xieguigang/mzkit

Mzkit is a mass spectrometry data analysis toolkit that processes and interprets complex spectral data from techniques like LC-MS, GC-MS, and NMR. It provides end-to-end capabilities for peak finding, alignment, and metabolite annotation by integrating with external chemical databases such as PubChem and KEGG. The system supports specialized workflows for lipidomics and single-cell analysis, offering robust visualization and statistical tools for biological discovery.

114 changes.

The project was rebranded from 'spectrum' to 'Mzkit' and restructured to support a comprehensive R package ecosystem for mass spectrometry data analysis. This period focused on developing core libraries for chemoinformatics, metabolite identification via the MetaDNA algorithm, and visualization of GCxGC and MSI data, alongside extensive documentation and test coverage for the new R modules.

125 changes.

This period focused on generating extensive R and .NET CLR documentation for the mzkit application, covering mass spectrometry, chemoinformatics, and genomics modules. It also involved adding comprehensive test suites for core functionalities like SMILES parsing, LC-MS workflows, and single-cell data processing, alongside new tools for 3D MSI and H&E stain analysis.

10 changes.

This period focused on expanding the mzkit package's documentation and demo scripts across cheminformatics, proteomics, and metabolomics domains. Significant work included adding man pages and HTML vignettes for .NET CLR classes, QSAR functions, and lipidomics modules, alongside new visualization reports and automated MSI pipeline scripts.

Introduced a new library for reading data files acquired on Bruker mass spectrometers. This addition includes a \DataReader\ class to parse binary mass spectrum data, a \BrukerSettingsFileReader\ to extract acquisition parameters from settings files (such as \acqus\ or \apexAcquisition.method\), and a suite of design-by-contract exception types to handle precondition, postcondition, and invariant failures during data loading.

src/assembly · high confidence

The visualize module now supports two-dimensional gas chromatography (GCxGC) imaging through new plot classes (GCxGCHeatMap, GCxGCTIC2DPlot, GCxGCTIC3DPeaks) that render 2D and 3D heatmaps and peak surfaces. Additionally, the GridScanner module introduces ion co-localization analysis and PCA-based clustering (PCAGroups) for spatial mass spectrometry imaging data, while MatrixExports provides parallel deconvolution for creating ion intensity matrices.

src/visualize · high confidence

A new demo script has been added to perform MS1 peak list annotation using the Mummichog algorithm. The script reads a list of m/z values, queries KEGG metabolite candidates, and runs pathway enrichment analysis (with the genetic algorithm disabled by default). It outputs the results as both JSON and CSV files, providing users with a concrete example of how to integrate mzkit's annotation capabilities with KEGG data.

Rscript/demo/Mummichog · high confidence

The R package 'ptw' (version 1.9-16) has been added to the repository. This package provides parametric time warping capabilities to align patterns, such as chromatograms or spectra, by searching for an optimal polynomial warping function. It supports aligning samples to a reference (individually or globally) using two optimization criteria: Root Mean Square (RMS) error and Weighted Cross Correlation (WCC). The package includes functions for baseline correction, peak list warping (stick spectra), and visualization, and depends on the RcppDE package for differential evolution optimization.

Rscript/R/ptw · high confidence

New graph query definition files have been added to the application to support parsing chemical data from PubChem. The \pubchem.graphquery\ file defines how to extract core record details (CID, CommonName) and cross-reference data from PubChem responses, while \section\_data.graphquery\ provides a reusable schema for parsing nested section structures and various data value types (String, Number, Boolean, etc.) found within chemical information records.

_Rscript/Library/mzkit\app/graphquery · high confidence

New R documentation pages have been added for the SMILES package, covering functions to parse SMILES strings, extract atoms and links, convert structures to graphs or matrices, and evaluate molecular similarity scores.

_Rscript/Library/mzkit\app/vignettes/mzkit/SMILES · high confidence

The metadb module introduces new data models for Chemical Markup Language (CML) serialization, including classes for molecules, atoms, and bonds, alongside a comprehensive ChemicalDescriptor model for storing physical properties like LogP and mass. It also adds a new Formula sub-namespace containing an element mass dictionary, search candidate definitions, and utilities for calculating exact mass and correcting empirical formula charges, enabling more robust chemical structure handling and annotation.

src/metadb · high confidence

This change adds 40 new \.Rd\ manual pages in the \Rscript/R/mzkit/man\ directory, generated via roxygen2 from source files in \R/\. The documentation covers a wide range of mzkit capabilities, including MS data processing (centroiding, alignment, matrix conversion), spectral similarity scoring (cosine, Jaccard, entropy), precursor type matching and mass calculation, and MGF file I/O. This makes these functions discoverable and usable via standard R help tools.

Rscript/R/mzkit/man · high confidence

New HTML documentation pages have been added for the SMRUCC.genomics.ComponentModel.Annotation namespace, specifically covering the CatalogProfiles, ClassProfiles, and PathwayBrief classes. These pages provide users with reference details on the class structures, properties, and inheritance relationships (such as PathwayBrief extending XmlDataModel) within the .NET CLR component model.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/genomics/ComponentModel/Annotation · high confidence

The vignette documentation now includes generated reference pages for several .NET CLR types used in the assembly and data parsing modules. This adds documentation for the ChEBI XML entity model (including synonyms, structures, and ontology parents), the Expasy Enzyme database record, and a comprehensive set of KEGG DBGET and WebServices models covering compounds, reactions, orthology terms, and pathway map data.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/genomics/Assembly · high confidence

The vignette now includes generated HTML documentation pages for the \BioNovoGene.BioDeep.Chemoinformatics.ChemicalMarkupLanguage\ namespace. Users can now view type definitions and reference trees for core CML structures, including \ArrayList\, \MarkupFile\, \atom\, \atomArray\, \bond\, \bondArray\, and \molecule\.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/ChemicalMarkupLanguage · high confidence

New HTML documentation pages have been added to the vignettes for the .NET CLR bindings in the Chemoinformatics module. Specifically, this includes documentation for the \Formula\ class (exposing properties like \CountsByElement\, \Elements\, \EmpiricalFormula\, and \ExactMass\) and the \FormulaComposition\ class (which extends \Formula\ and adds \charge\, \HCRatio\, \massdiff\, and \ppm\). Additionally, documentation for the \GlycosylNameSolver\ class in the NaturalProduct namespace has been added.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/Formula · high confidence

New HTML documentation pages have been added for the \DataFrameRow\ and \Matrix\ classes within the \SMRUCC.genomics.Analysis.HTS.DataFrame\ namespace. The \DataFrameRow\ page documents the gene expression data sample model, including properties for experiments, gene ID, MAD (Median Absolute Deviation), and sample count. The \Matrix\ page documents the data matrix model containing a collection of \DataFrameRow\ objects, detailing properties such as expression data, row names, sample count, and size. These pages provide reference information for users interacting with the .NET CLR components of the mzkit app.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/DataFrame · high confidence

New HTML documentation pages have been added for the \Microsoft.VisualBasic.Data.Framework.IO\ namespace, specifically covering the \DataSet\, \EntityObject\, and \Table\ classes. These pages provide TypeScript-style declarations and inheritance trees, clarifying that \Table\ extends \iterates(String)\, \EntityObject\ extends \Table\, and \DataSet\ extends \iterates(Double)\, thereby making these data structure definitions discoverable in the R package vignettes.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/Framework · high confidence

The vignette documentation for the Microsoft.VisualBasic.Math namespace now includes reference pages for the IVector numeric vector model and the NumberEqualityComparer class, which compares numbers based on a delta tolerance threshold.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Math · high confidence

The vignette site now includes generated documentation for the \BioNovoGene.BioDeep.Chemoinformatics.IUPAC.InChI\ namespace, covering the \InChI\ parser class and its constituent layers (Main, Charge, Stereochemical, Isotopic, Fixed-H, Reconnected) as well as supporting types like \InchiAtom\, \InchiBond\, and \InChIIKey\. This provides users with reference material for the structure and properties of International Chemical Identifier components within the .NET CLR environment.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/IUPAC · high confidence

New HTML documentation pages have been added for the \LinearDataSet\ and \QCData\ .NET CLR classes within the mzkit package. The \LinearDataSet\ page documents the class structure, while the \QCData\ page details its properties (\matchQC\, \model\, and \result\) and links to related types like \StandardCurve\ and \QuantifyScan\, providing users with reference material for these specific data models.

_Rscript/Library/mzkit\app/vignettes/clr/mzkit · high confidence

New documentation pages have been added for the \BioNovoGene.BioDeep.Chemistry.LipidMaps\ namespace, covering the \LipidClassReader\ helper module, the \LipidMapsCategory\ class, and the \MetaData\ data model. These pages provide API reference details for users accessing lipid maps compound class information and annotation data via .NET CLR.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LipidMaps · high confidence

The mzkit workbench now includes generated documentation pages for several .NET CLR types within the BioNovoGene.BioDeep.MSEngine namespace. Users can now view API details for the \AnnotationPack\ class (which structures annotation results including libraries, peaks, and XIC data), the \MzQuery\ class (representing MS1 m/z ion query results extending \MetID\), and interface/type stubs for \IMassSearch\, \IMetaDb\, \IMzQuery\, and \LibraryWorkspace\.

(repo-wide) · high confidence

The MetaDNA vignette now includes generated HTML documentation for several .NET CLR types, providing users with reference details for the underlying algorithm. New pages cover the core \Algorithm\ class (including its \ms1Err\ tolerance property), \AnnotatedSeed\ (representing metabolite annotation seeds with parent and product data), \CompoundSolver\ (the KEGG metabolite search engine extending \MSSearch\), \MetaDNARawSet\ (for peak alignment raw matrix data), \MetaDNAResult\ (the table output containing scores like entropy, jaccard, and ppm), \Networking\, \OntologyTree\, and \Visual.ReactionClass\.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA · high confidence

The vignette documentation for the BioNovoGene.BioDeep.Chemistry.MetaLib namespace has been expanded to include reference pages for four new types: AnnotationWorkspace (the temporary workspace file for the biodeep annotation pipeline), LocalRepository (a read-only metabolite annotation data repository implementing IMetaDb), RepositoryWriter (the data writer used to create the LocalRepository annotation database), and RefMet (a reference set of metabolite names with detailed naming conventions and properties like chebi\_id, smiles, and exactmass).

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/MetaLib · high confidence

The vignette documentation for the \Microsoft.VisualBasic.CommandLine\ namespace has been expanded to include reference pages for key types: \Interpreter\, \ExecuteEmptyCLI\, \ExecuteFile\, \ExecuteNotFound\, \ExecuteQuery\, \ArgumentCollection\, \APIDelegate\, \APIEntryPoint\, and \Namespace\. These new HTML pages provide users with the type declarations, property descriptions, and reference trees for the command-line interpreter's core components and reflection entry points.

(repo-wide) · high confidence

The vignette documentation for the BioNovoGene.BioDeep.Chemistry.NCBI.PubChem namespace has been expanded with new HTML pages for key data types. These pages document the structure and properties of classes such as CreateTable, PugViewRecord, Section, Information, and Value, providing users with reference material for the underlying .NET CLR types used in PubChem data handling.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/NCBI/PubChem · high confidence

The vignette now includes generated HTML documentation for the \BioNovoGene.BioDeep.Chemoinformatics.SDF.Models\ namespace. This adds reference pages for the \Atom\, \Bound\, \BoundStereos\, \BoundTypes\, \Point3D\, and \Structure\ classes, detailing their properties and relationships to support users working with SDF molecular structure data.

_Rscript/Library/mzkit\_app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF/Models, Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/MSEngine/Mummichog · high confidence

The package now includes generated documentation pages for four .NET CLR types within the \Microsoft.VisualBasic.Text.Xml.Models\ namespace: \Coordinate\, \KeyValuePair\, \NamedValue\, and \Property\. These new HTML vignettes describe the structure and usage of these classes, which are used for XML data storage and property management, providing users with reference material for these underlying data models.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Text · high confidence

The vignette documentation now includes generated reference pages for several .NET CLR types. This adds documentation for the \Microsoft.VisualBasic.ApplicationServices.Debugging.Diagnostics\ types (\Method\ and \StackFrame\), the \MSG\_TYPES\ enumeration for logging levels (DEBUG, FINEST, ERR, WRN, INF), and the comprehensive \ExpressionTypes\ enumeration for the R\# scripting language, covering literals, control flow, and operators.

_Rscript/Library/mzkit\_app/vignettes/clr/Microsoft/VisualBasic/ApplicationServices, Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/Rsharp/Development/Package · high confidence

The vignette documentation for the \Microsoft.VisualBasic.Math.LinearAlgebra.Matrix\ namespace has been updated to include reference pages for key matrix classes and decompositions. Users can now view detailed descriptions and type declarations for \NumericMatrix\, \GeneralMatrix\, \SparseMatrix\, and decomposition classes including \CholeskyDecomposition\, \LUDecomposition\, \QRDecomposition\, \SingularValueDecomposition\, and \EigenvalueDecomposition\.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Math/LinearAlgebra/Matrix · high confidence

New HTML documentation pages have been added for the \BioNovoGene.BioDeep.Chemoinformatics.Metabolite\ namespace, detailing the structure and usage of key data models including \MetaInfo\, \MetaLib\, \MetaboliteAnnotation\, \CompoundClass\, and \xref\ (cross-references). These pages provide TypeScript-style declarations for classes used in metabolite annotation, compound classification, and database integration (e.g., HMDB, KEGG, PubChem).

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/Metabolite · high confidence

The vignette documentation for the \Microsoft.VisualBasic.Data.visualize.Network\ namespace has been updated to include reference pages for key graph visualization classes. This adds documentation for the core graph model (\NetworkGraph\, \Node\, \Edge\), their associated data structures (\NodeData\, \EdgeData\, \GraphData\), and layout vector types (\AbstractVector\, \FDGVector2\, \FDGVector3\), providing users with details on properties such as node pinning, edge styling, and 2D/3D layout coordinates.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/visualize/Network/Graph · high confidence

The vignettes now include generated HTML documentation pages for a broad set of .NET CLR types within the System and System.Collections namespaces. This adds reference pages for core types such as Action, Array, Attribute, Boolean, Byte, Delegate, Double, Enum, Guid, and DateTime, as well as collections like CollectionBase, ICollection, IEnumerable, NameObjectCollectionBase, and NameValueCollection. Users can now consult these pages to see the declared properties, inheritance hierarchies, and type references for these .NET classes within the mzkit\_app context.

_Rscript/Library/mzkit\app/vignettes/clr/System · high confidence

The documentation site now includes generated reference pages for three .NET CLR types within the mzkit\_app vignettes: \XmlDataModel\ (which exposes \Stylesheet\ and \TypeComment\ properties for XML loading), \XmlStyleProcessor\ (defining CSS-like styling attributes), and \Byte\ (representing an 8-bit unsigned integer array pointer with buffer management properties). These pages provide TypeScript-style declarations and type reference trees to help users understand the underlying .NET components exposed by the package.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/ComponentModel · high confidence

The insilicons module now includes a new R script (ADP.R) that demonstrates simulating mass spectra for Adenosine 5'-diphosphate (ADP) using a custom energy-dependent fragmentation model, along with the corresponding KEGG compound data files (C00008.txt, C00008.xml) and generated output artifacts (ADP.mgf, energy.png).

dist/Rscript/insilicons · high confidence

The application now includes a new data source containing BioCyc pathway information. This change adds a CSV file (\biocyc.csv\) with over 15,000 rows of pathway data, including details on organism-specific and conserved pathways, associated genes, proteins, and reactions, thereby expanding the available biological context for users.

_Rscript/Library/mzkit\app/data · high confidence

Added a collection of MATLAB scripts and data files implementing Paul Eilers' signal processing algorithms, including the Whittaker Smoother (for equally and unequally spaced data, with and without weights), asymmetric least squares baseline estimation, parametric time warping, and Savitzky-Golay filtering. These files, located in Rscript/Manuscript, serve as reference implementations and demonstration scripts for the statistical methods described in Eilers' 2003 and 2004 publications.

Rscript/Manuscript · high confidence

New HTML documentation pages have been added for the BioNovoGene.BioDeep.Chemistry.TMIC.FooDB namespace, providing TypeScript-style class declarations for key data models including Compound, CompoundFlavor, Content, Flavor, and Food. These pages expose the structure of FooDB-related types (such as chemical identifiers, flavor categories, and food metadata) to R users via the mzkit\_app vignettes, enabling better discoverability and type checking for .NET CLR interop.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/TMIC/FooDB · high confidence

This update introduces new capabilities for processing and visualizing GCxGC data. A new Python script (2d\_cdf.py) has been added to extract 2D peaks from mzPack files, save them as CDF images, and generate PNG plots of the Total Ion Chromatogram (TIC) with customizable styling. The commit messages also indicate improvements to the HDF5 file reader and fixes for heatmap rendering offsets and axis ticks, enhancing the reliability of GCxGC imaging outputs.

_dist/Rscript/GCMS/GCxGC\TopMS · medium confidence

New HTML documentation pages have been added for the SMRUCC.genomics.Analysis.HTS.GSEA namespace, specifically covering the Background, BackgroundGene, and Cluster classes. These pages detail the data models used for Gene Set Enrichment Analysis, including the Background class which manages functional gene clusters, the BackgroundGene class representing individual gene members with alias and ID mappings, and the Cluster class which groups related genesets.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/genomics/Analysis/HTS/GSEA · high confidence

The workbench now includes a new R script, \mark\_nucleus.R\, in the H&E stain analysis module. This script automates the detection of cell nuclei from histology images by identifying specific purple color ranges, applying DBSCAN clustering to group nearby detections, and scanning tissue blocks for color density metrics. It outputs the results as CSV and JSON files containing nucleus coordinates, cluster assignments, and block-level color statistics, along with visualizations of the marked nuclei.

_dist/workbench/ms\_imaging/he\stain · high confidence

The vignette documentation for the \BioNovoGene.BioDeep.Chemistry.TMIC.HMDB\ namespace has been expanded to include generated reference pages for the underlying .NET CLR data models. New HTML documentation files cover core classes such as \MetaReference\, \MetaboliteTable\, and \MetaDb\, as well as supporting types for biological properties, concentrations, diseases, and spectra files. This provides users with detailed API reference material for the HMDB metabolite data structures used within the mzkit application.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/TMIC/HMDB · high confidence

The \Rscript/R/compound\_brites\ directory now includes new CSV data files (br08001.csv, br08002.csv, br08003.csv, br08005.csv) containing KEGG BRITE hierarchical classifications for various compound classes, including fatty acyls, alkaloids, organic acids, and lipids. These files provide structured metadata (ID, class, category, subcategory, entry, name) that supports the compound browsing and classification features within the application.

_Rscript/R/compound\brites · high confidence

This change introduces a new LIPIDMAPS annotation module within the mzkit application. It includes scripts to generate and pack the LIPIDMAPS database from SDF structures, create name mappings, and perform MS1 lipid searches against the database. The module outputs detailed search results, including lipid names, formulas, and classification data, into CSV files for specific m/z values.

dist/Rscript/lipidmaps · high confidence

The Linears package vignettes now include HTML documentation for key linear quantification functions, including ionPeaks, lines.table, load\_experiment, points, quantify, read.linearPack, report.dataset, result, scans.X, write.ionPeaks, and write.points. These pages provide usage syntax, argument descriptions, return types, and author information for the linear quantification workflow.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/Linears · high confidence

The ms\_imaging workbench now includes a set of R scripts and sample data files to support mass spectrometry imaging workflows. New additions include \imzML\_converts.R\ and \mzImageWrite.R\ for converting between CDF and imzML formats and writing mzImage files, \inspectImage.R\ and \inspect\_rawdata.R\ for inspecting raw data streams and total ion chromatograms (TIC), and \matrix\_test.R\ for exporting pixel matrices. These are accompanied by sample data files such as \data\_TIC.csv\, \results.csv\, and a \README.txt\ describing the HR2MSI mouse urinary bladder S096 dataset, enabling users to load, inspect, and export MS imaging data directly within the workbench.

_dist/workbench/ms\imaging · high confidence

New R scripts have been added to the MSI pipeline to automate the conversion of input files (such as imzML) into the mzPack format, extract specific ions based on mass and quality thresholds, and export the resulting peak matrix to CSV. These scripts demonstrate the usage of the mzkit library's MSI, math, and SingleCells modules for processing mass spectrometry imaging data.

_Rscript/Library/mzkit\app/pipeline/MSI · high confidence

New documentation pages have been added for the \MeshCategory\ and \Term\ classes within the NCBI MeSH Tree knowledge base. The \MeshCategory\ page details the 16 MeSH descriptor categories (A–Z) used to organize MeSH terms hierarchically, while the \Term\ page documents the structure of individual MeSH tree entries, including fields for accession ID, alias, category, description, term name, and tree path.

_Rscript/Library/mzkit\_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge\base/NCBI/MeSH · high confidence

The MoleculeNetworking package vignettes now include documentation for several new functions: \as.graph\ (converts a cluster tree into a graph model), \clustering\ (performs spectrum clustering on MS2 spectra), \grid\_assigned\ (assigns precursors to cluster nodes), \msBin\ (populates peak MS2 cluster data), \representative\ (creates representative spectrum data), \spectrum\_clusters\ (retrieves aligned spectrum clusters across raw data files), \spectrum\_grid\ (creates grid clustering of MS2 spectrum data), \splitClusterRT\ (splits cluster data by retention time windows), \tree\ (performs spectrum data clustering), \uniqueNames\ (ensures unique ID references for spectrum data), \unpack\_assign\ (unpacks spectrum data into file groups), and \unpack\_unmapped\ (unpacks unmapped grid data).

(repo-wide) · high confidence

The package now includes manual pages for several NMR-related functions, specifically FID, acquisition, nmr\_dft, read.nmrML, spectrum, and spectrumList. These new documentation files provide users with reference information on how to read Free Induction Decay data, retrieve acquisition data from raw files, perform discrete Fourier transforms, read nmrML files, and handle spectrum data matrices.

_Rscript/Library/mzkit\app/man/mzkit/NMR/NMR · high confidence

A new R script (readRaw.R) has been added to the NMR module to demonstrate reading raw NMR data files (specifically nmrML format) and generating visualizations. The script utilizes the NMR package from both mzplot and mzkit to parse spectrum lists and acquisition data, producing demo plots for spectra, FID (Free Induction Decay) signals, and frequency-domain representations.

dist/Rscript/raw/NMR · high confidence

New HTML documentation pages have been added for the OBO file reader models within the SMRUCC.genomics.foundation.OBO\_Foundry.IO namespace. The 'OBOFile' page details the structure of OBO version 1.2 files, including headers, terms, typedefs, and instances, while the 'header' page defines the corresponding .NET CLR class properties (such as Author, DataVersion, and Ontology) for parsing these files.

_Rscript/Library/mzkit\_app/vignettes/clr/SMRUCC/genomics/foundation/OBO\Foundry/IO · high confidence

A new R script (metadata.R) has been added to the dist/Rscript/raw/flexImaging directory. This script utilizes the mzkit library to import flexImaging functionality and reads metadata from a data.mcf\_idx file, converting the result into a list structure for inspection.

dist/Rscript/raw/flexImaging · high confidence

New R scripts have been added to the mzPack v2 directory to support reading, writing, and upgrading mzPack files. The \read\_v2.R\ script demonstrates opening and inspecting mzPack data using the HDS and mzkit libraries. The \write\_v2.R\ script shows how to pack stream data into an mzPack file and inspect its metadata. The \upgrade.R\ script provides an example of opening an existing mzPack file and writing it back, likely for format upgrades. The \samplefiles.R\ script includes a sample operation for splitting samples from an mzPack file.

_dist/Rscript/raw/mzpack\v2 · high confidence

A new build script (build-unix.cmd) has been added to the mzkit\_app package to automate the packaging and installation process on Unix-like systems. This script configures the R environment paths, downloads syntax highlighting assets, builds the package source into a zip file, and installs it, streamlining the deployment workflow for users on non-Windows platforms.

_Rscript/Library/mzkit\app/.pkg · high confidence

A new build.cmd file has been added to the Rscript/R directory, providing a Windows-specific command to execute Rcmd.exe for building the MetaDNA package.

Rscript/R · high confidence

The .pkg directory now includes two new automation scripts. publish.R enables users to publish NuGet packages by iterating through .nupkg files in the .nuget directory and pushing them to a specified NuGet source using an API key. update\_banner.cmd automates the process of updating source file header banners across multiple project folders (Rscript, assembly, metadb, metadna, mzkit, mzmath, visualize) by invoking an R script with a specific XML banner file and committing the changes.

.pkg · high confidence

The DATA directory now includes several new reference files to support chemical identification and classification: ChemOnt\_2\_1.obo.TXT provides the Chemical Ontology structure for categorizing compounds; VF-NPL-QEHF007898.json contains metadata for the compound albiflorin, including its InChI, SMILES, and theoretical adducts; pubchem\_ftp\_xml.Xml adds PubChem compound structure data; GUCA.csv provides time-intensity data; and NADPH\_insilicons.txt includes MS/MS matrix data.

DATA · high confidence

The dist folder now includes buildPdf.cmd to generate the README.pdf from the website using wkhtmltopdf, and two new command-line scripts (kegg\_metaDNA.cmd and metadna\_lib.cmd) that invoke KEGG\_MetaDNA.exe to process KEGG compound and reaction class data into R data files.

dist · high confidence

New HTML documentation pages have been added for the \APICategories\ enum and the \PackageAttribute\ class within the \Microsoft.VisualBasic.Scripting.MetaData\ namespace. The \APICategories\ page details the available categories for API facilities (SoftwareTools, ResearchTools, UtilityTools, CLI\_MAN), while the \PackageAttribute\ page describes the metadata properties available for scripting plugin modules, such as category, description, and publisher information.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Scripting · high confidence

A new HTML documentation page has been added for the \AtomLink\ class within the \BioNovoGene.BioDeep.Chemoinformatics.SMILES.Embedding\ namespace. This page details the class structure, including its properties (\atom1\, \atom2\, \score\, \v0\, \vertex\, \vk\) and its usage in the type reference tree, providing users with a reference for this chemoinformatics embedding component.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SMILES/Embedding · high confidence

The mzkit app now includes generated documentation for the BooleanVector class within the Microsoft.VisualBasic.Language.Vectorization namespace. This new HTML page details the class's inheritance from Vector\`1 and lists its available properties, such as Any, Array, First, IsLogical, IsScalar, Last, and Length, allowing users to reference the .NET CLR type structure directly in the vignettes.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Language · high confidence

New HTML documentation pages have been added for the \BufferRegion\ and \ByteOrder\ classes within the \Microsoft.VisualBasic.Data.IO\ namespace. The \BufferRegion\ page describes a binary data region structure with properties for block index, position, and size, while the \ByteOrder\ page documents the \BigEndian\ and \LittleEndian\ constants for binary data endianness.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/IO · high confidence

New HTML documentation pages have been added for the \dataframe\, \list\, and \pipeline\ classes within the \SMRUCC.Rsharp.Runtime.Internal.Object\ namespace. These pages provide type declarations and descriptions for users interacting with the .NET CLR runtime internals, detailing properties such as column handling for dataframes, slot management for lists, and error/message states for pipelines.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/Rsharp/Runtime/Internal · high confidence

New HTML documentation pages have been added for the \BioNovoGene.BioDeep.Chemoinformatics\ namespace, specifically covering the \Value\, \UnitValue\, \CCS\, and \ChemicalDescriptor\ classes. These pages detail the TypeScript declarations and property structures for chemical descriptor data, including support for unit-tagged values and collision cross-section (CCS) data.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics · high confidence

New R documentation pages have been added for the DIA package, specifically covering the \dia\_nmf\ function (which decomposes spectrum sets into groups using NMF), the \peptide\_lib\ function (which generates peptide mass data objects), and the \peptide\_q3\ function (which returns metabolite annotation data objects).

_Rscript/Library/mzkit\app/vignettes/mzDIA/DIA · high confidence

The vignette documentation for the \IDynamicsObject\ interface within the \Microsoft.VisualBasic.ComponentModel.DataSourceModel\ namespace has been added. This new HTML page provides a description of the interface, which is used to cast .NET CLR objects to lists in R, along with its R\# class declaration and type reference information.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/ComponentModel/DataSourceModel · high confidence

The mzkit app vignettes now include generated HTML documentation for the Microsoft.VisualBasic.Data.Bootstrapping namespace, specifically covering the IFitError and IFitted interfaces. IFitError defines the structure for fit error data (Y and Yfit values), while IFitted provides a unified model for linear fitting results, including error tests, polynomial formulas, and R-squared coefficients.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/Bootstrapping · high confidence

The vignette documentation for the \Microsoft.VisualBasic.ComponentModel.Collection.Generic\ namespace now includes pages for the \INamedValue\ and \IReadOnlyId\ interfaces. \INamedValue\ is documented as an interface inheriting from \IKeyedEntity\1\ that allows objects to be uniquely identified by a key, while \IReadOnlyId\ is documented as an interface providing a read-only \Identity\` string property for unique identification within a collection.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/ComponentModel/Collection · high confidence

The vignette now includes a new HTML page documenting the \ITimeSignal\ interface within the \Microsoft.VisualBasic.ComponentModel.TagData\ namespace. This documentation explains that the interface represents time series data, exposing \intensity\ and \time\ properties as double values, providing users with a reference for this specific data structure.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/ComponentModel/TagData · high confidence

New R documentation pages have been added to the visualPlots vignette for three plotting functions: MRM.chromatogramPeaks.plot (for visualizing MRM chromatogram peaks), chromatogram.plot (for plotting MRM chromatogram overlaps in specific raw data files), and standard\_curve (for drawing standard curves from linear models). These pages detail the function signatures, arguments, and return types (GraphicsData) for users generating these specific visualizations.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/visualPlots · high confidence

Added man pages for the MsImaging module, documenting functions for loading and rendering MSI data (viewer, render, layer, rgb), extracting and filtering ion layers (FilterMz, MSIlayer, ionLayers, apply\_raster\_filter, defaultFilter), and managing data summaries and tags (MSI\_summary.scaleMax, tag\_layers, sum\_layers, knnFill).

_Rscript/Library/mzkit\app/man/mzplot/MsImaging/MsImaging · high confidence

The vignette documentation for the \BioNovoGene.BioDeep.MetaDNA.Infer\ namespace now includes reference pages for the \Candidate\, \CandidateInfer\, \InferLevel\, and \InferLink\ classes. These pages detail the structure of inference results, including properties for alignment scores, KEGG identifiers, and MS1/MS2 level indicators, providing users with clear definitions for the data structures returned by the inference engine.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/MetaDNA/Infer · high confidence

New HTML documentation pages have been added for the MsImaging and ChemicalDraw packages, covering functions such as FilterMz, MS1, TrIQ, layer, and KCFDraw. These pages provide usage details, argument descriptions, and return type information for mass spectrometry imaging and chemical structure drawing capabilities.

_Rscript/Library/mzkit\app/vignettes/mzplot/MsImaging · high confidence

New R documentation pages have been added for the NMR package (covering FID, acquisition, nmr\_dft, read.nmrML, spectrum, and spectrumList) and the math package (covering centroid, cluster.nodes, cosine, cosine.pairwise, defaultPrecursors, exact\_mass, find\_precursor, intensity\_vec, ions.unique, jaccard, jaccardSet, mrm\_array, mz, mz\_index, norm\_msdata, and ppm). These pages provide usage details, argument descriptions, and return value types for the respective functions.

_Rscript/Library/mzkit\app/vignettes/mzkit/math · high confidence

A new HTML documentation page has been added for the \NaturalProduct\ class within the \BioNovoGene.BioDeep.Chemistry.LOTUS\ namespace. This page details the class structure, including properties such as \lotus\_id\, \smiles\, \inchi\, and \taxonomyReferenceObjects\, and provides context on the LOTUS database for natural products research.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/LOTUS · high confidence

New documentation pages have been added for the \Node\ and \NodeDegree\ classes within the \Microsoft.VisualBasic.Data.GraphTheory.Network\ namespace. The \Node\ page describes the network node model, including its inheritance from \Vertex\ and properties for degree, ID, and label. The \NodeDegree\ page documents the structure for tracking in-degree, out-degree, and total connections.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/GraphTheory/Network · high confidence

New HTML documentation pages have been added for the BioNovoGene.BioDeep.Chemistry.NCBI.PubChem.Graph namespace, detailing the structure of the knowledge graph data model. This includes the Article class for bibliographic metadata, the Evidence class for linking chemical, gene, and disease entities, the GraphId class for managing identifiers (CID, MeSH, GeneSymbol), the MeshGraph class for representing evidence-backed relationships, and the PubChemGraph class for aggregating article counts and co-occurrence scores.

_Rscript/Library/mzkit\_app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/NCBI/PubChem/Graph, Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SMILES · high confidence

A new documentation page has been added for the \QueryXml\ class within the \BioNovoGene.BioDeep.Chemistry.NCBI.PubChem.Web\ namespace. This page details the data structure used for PubChem query summaries in XML format, listing properties such as CID, IUPAC name, InChI, and various chemical descriptors, helping users understand the schema for retrieved compound data.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/NCBI/PubChem/Web · high confidence

A new HTML documentation page has been added for the \PubMedTextTable\ class within the \SMRUCC.genomics.GCModeller.Workbench.Knowledge\_base.NCBI.PubMed\ namespace. This page details the class structure, which represents a publication record exported from the PubMed database (associated with PubChem data), including fields for article metadata such as title, authors, abstract, DOI, and related compound IDs.

_Rscript/Library/mzkit\_app/vignettes/clr/SMRUCC/genomics/GCModeller/Workbench/Knowledge\base/NCBI/PubMed · high confidence

Added man pages for the \fingerprint\ and \morgan\_fingerprint\ functions within the QSAR module. The \morgan\_fingerprint\ documentation details the generation of circular molecular fingerprints, specifying parameters for molecule structure and radius, while the \fingerprint\ page provides a basic reference. These files serve as the user-facing documentation for these cheminformatics capabilities.

_Rscript/Library/mzkit\_app/man/mzkit/QSAR, Rscript/Library/mzkit\app/vignettes/mzkit/QSAR · high confidence

New HTML documentation pages have been added for the SMRUCC.Rsharp.Runtime.Interop namespace, covering key types such as IRType, RType, RMethodInfo, RMethodArgument, RReturn, RInteropAttribute, RDefaultExpressionAttribute, and RDefaultFunction. These pages provide API reference details for the .NET CLR type and method wrappers used in the R\# runtime interop layer.

_Rscript/Library/mzkit\app/vignettes/clr/SMRUCC/Rsharp/Runtime/Interop · high confidence

This change adds man pages for the SMILES module in the mzkit R package, documenting functions for parsing SMILES strings (parse), converting structures to formulas or graphs (as.formula, as.graph), extracting atomic and bond data (atoms, links), generating graph matrices (graph\_matrix), creating graph embeddings (links), converting to markup (as.markup), and evaluating structural similarity scores (score).

_Rscript/Library/mzkit\app/man/mzkit/SMILES/SMILES · high confidence

The vignette documentation now includes the \ScalerPalette\ class, which defines the available color palettes for visualizing linear scale data. This enum exposes standard patterns (Jet, Autumn, Cool, Gray, Hot, Spring, Summer, Winter), channel options (Red, Green, Blue), ColorBrewer sets (OrRd, PuBu, BuPu, Oranges, BuGn, YlOrBr, YlGn, RdPu, YlGnBu, Purples, GnBu, YlOrRd, PuRd, PuBuGn), and perceptually uniform colormaps (Rainbow, FlexImaging, Typhoon, Icefire, Seismic, viridis, magma, inferno, plasma, cividis, mako, rocket, turbo).

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Imaging/Drawing2D/Colors · high confidence

New R documentation pages have been added for the cellsPack package, specifically detailing the \pack\_cells\ and \pack\_cells.group\ functions. These pages describe how to pack multiple raw data files into a single data pack or organize single-cell metabolomics data across multiple sample groups, including usage syntax, argument definitions, and example code for creating .mzPack files.

_Rscript/Library/mzkit\app/vignettes/mzkit/cellsPack · high confidence

This update adds man pages for a suite of new functions within the massbank module, covering the reading and writing of metabolite data from various sources (MoNA, LipidMaps, ChEBI, HERB, RefMet, Lotus, Coconut) and the processing of lipid and metabolite annotations. Users can now consult the documentation for functions such as read.MoNA, read.lipidmaps, as.lipidmaps, lipid.class, and write.metalib, which facilitate loading, parsing, and saving metabolite and spectral data in formats like SDF, MSP, and MessagePack.

_Rscript/Library/mzkit\app/man/mzkit/massbank/massbank · high confidence

This change adds a set of new man pages to the \mzkit/metadb\ module, documenting functions for metabolite annotation workflows. These include \annotationStream\ and \annotationStream.compounds\ for constructing annotation data collections, \excludeFeatures\ and \uniqueFeatures\ for filtering and deduplicating annotation results, and utility functions like \has.metal\_ion\, \is.organic\, and \parseLipidName\ for chemical formula validation. It also documents search and query capabilities such as \ms1\_search\, \queryByMass\, \searchMz\, and \mass\_search.index\, alongside helper functions like \getMetadata\, \load\_asQueryHits\, \precursorIon\, and CAS number verification (\verify\_cas\_number\, \select\_cas\_number\).

_Rscript/Library/mzkit\app/man/mzkit/metadb/metadb · high confidence

Added man pages for the mzDeco module, documenting functions for MS1 peak detection (find\_peaks, mz\_deco), retention index calculation (RI\_cal, RI\_reference), peak alignment (peak\_alignment), and data conversion utilities (as.peak\_set, to\_matrix).

_Rscript/Library/mzkit\_app/man/mz\quantify/mzDeco/mzDeco · high confidence

This change adds man pages for several mzPack utility functions, including convertTo\_mzXML, getSampleTags, ls, metadata, mzpack, mzwork, open.mzwork, packData, packStream, pack\_ms1, readFileCache, removeSciexNoise, scaninfo, and split\_samples. These documents provide users with information on how to use these functions to interact with mzpack data objects, such as opening files, retrieving metadata, packing data, and removing noise.

_Rscript/Library/mzkit\app/man/mzkit/mzPack/mzPack · high confidence

The mzkit package now includes man pages for its annotation module, covering functions for validating adducts, checking in-source fragments, managing annotation workspaces and repositories, assigning peaks, and creating cross-references to external databases like KEGG, PubChem, and HMDB.

_Rscript/Library/mzkit\app/man/mzkit/annotation/annotation · high confidence

The package now includes man pages for several new visualization capabilities: \gcxgc\_heatmap\ for two-dimensional GCxGC data, \mass\_spectrum.plot\ for mass spectrum bar charts with highlighting options, \parse.spectrum\_alignment\ for parsing alignment details, \plot.UV\_signals\ for UV spectrum visualization, \plotNetworkClusterHistogram\ for molecular networking cluster histograms, \raw\_scatter\ for MS1 scan scatter matrices, \raw\_snapshot3D\ for 3D XIC matrix plots, and \xic\_scatter\_density\ for XIC scatter visualizations.

_Rscript/Library/mzkit\app/man/mzplot/visual/visual · high confidence

The documentation site now includes a dedicated page for the \Microsoft.VisualBasic.Data.GraphTheory.Vertex\ class, detailing its properties (\ID\ and \label\) and its role as a node within a graph structure.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/Data/GraphTheory · high confidence

A new HTML documentation page has been added for the \PathwayGraph\ class within the \BioNovoGene.BioDeep.Chemistry.NCBI.PubChem.ExtensionModels\ namespace. This page details the class structure, listing its properties such as \annotation\, \category\, \cids\, \name\, and \url\, providing users with a reference for this specific extension model.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemistry/NCBI/PubChem/ExtensionModels · high confidence

A new HTML documentation page has been added for the \readFile\ function within the RamanSpectroscopy package. This page details how to parse Raman Spectroscopy data from an ASCII text file, specifying the \file\ argument for the input path and the optional \env\ argument for the execution environment. It also clarifies that the function returns a \Spectroscopy\ data object.

_Rscript/Library/mzkit\app/vignettes/mzkit/RamanSpectroscopy · high confidence

A new HTML vignette has been added for the \BioNovoGene.BioDeep.Chemoinformatics.SDF.SDF\ class, providing users with a reference for the Structure-data file format. The documentation details the class properties, including \Comment\, \ID\, \MetaData\, \name\, \Software\, and \Structure\, and includes external links to resources like LipidMaps, PubChem, and the SDF Toolkit.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/BioDeep/Chemoinformatics/SDF · high confidence

A new HTML documentation page has been added for the \Microsoft.VisualBasic.ValueTypes.TimeScales\ enumeration. This page details the available time scale options (Millisecond, Second, Minute, Hour, Day, Month, Year) and their underlying integer values, providing users with a reference for this .NET CLR type within the mzkit application.

_Rscript/Library/mzkit\app/vignettes/clr/Microsoft/VisualBasic/ValueTypes · high confidence

A new HTML documentation page has been added for the \exact\_mass\ function within the \Oligonucleotide\_MS\ package. This page details the function's usage, which accepts a collection of gene sequences as input, and describes its return value as a data object of any kind. This provides users with reference material for calculating exact masses of gene sequences.

_Rscript/Library/mzkit\_app/vignettes/mzDIA/Oligonucleotide\MS · high confidence

A new HTML vignette page has been added to document the \loadFoods\ function from the \foodb\ package. This page details the function's usage, specifying that it accepts a \dir\ argument (string) and an optional \env\ argument (Environment), and explains that it returns a data object of any kind. This provides users with reference material for loading food database CSV dumps within the mzkit application.

_Rscript/Library/mzkit\app/vignettes/mzkit/foodb · high confidence

The libraryTest demo now includes a new R script (leucine\_anno.R) and a corresponding MGF data file (leucine.mgf) to demonstrate peptide annotation using the mzkit package. The script reads the provided leucine spectrum, extracts precursor types, and applies peak annotations for the leucine formula (C6H13NO2), providing a concrete example of how to use the formula and assembly modules for mass spectrometry data processing.

Rscript/demo/libraryTest · high confidence

A new R script (mzxml\_cache.R) has been added to the workbench to convert raw mzXML files into a data cache format. This utility accepts an input mzXML file via the --mzxml argument and writes the processed cache to a file (defaulting to a .mzweb\_cache.txt file in the same directory), leveraging the mzkit library for stream loading and cache writing.

dist/workbench/mzweb · high confidence

This update adds the man pages (documentation) for the mzweb R package, covering functions for opening and converting raw data files (open, open.mzpack, as.mzpack), extracting chromatogram and scan data (load.chromatogram, load.stream, ms1\_scans, ms2\_peaks), processing spectra (ms1\_peaks, mass\_calibration, parse.scanMs, parse\_base64), and managing data persistence (write.mzPack, write.cache, read.cache, write.text\_cache, packBin, setThumbnail).

_Rscript/Library/mzkit\app/man/mzkit/mzweb/mzweb · high confidence

The butyryl-CoA chemoinformatics module now includes a network model defined by two new data files: \nodes.csv\ and \network-edges.csv\. The node file defines 53 chemical entities (including Carbon, Nitrogen, Oxygen, Sulfur, and Phosphorus) with their atomic weights and spatial coordinates, while the edge file specifies the connections between these nodes, including interaction types such as up-regulation and down-regulation. This data provides the structural and relational basis for visualizing or analyzing the butyryl-CoA pathway within the application.

dist/Rscript/chemoinformatics/butyryl-CoA · high confidence

The vignettes directory now includes an index.html page that lists the available R package symbols and links to the various mzkit library modules (such as mzDIA, mzkit, mzplot, and mz\_quantify), along with a keywords.html page that organizes symbols by topic (e.g., 'read data', 'metadna', 'pubchem') to improve discoverability of functions within the MZKit toolkit.

_Rscript/Library/mzkit\app/vignettes · high confidence

New R scripts have been added to the proteomics demo directory to support peptide mass library workflows. The \peptide\_libs.R\ script generates BSON-formatted peptide mass libraries for various amino acid lengths (2-5 aa) using the \mzkit\ and \mzDIA\ packages. The \MRM\_peptide.R\ script provides a demo for annotating MRM ions by matching precursor and product ions against these libraries, allowing users to process raw mzML data and export annotation results to CSV.

Rscript/demo/proteomics · high confidence

The dist/Rscript/spectra directory now includes several new R scripts that enable spectral clustering and molecular networking workflows. MNclustering.R and molecularNetworking.R provide pipelines for loading mzPack files, extracting MS2 peaks, and performing clustering using the MoleculeNetworking package (with Louvain clustering in the latter). cluster.R and cluster2.R offer alternative clustering approaches: the former clusters MGF files and generates individual spectrum plots, while the latter processes Excel-defined lipid targets, unions peaks, generates annotations, and outputs summary CSVs alongside union and top-ion visualizations. Additional scripts include distance.R (listing available distance metrics), tree.R (querying a spectrum tree library), plot\_new.R (plotting aligned MS/MS spectra), and supporting plot assets (plotMs.svg, plot\_msms.svg).

dist/Rscript/spectra · high confidence

New JavaScript and CSS assets have been added to the vignettes assets folder to enable syntax highlighting for R code examples. The \R\_syntax.js\ file defines tokenization rules for R keywords, operators, and colors, while \highlights.js\ provides the function to apply these styles to code blocks. The accompanying \page.css\ file styles the highlighted code elements (keywords, comments, numbers, etc.) and general vignette layout.

_Rscript/Library/mzkit\_app/vignettes/\assets · high confidence

New HTML documentation pages have been added for the \taxonomy\ package within the mzDIA vignettes. These pages document the \clusters\ function for getting spectrum clusters, the \tree\ function for creating a single spectrum taxonomy tree, the \parallel\_tree\ function for building trees from multiple samples in parallel, and the \vocabulary\ function for extracting spectrum vocabulary from a tree.

_Rscript/Library/mzkit\_app/vignettes/mzDIA/taxonomy, Rscript/Library/mzkit\app/vignettes/mzkit/ThermoRaw · high confidence

New man pages have been added to document the xcms interop and data handler functions within the mzkit application. These include parse\_xcms\_samples for converting input files to mzkit peakset objects, cast\_findpeaks\_raw for transforming xcms find peaks results, set\_annotations for assigning metabolite annotations to ion features, expression\_df for creating expression dataframes, and make\_group\_peaks for grouping peaks by mass-to-charge and retention time.

_Rscript/Library/mzkit\_app/man/mz\quantify/xcms · high confidence

New HTML documentation pages have been added to the mzkit\_app vignettes for the xcms package, covering functions such as cast\_findpeaks\_raw, expression\_df, make\_group\_peaks, parse\_xcms\_samples, and set\_annotations.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/xcms · high confidence

The \mzkit\_app\ vignettes for the \assembly\ package now include generated R documentation for key mass spectrometry data handling functions. Users can now reference API details for reading and writing MGF files (\read.mgf\, \write.mgf\), parsing MSL and MSP formats (\read.msl\, \read.msp\), and accessing raw scan data from mzXML/mzML files (\raw.scans\, \ms1.scans\). Additional documentation covers utility functions for polarity detection, file indexing, and XML seeking.

_Rscript/Library/mzkit\app/vignettes/mzkit/assembly · high confidence

Added HTML documentation for the \OutFileTypes\ class within the \ProteoWizard.Interop\ namespace. This new page details the available file format options for output, including mzXML, mzML, mz5, MGF, text, MS1, CMS1, MS2, and CMS2, providing users with a reference for the supported export types.

_Rscript/Library/mzkit\app/vignettes/clr/ProteoWizard/Interop · high confidence

This change adds HTML documentation pages for the spectrumTree package, covering functions for managing reference spectrum databases (new, open, readpack, addBucket, compress, export\_spectrum), performing spectral searches and alignments (query, top\_candidates, candidate\_ids, as.annotation\_result, jaccardSet), and configuring search parameters (dotcutoff, parallel, discard\_precursor\_filter). It also includes documentation for utility functions like embedding and get\_testSample.

_Rscript/Library/mzkit\app/vignettes/mzkit/spectrumTree · high confidence

This update adds comprehensive man pages for the MRMLinear module, documenting functions for ion pair extraction, peak area calculation, linear fitting, and sample quantification. It also introduces a new \joint\_peaks\ boolean parameter (defaulting to TRUE) to the MRM arguments and peak finding functions, allowing users to control whether peaks are processed jointly, alongside a new \from\_arguments\_json\ helper for loading configuration from JSON strings.

_Rscript/Library/mzkit\_app/man/mz\quantify/MRMLinear/MRMLinear · high confidence

Added man pages for the \cellsPack\ module, documenting the \pack\_cells\ and \pack\_cells.group\ functions. These tools allow users to pack multiple single-cell flow cytometry raw data files into a single data pack, with \pack\_cells.group\ supporting the organization of data across multiple sample groups.

_Rscript/Library/mzkit\app/man/mzkit/cellsPack · high confidence

Added man pages for the FoodB module, specifically documenting the loadFoods function which allows users to load a FoodB database CSV dump. The documentation details the function's name, synopsis, description, and parameters (dir and env), clarifying how to access this data source within the application.

_Rscript/Library/mzkit\app/man/mzkit/foodb · high confidence

Added a new GC-MS quantification script (GCMS\_quantify.R) that automates the targeted quantification of samples using reference standards. The tool reads raw mzML data and ion lists, performs linear fitting on reference samples to generate calibration curves, and then quantifies target ions in sample data using the NetPeakSum integrator. It outputs quantification results, raw scan data, linear regression parameters, and ion peak data as CSV files, and generates an HTML report containing standard curve plots and chromatograms for each ion.

dist/Rscript/GCMS · high confidence

The mzkit application now includes HTML documentation for the GCMS package's quantification functions, covering peak detection (ROIlist), ion extraction (SIMIonExtractor, ScanIonExtractor), data parsing (parseContents), raw data reading (read.raw), and linear quantification workflows (linear\_algorithm, linears, contentTable, as.quantify.ion, peakRaw).

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/GCMS · high confidence

The MSI package documentation has been added, providing reference pages for functions that handle mass spectrometry imaging (MSI) data. This includes capabilities to open imzML files, extract ion data matrices, calculate spatial statistics (such as Moran's I), manage pixel layers, and perform data correction and convolution.

_Rscript/Library/mzkit\app/vignettes/mzkit/MSI · high confidence

Added static data files for three PubChem compounds (ATP/CID 5957, Cyanidin/CID 128861, Aspirin/CID 2244). The dump includes HTML records with structure, names, and safety information, alongside JSON index files mapping identifiers to their respective CIDs.

DATA/pubchem/.pubchem · high confidence

The mzkit package (version 1.1.5) is introduced as a pure R API toolkit for processing mass spectrometry data, featuring an in-memory periodic table for exact mass calculations and a C++ backend via Rcpp to support reading mzPack binary data files.

Rscript/R/mzkit · high confidence

The MetaDNA package is introduced to identify unknown metabolites using the metaDNA algorithm. This initial release (version 1.315.20963) establishes the core package structure, including the DESCRIPTION, NAMESPACE, and R project configuration, and lists VisualBasic.R as a suggested dependency.

Rscript/R/MetaDNA · high confidence

The mzkit R package is introduced as a new toolkit for processing NMR, MALDI MSI, MALDI single cell, LC-MS, and GC-MS raw data, along with chemoinformatics analysis and visualization. This initial release (version 3.2.56.56444) includes the core package structure (DESCRIPTION, NAMESPACE) and the mzDIA module, which provides APIs for DIA spectrum data annotation (including NMF-based decomposition), lipidomics annotation (parsing lipid names, generating SMILES, and mapping to LipidMaps), and molecular networking (clustering, graph creation, and spectrum inference via cloud services).

_Rscript/Library/mzkit\app · high confidence

This change adds two new Visual Studio solution projects to the metadna module: KEGG\_MetaDNA and MetaDNA\_visual. The KEGG\_MetaDNA project provides a command-line interface to compile KEGG reaction and compound data into an RDA-format network database, including data models for KEGG metadata and reaction links. The MetaDNA\_visual project introduces the infrastructure for visualizing these metabolic networks, featuring extension methods to translate graph data into table formats for rendering.

src/metadna · high confidence

Adds the MetaDNA algorithm for identifying unknown metabolites by leveraging KEGG reaction networks and MS/MS spectral alignment. The implementation includes core logic for iterative network expansion (metaDNA.R, metaDNA\_iteration.R), KEGG compound matching and partner lookup (KEGG\_handler.R), MS/MS similarity scoring and alignment (algorithm.R), seed management and scoring (metaDNA\_seeds.R), and network debugging/visualization output (debugger.R). It also adds support for appending KEGG Brite classification data to results (keggBrite.R) and provides parallel execution support via foreach/doParallel in the iteration step.

Rscript/R/MetaDNA/R · high confidence

The MRMLinear package vignettes are now available, providing R documentation for functions that support MRM quantification workflows. This includes utilities for reading ion pair definitions and internal standards from files, extracting ion peaks and regions of interest from raw mzML data, performing peak area calculations, and executing sample quantification against linear calibration models.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/MRMLinear · high confidence

Added HTML documentation pages for several new .NET CLR types used in mass spectrometry data handling. This includes models for MGF and MSL ion formats, MSP spectrum data, Raman spectroscopy data, 2D chromatograms, and mass spectrometry imaging (MSI) corrections. The update also introduces documentation for imzML-related classes, covering binary data pointers, pixel intensity summaries, scan data structures, and metadata handling, as well as XML-based data seeking utilities.

_Rscript/Library/mzkit\app/vignettes/clr/BioNovoGene/Analytical · high confidence

Added a set of R scripts to the 3D imaging workbench to support 3D mass spectrometry imaging workflows. These include \embedding.R\ for performing cell embedding and exporting cluster data, \nrrd\_3dmodel.R\ for assembling NRRD 3D models from ion layers, \volume.R\ for applying intensity filters and generating 3D volume visualizations, and \z\_reader\_test.R\ and \z\_single\_test.R\ for testing single-layer data reading and assembly. A \.vscode/settings.json\ file was also added to configure the development environment.

_dist/workbench/ms\imaging/3d · high confidence

This change introduces a new set of scripts for targeted mass spectrometry analysis, specifically supporting GC-MS SIM and MRM workflows. The new \GCMS\_SIM.R\ module provides functions to create reference linears, parse content levels from calibration file names, perform quantification, and generate HTML reports. The \MRM.R\ module adds support for reading ion pair data from MSL datasets. Additionally, \html.R\ enables the generation of MRM data reports including XIC data and PCA plots, while \linears.R\ handles the plotting of linear calibration curves and the export of quantification results (quantify, raw peak areas, linear equations, and ion peaks) to CSV files.

_Rscript/Library/mzkit\app/R/targeted · high confidence

Added two new R scripts to the GCMS module: \deconv.R\ introduces a \deconv\_gcms\ function that processes raw GCMS data (\.mzPack\ files) to extract peak features, align them across samples, and export the results as a peak table CSV, retention time shift data, and a shift plot; \cfmid\_3\_EI.R\ adds a \read.cfmid\_3\_EI\ helper to parse prediction result files from the cfm-id EI model, returning spectral data and fragment annotations.

_Rscript/Library/mzkit\app/R/GCMS · high confidence

Added new HTML report templates (linears.html, peaksdata.html) for viewing MRM chromatogram and peak data. The peaksdata report includes a File Viewer tab for XIC data and an Ion Viewer tab for ion overlaps, along with a section for displaying PCA plots and a table of peak data (rt, area, sn, etc.).

_Rscript/Library/mzkit\app/data/MRM · high confidence

This change introduces a new set of R scripts in the LCMS module to handle MS1-level data processing and visualization. Users can now generate Total Ion Current (TIC) and Base Peak Chromatogram (BPC) plots for individual samples and overlaid groups via the new \chromatogram.R\ module. Additionally, a complete MS1 deconvolution workflow is provided: \ms1\_xic\_bins.R\ extracts ion chromatograms with caching, \ms1\_mz\_bins.R\ identifies ion features, \deconv\_xicfile.R\ and \make\_peak\_samples.R\ perform parallel peak detection, and \ms1\_peaktable.R\ assembles and aligns the final peak table. The \spectrum\_cluster.R\ module adds the ability to select representative MS2 spectra using molecular networking.

_Rscript/Library/mzkit\app/R/LCMS · high confidence

This change introduces new R modules for interacting with PubChem data, specifically enabling the retrieval of knowledge graph networks and structured metadata. The \pubchem.R\ module adds a \knowledge\_graph\ function that queries relationships between compounds, genes, and diseases, returning structured tables with PubMed evidence. The \pugView.R\ module provides functions to parse PubChem HTML responses into standardized metadata objects, including identifiers, synonyms, and cross-references. Additionally, \graph\_json.R\ and \load\_metadata.R\ support the conversion of these data objects into JSON formats and the loading of local cached repositories, respectively.

_Rscript/Library/mzkit\app/R/pubchem · high confidence

The mz\_quantify math vignette now includes generated R documentation pages for several functions, including chromatogram creation, sample name mapping, peakset table merging, peak ROI extraction, data preprocessing (with options for imputation, normalization, and batch correction), missing value removal, chromatogram resampling, and top peak selection. These pages provide usage syntax, argument descriptions, and return type information for users working with mass spectrometry data analysis in R.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/math · high confidence

The \pubchem\_kit\ vignette now includes generated R documentation pages for a comprehensive set of functions, enabling users to understand how to query PubChem data, parse MeSH ontology trees, read Pubmed and PUG-View files, and handle local repositories. New documentation covers CID and SID mapping, pathway graph parsing, knowledge graph queries, and metabolite image retrieval, providing usage signatures and argument details for the package's chemical and biological data integration capabilities.

_Rscript/Library/mzkit\_app/vignettes/mzkit/pubchem\kit · high confidence

The dist/workbench directory now includes a set of R scripts that provide new capabilities for mass spectrometry imaging and data analysis. Users can generate ion statistics and histograms via IonStat.R, and create multi-layer MS imaging visualizations (including PDF output) using MsImaging.R, MsImaging2.R, and pdfMSI.R. The new MSICache.R and readMSICache.R scripts enable caching and retrieval of MSI data layers, while kegg.R and pubchem\_script.R offer utilities for importing and annotating compound data from KEGG and PubChem sources.

dist/workbench · high confidence

This update adds a suite of new R\# scripts and Windows batch files to the dist/Rscript directory to support Mass Spectrometry workflows. Key additions include MRM-specific tools: MRM-quantify.cmd and mrm\_quantify.R for quantification, MRM\_rt\_shifts.R for retention time alignment, and mzML\_chromatogramPlots.R for generating chromatogram plots from mzML files. Data conversion capabilities are expanded with wiff2mzML.R (Wiff to mzML) and raw2mzXML.R (Thermo Raw to mzXML), both utilizing ProteoWizard. Additional scripts provide visualization and analysis features: plot\_chromatogram.R and plotSamples.cmd for plotting ion chromatograms, denovo.py for MS2 product ion filtering, contour.R for scatter plots, and adducts.R for adduct annotation. Several .cmd files (test.cmd, plotSamples.cmd, mzML.cmd) are provided to orchestrate these scripts with specific data paths.

dist/Rscript · high confidence

The SingleCells package documentation has been updated with new HTML vignettes for key single-cell metabolomics functions. Users can now find detailed reference pages for data handling and analysis, including \cell\_matrix\ and \write.matrix\ for exporting and saving ion feature data, \read.mz\_matrix\ and \open.matrix\ for loading data, \cell\_embedding\ and \embedding\_sample\ for creating spot cell embeddings, and \cell\_clusters\ for exporting clustering results. Additional vignettes cover utility functions such as \apply.scale\ for matrix scaling, \as.expression\ for casting to expression matrices, \df.mz\_matrix\ for dataframe conversion, and \total\_peaksum\ for normalization.

_Rscript/Library/mzkit\app/vignettes/mzkit/SingleCells · high confidence

The TissueMorphology package (version 1.0.0.0) now includes generated R documentation for its core functions. Users can now reference the API for creating tissue region datasets (TissueData), handling UMAP spatial data (UMAPsample, loadUMAP), managing spatial mappings (gridding, read.spatialMapping, splitMapping), and processing tissue regions (intersect\_layer, loadTissue, tag\_samples, writeCDF).

_Rscript/Library/mzkit\app/vignettes/mzkit/TissueMorphology · high confidence

Added TypeScript declaration files (.d.ts) for multiple mzkit modules, including ChemicalDraw, DIA, GCMS, GCxGC, InChI, Linears, MRMLinear, MSI, MoleculeNetworking, MsImaging, Mummichog, NMR, Oligonucleotide\_MS, and ProteoWizard. These files expose the public API surface of the underlying R\# packages to JavaScript/TypeScript consumers, enabling type-safe integration and IDE support for functions such as GCMS peak detection, MRM ion pair extraction, MSI layer rendering, and InChI parsing.

_Rscript/Library/mzkit\app/@export · high confidence

This update introduces several new R helper scripts to the mzkit application library. annotation.R adds a function to load KEGG compound databases for mass spectrometry annotation, supporting both local MessagePack files and the default GCModeller repository. lipidmaps.R provides utilities to load the LIPIDMAPS repository from internal data packs and parse raw SDF structure files. math.R introduces functions for creating m/z tolerance values, normalizing matrix sample data with missing value imputation, and preparing data for ANOVA statistical testing. mummichog.R implements a wrapper for the Mummichog workflow to perform pathway enrichment analysis using KEGG background data. rawfile.R adds a method to convert raw mass spectrometry files (mzXML, mzML, raw) into mzpack data objects with thumbnail generation. Finally, zzz.R updates the package startup message to display mzkit title, description, and feature highlights upon loading.

_Rscript/Library/mzkit\app/R · high confidence

Added \github\_page.cmd\ and \update.cmd\ scripts to automate the build and documentation generation for the MSI\_app and mzkit\_app modules. The \github\_page.cmd\ script invokes the R\# runtime to build the source code and generate GitHub page documentation, while \update.cmd\ extends this by saving the built packages as zip files and installing them as R packages. These scripts also reference the newly added \MSI\_app\ and \mzkit\_hpc\ submodules, integrating them into the build workflow.

Rscript/Library · high confidence

This update adds a collection of R and Python scripts to the chemoinformatics module, providing new capabilities for molecular formula handling, graph similarity analysis, and isotope distribution. The new R scripts (KCF.R, KCF.network.R, formulaTest.R, literalTest.R, eval\_exact\_mass\_test.R, Isotope\_Distribution.R, drawSMILES.R, exportChemicalDescriptors.R, testNameParser.R) demonstrate reading KCF molecular graphs, calculating graph Jaccard similarity, performing formula arithmetic and canonicalization, evaluating exact mass, generating isotope distributions, drawing SMILES structures, exporting chemical descriptors from PubChem, and parsing glycosyl names. Additionally, Python scripts (search.py, searchFormula.py) are introduced for searching formulas by exact mass. Several sample molecular structure files in KCF format (2-butenoyl-CoA.txt, AMP.txt, ATP.txt, butyrate.txt, butyryl-CoA.txt) are also added to support these examples.

dist/Rscript/chemoinformatics · high confidence

This change introduces a suite of new R and Python scripts in the \mzkit\_app/tools\ directory to automate common mass spectrometry workflows. Users can now convert raw data files (mzXML, mzML, imzML, raw) to ASCII text caches or mzPack formats via \ascii\_cache.R\ and \msconvert.R\. The \inspect\_files.R\ script enables targeted inspection by generating XIC plots for specific metabolites across multiple samples, while \viz\_raw.R\ and \viz\_raw\_func.R\ provide batch visualization of Total Ion Current (TIC) and Base Peak Chromatograms (BPC). For data integration, \single\_xcms.R\ and \merge\_xcms.R\ facilitate peak detection and alignment of xcms outputs into unified peak tables. Additional utilities include \exportLibrary.R\ for exporting spectral libraries to MGF format, \imzml\_metadata.R\ for extracting imaging metadata, \pubchem\_query.R\ for batch PubChem CID lookups, and \peptide\_libs.R\ for generating peptide library references.

_Rscript/Library/mzkit\app/tools · high confidence

The mzmath library introduces new data structures and processing capabilities for comprehensive mass spectrometry analysis. It adds a dedicated GCxGC module featuring models for 2D chromatogram meshes, dimensional spectra, and 2D peak detection algorithms to handle complex two-dimensional gas chromatography data. Additionally, it implements a new MS2 annotation reporting system, including binary serialization for MS2 alignment scores and a report rendering interface that generates HTML tables for visualizing metabolite annotations and ion data.

src/mzmath · high confidence

Added a suite of R demo scripts in Rscript/demo that showcase mzkit capabilities, including spectral entropy calculation and similarity scoring (entropy.R), formula scanning (formula.R), ID mapping for ChEBI and HMDB (idmapping.R), MRM ion extraction (mrm.R), raw file listing and linear group detection (rawfiles.R, multipleReferenceTest.R), m/z object creation (mz.R), matrix packing (pack\_matrix.R), and spectrum plotting from CSV or MGF inputs (plot\_spectrum.R, plot.mgf\_Ion.R). Also included tolerance calculation examples (tolerance\_test.R) and sample CSV data files for centroid and MZI matrices.

Rscript/demo · high confidence

Added R documentation pages for the \tissue\ package, introducing guides for \RSD\ (spatial RSD evaluation), \heatmap\_layer\ (heatmap generation from tissue scans), \mark\_nucleus\ (nucleus pixel extraction), and \scan\_tissue\ (HE-stain image block analysis).

_Rscript/Library/mzkit\app/vignettes/mzplot/tissue · high confidence

Added HTML documentation pages for several mzkit modules, including GCMS, GCxGC, InChI, MSI, Mummichog, NMR, ProteoWizard, QSAR, RamanSpectroscopy, and SMILES. These pages provide user-facing descriptions and lists of exported functions and types for each module.

_Rscript/Library/mzkit\app/vignettes/mzkit · high confidence

A new CSV dataset (2244\_compounds.csv) has been added to the PubChem knowledge graph output, providing structured co-occurrence data linking specific compounds (such as Clopidogrel, Warfarin, and Aspirin) to related medical literature. This file contains columns for relevance scores, article counts, and co-occurrence metrics, enabling users to explore relationships between drugs and research topics directly from the query results.

dist/Rscript/pubchem · high confidence

The lipidomics vignette now includes generated R documentation pages for several new functions: \adduct\ (creates adduct ion data models), \lipid\_ions\ (generates lipid ion collections based on class and structural constraints), \lipid\_smiles\ (returns lipid SMILES data), \lipidmaps\ (creates a LipidMaps metabolite data indexer), \mapping\ (maps LipidMaps reference IDs via lipid name), and \parse\_lipid\ (parses lipid names into structure objects). These pages provide usage syntax, argument details, and return type information for users working with lipid identification and data modeling.

_Rscript/Library/mzkit\app/vignettes/mzDIA/lipidomics · high confidence

The mzkit R package introduces a comprehensive suite of functions for mass spectrometry data processing and analysis. This includes utilities for converting profile spectra to centroid mode, calculating m/z values for various precursor types (adducts, ions), and matching precursor types based on mass and charge. The package also provides algorithms for spectral similarity scoring (cosine, Jaccard, entropy), global alignment of spectra, and molecular networking via clustering. Additional features cover atomic group enumeration, molecular weight calculation, formula parsing, and ASCII visualization of spectra.

Rscript/R/mzkit/R · high confidence

The massbank package vignettes now include comprehensive documentation for a suite of new functions supporting metabolite annotation and lipidomics. Users can now reference guides for loading and parsing external databases (ChEBI, HMDB, MONA, HERB), converting SDF data to lipidmaps objects, and creating annotation helpers for lipid classes and names. Additional documentation covers utility functions for parsing glycosyl names, extracting metabolite information, and constructing metabolite annotation records with cross-references.

_Rscript/Library/mzkit\app/vignettes/mzkit/massbank · high confidence

The \metadna\ package vignettes have been generated, providing R documentation for the metaDNA annotation workflow. This includes functions to create the algorithm module (\metadna\), load reference data such as KEGG compounds and reaction classes (\kegg.library\, \load.kegg\, \load.kegg\_network\), configure precursor adducts (\range\), and process MS2 spectrum data (\load.raw\). The documentation also covers result handling, including extracting annotation tables (\as.table\), reading inference details (\read.infer\_details\), and visualizing results as network graphs (\as.graph\, \read.metadna.infer\).

_Rscript/Library/mzkit\app/vignettes/mzDIA/metadna · high confidence

The \mzDeco\ package vignettes have been added, providing user-facing documentation for a suite of mass spectrometry analysis functions. This includes \mz\_deco\ for chromatogram data deconvolution to peak tables, \peak\_alignment\ for COW-based time alignment of multiple samples, and \mz.groups\ for m/z grouping. The documentation also covers helper utilities for peak finding (\find\_peaks\, \find\_peaks.simple\), retention index calculation and reference creation (\RI\_cal\, \RI\_reference\, \RI\_batch\_join\), and data manipulation (\as.peak\_set\, \filter\_noise\_spectrum\, \pull\_xic\).

_Rscript/Library/mzkit\_app/vignettes/mz\quantify/mzDeco · high confidence

The mzPack package documentation has been updated with new HTML reference pages for key functions, including \convertTo\_mzXML\ for writing data to mzXML format, \packData\ and \packStream\ for creating and saving mzPack objects, \mzpack\ and \mzwork\ for opening data readers and workspaces, and \ls\, \metadata\, and \scaninfo\ for inspecting scan IDs and metadata. Additional pages cover \getSampleTags\ for retrieving sample tags, \split\_samples\ for dividing files by tags, \readFileCache\ for extracting data from mzwork archives, \removeSciexNoise\ for cleaning MS2 data, and \pack\_ms1\ for aggregating MS2 spectra.

_Rscript/Library/mzkit\app/vignettes/mzkit/mzPack · high confidence

Added HTML documentation pages for the mz\_quantify module, covering targeted metabolomics workflows including GCMS quantification, MRM linear regression, peak analysis, and data visualization. The new vignettes document functions for reading raw data, extracting ion peaks, performing linear quantification, and plotting chromatograms, providing users with reference material for the mzkit package's mass spectrometry capabilities.

_Rscript/Library/mzkit\_app/vignettes/mz\quantify · high confidence

The mzweb package vignettes now include comprehensive R documentation for a suite of functions designed to interact with mass spectrometry data. Users can now reference guides for opening raw data files (such as mzXML, mzML, and mzPack) via \open\ and \open.mzpack\, loading chromatogram and scan stream data with \load.chromatogram\ and \load.stream\, and extracting specific spectral data using \ms1\_peaks\, \ms1\_scans\, and \ms2\_peaks\. The documentation also covers data conversion and I/O operations, including \as.mzpack\ for converting assembly files, \write.mzPack\ for exporting data, and utilities for parsing base64 or binary streams like \parse\_base64\ and \parse.scanMs\. Additional functions for mass calibration, thumbnail generation, and caching are also documented.

_Rscript/Library/mzkit\app/vignettes/mzkit/mzweb · high confidence

A new \pack\_singleCells\ function has been added to the \mzkit\_app\ library, allowing users to combine multiple single-cell sample files into a single dataset. The function accepts a directory path or a list of raw data file paths, automatically detects \.mzPack\ files if a directory is provided, and uses the \cellsPack\ package to merge the opened files into one unified object.

_Rscript/Library/mzkit\app/R/singleCells · high confidence

Added a suite of new pipeline scripts in the \Rscript/Library/mzkit\_app/pipeline\ directory to support various mass spectrometry workflows. These include \GCxGC.R\ for processing GCxGC raw data (CDF to mzPack conversion, 2D TIC extraction, and rendering), \MSI.R\ and \MSIsummary.R\ for mass spectrometry imaging ion layer rendering and joint matrix generation across multiple samples, and \Mummichog.R\ for MS1 peak annotation using the Mummichog algorithm against KEGG data. Additional scripts provide functionality for creating spectral reference libraries (\KEGG\_reference.R\, \hmdb\_reference.R\), performing targeted MRM quantification (\mrm\_quantify.R\), batch converting raw files to mzPack format (\mzPack.R\), extracting UV signals (\UV.R\), running metaDNA annotation (\metaDNA.R\), converting raw data via PWIZ (\pwiz.R\), and exporting chromatogram images (\chromatogram\_exports.py\).

_Rscript/Library/mzkit\app/pipeline · high confidence

Added a suite of R scripts in the \dist/Rscript/raw\ directory to support raw mass spectrometry data workflows. These include \TIC\_overlaps.R\ and \TIC\_overlapsFast.R\ for generating Total Ion Current and Base Peak Chromatogram overlap plots, \mzPack.R\ and \packSingle.R\ for converting raw files (mzML/mzXML) into the proprietary mzPack binary format, and \mzwork.R\/\mzwork2.R\ for extracting and clustering specific lipid ions from mzWork files. Additional utilities cover UV signal extraction (\rawPipeline.R\), chromatogram packing (\pack\_chromatogram.R\), and pixel data export for MSI (\exportPixels.R\).

dist/Rscript/raw · high confidence

Added R scripts in the single\_cells directory to process raw MALDI-TOF mass spectrometry data into single-cell metabolomics matrices. The new matrix.R and mzpack\_raw.R files provide workflows to read raw XML/mzPack files, perform centroiding, pack the data, and export the resulting cell expression matrices as CSV files. Supporting test files (matrix\_test.R, matrix\_reader\_test.R) were also added to validate the matrix reading and writing logic.

_dist/Rscript/single\cells · high confidence

The \spectrumPool\ vignette now includes generated R documentation pages for key functions, enabling users to understand how to manage spectrum clustering pools and perform inference. The new documentation covers lifecycle operations (\createPool\, \openPool\, \closePool\, \commit\), data management (\addPool\, \getClusterInfo\), and analysis workflows (\infer\, \load\_infer\, \conservedGuid\, \set\_conservedGuid\).

_Rscript/Library/mzkit\app/vignettes/mzDIA/spectrumPool · high confidence

A change to existing behaviour in src — 4455 commits (555 fixs), 2 files.

src · medium confidence · unverified

Added a configuration file for the Clearcore2.Data.AnalystDataProvider assembly that specifies .NET Framework 4.8 as the supported runtime and redirects dependencies for Clearcore2.ProjectUtilities from versions 0.0.0.0-3.0.0.0 to version 2.0.0.0. Also added a license text file directing users to the Sciex website for the Clearcore MD Software license and stating that other products are for research use only.

Sciex · high confidence

The metaDNA result export now includes additional columns in the KEGG reaction data model, specifically \precursorType\, \parentTrace\, \inferSize\, \score1\, \score2\, \pvalue\, \seed\, \partnerKEGGId\, \KEGG\_reaction\, and \reaction\. This change enhances the compatibility and detail of the exported data by providing more granular scoring, inference, and reaction context for each metabolite entry.

dist/Rscript/metaDNA · high confidence

The \formula\ package vignettes have been updated to reflect the current API surface. New documentation pages have been added for \KCF.graph\ (creating molecular network graph models) and \SDF.convertKCF\ (converting SDF models to KCF). Several existing functions have been refined: \candidates\ now explicitly documents the \candidateElements\ argument for configuring formula candidates; \canonical\_formula\ includes an example showing conversion of input strings to canonical format; \eval\ now clarifies that it returns -1 for empty or invalid formulas and details its return type behavior based on input; \isotope\_distribution\ exposes additional parameters for probability thresholds, FWHM, padding, and grid interpolation; \parse.SDF\ adds a \parseStruct\ boolean argument; \peaks\_annotation\ adds \massDiff\, \isotopeFirst\, \as.list\, and \unset.scalar\ arguments; and \registerAnnotations\ adds a \debug\ argument. These changes improve the clarity and usability of the chemical formula and structure handling tools.

_Rscript/Library/mzkit\app/vignettes/mzkit/formula · high confidence

The project has been rebranded from 'spectrum' to 'Mzkit' (a mass spectrometry data toolkit by BioNovoGene), updating the README, LICENSE, and CITATION.cff files to reflect the new name, copyright holder, and DOI. The repository structure was reorganized by adding a .gitmodules file to include external submodules for MSI imaging and KEGG visualization, while the .gitignore was expanded to exclude build artifacts, test data, and NuGet symbol packages. Additionally, new metadata files were introduced, including a SECURITY.md policy, a CODE\_OF\_CONDUCT.md, a Jekyll theme configuration (\_config.yml), and a web manifest (manifest.json) to support the project's documentation site and community standards.

(repo-wide) · high confidence

The NMR data directory now includes several new sample files (FAM013, HMDB00005, MMBBI, biosample\_quantification, bmse000400) and a README for context. The nmrML2batman.R script has been updated to handle changes in the content file format, and a test script along with a fix for the NMR test file have been added to ensure processing accuracy.

DATA/nmr · medium confidence · unverified

The vignettes for the ProteoWizard and annotation packages have been updated to reflect current API signatures and behaviors. The ProteoWizard documentation now includes \MRM.mzML\ for converting wiff files, \convert.thermo.raw\ with explicit \filetype\ and \filters\ arguments, and specific filter functions (\filter.msLevel\, \filter.scanTime\) alongside a \msconvert.ready\ status check. The annotation package documentation has been refreshed to clarify usage for \open.annotation\_workspace\ (including \meta.allocated\ pre-allocation), \open\_repository\ (with \mode\ and \mapping\ options), and \push\_temp\ (detailing alignment score fields like \jaccard\ and \entropy\). Additionally, \checkInSourceFragments\ now explicitly documents its \da\ and \rt.win\ parameters, and \make.annotation\ clarifies the \xref\ argument type.

_Rscript/Library/mzkit\app/vignettes/mzkit/annotation · high confidence

The package documentation vignettes in the \data\ module have been regenerated to reflect the current API. This update refreshes the reference pages for core spectral data handling functions, including \XIC\ and \XIC\_groups\ for extracted ion chromatogram operations, \peakMs2\ and \libraryMatrix\ for object construction, \groupBy\_ROI\ and \make.ROI\_names\ for region-of-interest management, and \representative\ and \unionPeaks\ for spectrum aggregation. It also updates documentation for utility functions such as \intensity\, \scan\_time\, \rt\_slice\, \nsize\, \linearMatrix\, \logfc\, \search\, \splash\_id\, \alignment\_ref\, \alignment\_str\, \read.MsMatrix\, and \msn\_matrix\, ensuring that argument descriptions, usage examples, and return value types are consistent with the underlying implementation.

_Rscript/Library/mzkit\app/vignettes/mzkit/data · high confidence

The \metadb\ package vignettes have been regenerated to reflect current function signatures and behaviors. Key updates include the addition of the \annotationStream.compounds\ function for creating metabolite annotation collections, new utility functions \has.metal\_ion\ and \is.metal\_ion\ for checking formula composition, and the introduction of \parseLipidName\ for lipid name parsing. The \ms1\_search\ function now supports \uniqueByScore\ and custom field mapping (\field.mz\, \field.score\), while \uniqueFeatures\ has added parameters for score-based deduplication (\scoreFactors\, \uniqueByScore\) and zero-score removal (\removesZERO\). Other updates include \load\_asQueryHits\ for casting dataframes to ion feature results, \queryByMass\ for exact mass index queries, and \verify\_cas\_number\ for CAS registry validation.

_Rscript/Library/mzkit\app/vignettes/mzkit/metadb · high confidence

1 commit adding/updating tests in DATA/test/wiff; 3 commits adding/updating tests in DATA/test/PANOMIX; Added CFM-ID test data files for GCMS testing; Added Orbitrap CID mass spectrometry test data; Added PubChem data reader and graph tests with sample datasets; Added SMILES parsing test suite and debug scripts; Added TIC test data and documentation for GCxGC analysis; Added imzML test fixtures for continuous and processed imaging data; Added test file for MoNA MSP data reading; Added test for lipid name parsing and SMILES generation; Added test scripts and data for mass spectrometry scoring and centroiding; Added test scripts for GC-MS and UV data processing; Added test scripts for LC-MS/MS analysis workflows; Added test scripts for XIC processing and peak deconvolution workflows; Added test scripts for peaktable operations; Added test scripts for single-cell matrix and data packing workflows; Added test suite for MGF file handling in MetaDNA; Added test suite for lipid mass spectrometry peak annotation; Added test suite for mzkit core modules; Added tests for DIA spectrum decomposition and lipid clustering; Added tests for SMILES structure similarity scoring; Updated test suite and data files for PubChem integration.

New .NET SDK project files (mzDIA, mzkit, mzplot, mz\_quantify, BrukerDataReader, Comprehensive) have been added to the build system, targeting .NET 10.0 and configuring multi-platform runtime identifiers (win-x64, linux-x64, linux-arm64, osx-x64). These project definitions establish the build structure and internal project references for the mzkit application modules and data readers, enabling their compilation and packaging as NuGet libraries.

(dependencies) · high confidence

Added .NET CLR documentation for Microsoft.VisualBasic.Data.GraphTheory.T; Added .NET CLR documentation for R\# interpreter components; Added MSI function documentation; Added R history file for development tracking; Added chromatogram API documentation; Added documentation for AdductIon class; Added documentation for BitmapBuffer class; Added documentation for ClusterTree class; Added documentation for DBLink and Synonym CLR types; Added documentation for DirectedVertex class; Added documentation for DoubleRange class; Added documentation for EdgeBundling Handle and WayPointVector types; Added documentation for Equation and CompoundSpecieReference types; Added documentation for Fisher's Exact test types; Added documentation for GCxGC data I/O and processing functions; Added documentation for GeneralSignal class; Added documentation for GenericTree class; Added documentation for HeatMap PixelData and RasterMatrix classes; Added documentation for InChI parsing and analysis functions; Added documentation for IsotopeCount and IsotopeDistribution classes; Added documentation for Linears module functions; Added documentation for MoleculeNetworking spectrum clustering functions; Added documentation for PoolData CLR types; Added documentation for ProteoWizard.Interop.filters.Filter class; Added documentation for R\# Runtime Environment and SymbolSet classes; Added documentation for R\# runtime components; Added documentation for RFunction, RNameIndex, and RNames interface types; Added documentation for RawFileReader library; Added documentation for SVG XML enum types; Added documentation for SampleGroup and SampleInfo classes; Added documentation for TissueMorphology helper functions; Added documentation for UV spectroscopy signal processing functions; Added documentation for Word2Vec TrainMethod and VectorModel classes; Added documentation for mzDIA package tools; Added documentation for mzkit assembly functions; Added documentation for mzkit spectral data functions; Added documentation for single-cell metabolomics analysis functions; Added documentation for spectrum taxonomy functions; Added documentation for the plot\_nmr function; Added documentation for the readFile function; Added documentation for z\_assembler package functions; Added man pages for KCFDraw and as.kcf functions; Added man pages for ThermoRaw helper functions; Added project statistics report; Added spectral\_simulator documentation pages; Document spectral\_simulator API functions; Documentation added for AggregateFunction component; Documentation for GCMS features data object creation; Documentation for spectrum pool management and inference functions; Documented exact\_mass function for gene sequence mass evaluation; Initial documentation for hmdb\_kit package functions; Initial release of MetaDNA package documentation; New documentation for tissue analysis functions; Updated ProteoWizard manual pages for R package documentation; Updated R documentation for visual package plotting functions; Updated documentation for pubchem\_kit functions; Updated man pages for the metadna package; Updated mzDIA package documentation pages; Updated mzplot package documentation.

Written by watchdog.canine.dev from the codebase's own history, inside the signed delivery this page is composed from.

• First survey — no prior run to compare against. CAI 52.

• Code Health 79
• Architecture 98
• Maturity 49
• Readiness 43
• Security 57

• 300 commits — 242 feature/other, 58 fixes

• Rscript/Library — 107 commits
• src/mzmath — 79 commits
• src/mzkit — 78 commits
• src/assembly — 16 commits
• src/metadb — 9 commits
• src/visualize — 9 commits
• Rscript/demo — 1 commit
• ThermoFisher/Libs — 1 commit

• fix: fix fo the missing pathway enrichment result
• fix: fix for buffer copy
• fix: fix for test data
• fix: fix for the fisher test function reference
• fix: fix for the math function reference
• fix: fix of cast gdi+ image object type error
• fix: fix of cast object
• fix: fix of symbol reference erro
• fix: fix of the base line
• fix: fix of the bug of parse kegg compound id pattern
• fix: fix of the component reference error
• fix: fix of the data error
• fix: fix of the demo
• fix: fix of the gdi+ image interop with skia
• fix: fix of the gdi+ image object reference conflicts between the winform and skia
• fix: fix of the invalid namespace reference error
• fix: fix of the methodf overloads
• fix: fix of the missing component reference
• fix: fix of the missing data model
• fix: fix of the missing method reference error
• …and 280 more

• 5 containers · 0 bounded contexts · 0 dependency edges (baseline)

Written by watchdog.canine.dev from the codebase's own history, inside the signed delivery this page is composed from.

xieguigang/mzkit was measured the same way every project in this corpus was: the same rubric, at a pinned commit, with the result published in full. Point a surveyor at a repository you know and see whether you agree with it.