excel file uploaded by a user following the InjectionDesign template schema and need to convert it into a modifiable, structured sample list that preserves up to three classification dimensions and QC type assignments for LC/GC-MS multi-omics experiments.

holobiomicslab Skill

Use when when you have Parquet-encoded tabular data (e.

holobiomicslab Skill

Use when you have generated one or more MemoMatrix objects (MS2 fingerprint matrices from separate sample sets) and need to combine them for cross-cohort alignment, validate structural consistency after merging, or prepare merged matrices for downstream filtering and visualization.

holobiomicslab Skill

Use when when you have LC-MS/MS data in MZmine-generated MGF and CSV files (for positive and/or negative ionization modes) and need to apply a sequence of deduplication, annotation, and dereplication steps defined in a MolNotator YAML configuration file to predict actual molecules and build.

holobiomicslab Skill

Use when after duplicate filtering of MZmine-exported MGF and CSV files, when you have combined spectra from multiple samples in a single MGF and need to segregate them by sample identifier before fragment annotation or adduct assignment.

holobiomicslab Skill

Use when you have NMR metabolite measurements from peripheral blood samples (plasma/serum) paired with processing delay metadata (pre-centrifugation and post-centrifugation times) and need to benchmark metabolic parameter stability across delay windows.