Spectra - Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
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Spectra - Spectra Infrastructure for Mass Spectrometry Data
The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.
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12.35 score 46 stars 70 dependents 826 scripts
QFeatures - Quantitative features for mass spectrometry data
The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.
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11.46 score 29 stars 57 dependents 397 scripts
MsCoreUtils - Core Utils for Mass Spectrometry Data
MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.
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11.15 score 17 stars 86 dependents 90 scripts 5.5k downloads
MsCoreUtils - Core Utils for Mass Spectrometry Data
MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...), misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.
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10.37 score 17 stars 86 dependents 83 scripts
MetaboCoreUtils - Core Utils for Metabolomics Data
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
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10.28 score 9 stars 71 dependents 99 scripts 3.7k downloads
MetaboCoreUtils - Core Utils for Metabolomics Data
MetaboCoreUtils defines metabolomics-related core functionality provided as low-level functions to allow a data structure-independent usage across various R packages. This includes functions to calculate between ion (adduct) and compound mass-to-charge ratios and masses or functions to work with chemical formulas. The package provides also a set of adduct definitions and information on some commercially available internal standard mixes commonly used in MS experiments.
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9.72 score 9 stars 71 dependents 99 scripts
QFeatures - Quantitative features for mass spectrometry data
The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.
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9.68 score 29 stars 57 dependents 392 scriptsPSMatch - Handling and Managing Peptide Spectrum Matches
The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.
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9.13 score 6 stars 40 dependents 52 scriptsPSMatch - Handling and Managing Peptide Spectrum Matches
The PSMatch package helps proteomics practitioners to load, handle and manage Peptide Spectrum Matches. It provides functions to model peptide-protein relations as adjacency matrices and connected components, visualise these as graphs and make informed decision about shared peptide filtering. The package also provides functions to calculate and visualise MS2 fragment ions.
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9.13 score 6 stars 40 dependents 52 scripts
CompoundDb - Creating and Using (Chemical) Compound Annotation Databases
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
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8.80 score 19 stars 3 dependents 92 scripts
CompoundDb - Creating and Using (Chemical) Compound Annotation Databases
CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.
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8.66 score 19 stars 3 dependents 84 scripts
MsExperiment - Infrastructure for Mass Spectrometry Experiments
Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.
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8.53 score 5 stars 18 dependents 311 scriptsPTMods - Managing Post-Translational Modifications in R
An interface to the community supported database for amino acid/protein modifications using mass spectrometry.
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8.51 score 11 stars 41 dependents 5 scripts 1.6k downloads
MsExperiment - Infrastructure for Mass Spectrometry Experiments
Infrastructure to store and manage all aspects related to a complete proteomics or metabolomics mass spectrometry (MS) experiment. The MsExperiment package provides light-weight and flexible containers for MS experiments building on the new MS infrastructure provided by the Spectra, QFeatures and related packages. Along with raw data representations, links to original data files and sample annotations, additional metadata or annotations can also be stored within the MsExperiment container. To guarantee maximum flexibility only minimal constraints are put on the type and content of the data within the containers.
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8.11 score 5 stars 18 dependents 240 scripts
MsFeatures - Functionality for Mass Spectrometry Features
The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.
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7.80 score 7 stars 15 dependents 50 scripts
SpectriPy - Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python MS data structures. In addition, SpectriPy integrates and wraps the similarity scoring and processing/filtering functions from the Python matchms package into R.
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7.80 score 13 stars 31 scripts
SpectriPy - Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python
The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python MS data structures. In addition, SpectriPy integrates and wraps the similarity scoring and processing/filtering functions from the Python matchms package into R.
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7.79 score 13 stars 28 scriptsProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
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7.77 score 8 stars 210 dependents 13 scriptsProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages
S4 generic functions and classes needed by Bioconductor proteomics packages.
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7.77 score 8 stars 210 dependents 13 scripts
MetaboAnnotation - Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
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7.77 score 20 stars 1 dependents 65 scripts
MetaboAnnotation - Utilities for Annotation of Metabolomics Data
High level functions to assist in annotation of (metabolomics) data sets. These include functions to perform simple tentative annotations based on mass matching but also functions to consider m/z and retention times for annotation of LC-MS features given that respective reference values are available. In addition, the function provides high-level functions to simplify matching of LC-MS/MS spectra against spectral libraries and objects and functionality to represent and manage such matched data.
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infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry
7.67 score 20 stars 1 dependents 65 scripts
MsFeatures - Functionality for Mass Spectrometry Features
The MsFeature package defines functionality for Mass Spectrometry features. This includes functions to group (LC-MS) features based on some of their properties, such as retention time (coeluting features), or correlation of signals across samples. This packge hence allows to group features, and its results can be used as an input for the `QFeatures` package which allows to aggregate abundance levels of features within each group. This package defines concepts and functions for base and common data types, implementations for more specific data types are expected to be implemented in the respective packages (such as e.g. `xcms`). All functionality of this package is implemented in a modular way which allows combination of different grouping approaches and enables its re-use in other R packages.
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7.45 score 7 stars 15 dependents 45 scripts
MsBackendMgf - Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.
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7.28 score 5 stars 2 dependents 126 scripts
MsBackendMgf - Mass Spectrometry Data Backend for Mascot Generic Format (mgf) Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS spectra data from Mascot Generic Format (mgf) files. Objects defined in this package are supposed to be used with the Spectra Bioconductor package. This package thus adds mgf file support to the Spectra package.
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7.27 score 5 stars 2 dependents 83 scripts
Chromatograms - Infrastructure for Chromatographic Mass Spectrometry Data
The Chromatograms packages defines an efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.
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7.07 score 3 stars 1 dependents 27 scripts
Chromatograms - Infrastructure for Chromatographic Mass Spectrometry Data
The Chromatograms packages defines an efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.
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7.07 score 3 stars 1 dependents 27 scripts 197 downloads
MsBackendMsp - Mass Spectrometry Data Backend for NIST msp Files
Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.
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6.70 score 5 stars 2 dependents 42 scriptsMsDataHub - Mass Spectrometry Data on ExperimentHub
The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.
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6.53 score 1 stars 1 dependents 94 scriptsMsDataHub - Mass Spectrometry Data on ExperimentHub
The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.
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6.41 score 1 stars 1 dependents 85 scripts
MsBackendMsp - Mass Spectrometry Data Backend for NIST msp Files
Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.
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6.40 score 5 stars 2 dependents 42 scripts
MsBackendMetaboLights - Retrieve Mass Spectrometry Data from MetaboLights
MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.
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5.89 score 2 stars 32 scripts 320 downloads
MsBackendMassbank - Mass Spectrometry Data Backend for MassBank record Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.
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MsBackendMetaboLights - Retrieve Mass Spectrometry Data from MetaboLights
MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.
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MsBackendSql - SQL-based Mass Spectrometry Data Backend
SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.
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5.72 score 4 stars 33 scripts
MsBackendSql - SQL-based Mass Spectrometry Data Backend
SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.
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5.66 score 4 stars 33 scripts
MsBackendMassbank - Mass Spectrometry Data Backend for MassBank record Files
Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.
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5.57 score 3 stars 31 scriptsRuSirius - R Implementation of the Sirius software
The RuSirius package allows the user to interact with the Sirius software from R. Sirius is a software for the analysis and annotation of mass spectrometry data. RuSirius makes use of the API present in RSirius. It is dependent on Sirius 6.4, please ensure you have the right version downloaded.
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5.31 score 2 stars 17 scripts
SpectraQL - MassQL support for Spectra
The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects.
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5.30 score 10 stars 8 scripts
SpectraQL - MassQL support for Spectra
The Mass Spec Query Language (MassQL) is a domain-specific language enabling to express a query and retrieve mass spectrometry (MS) data in a more natural and understandable way for MS users. It is inspired by SQL and is by design programming language agnostic. The SpectraQL package adds support for the MassQL query language to R, in particular to MS data represented by Spectra objects. Users can thus apply MassQL expressions to analyze and retrieve specific data from Spectra objects.
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5.30 score 10 stars 8 scriptsMsStash - Infrastructure to serialize and restore mass spectrometry data objects
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsStash package defines classes and method to enable serializing and restoring, or importing, mass spectrometry data objects to and from language agnostic file formats. A variety of different file types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods. Additional packages extending MsStash provide the implementations to serialize/restore MS data objects.
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5.26 score 3 dependentsMsStash - Infrastructure to serialize and restore mass spectrometry data objects
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsStash package defines classes and method to enable serializing and restoring, or importing, mass spectrometry data objects to and from language agnostic file formats. A variety of different file types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods. Additional packages extending MsStash provide the implementations to serialize/restore MS data objects.
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5.08 score 2 dependents 22 downloads
MsBackendMassIVE - Retrieve Mass Spectrometry Data from MassIVE
MassIVE is one of the main public repositories for storage of metabolomics experiments. The MsBackendMassIVE package provides functionality to retrieve and represent mass spectrometry (MS) data from MassIVE. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMassIVE package.
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5.04 score 1 stars 2 scriptsQFeaturesGUI - A suite of shiny apps to use the main functionalities of the QFeatures package
"QFeaturesGUI is a suite of shiny apps that serve as graphical interfaces for the QFeatures package. Currently, the package contains the following shiny apps: 'importQFeatures'."
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4.93 score 3 stars 10 scriptsRforMassSpectrometry - R for MassSpectrometry meta-package
The RforMassSpectrometry meta-package loads and manages the core packages of the R for Mass Spectrometry initiative, that provide efficient, thoroughly documented, tested and flexible R software for the analysis and interpretation of high throughput mass spectrometry assays.
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4.72 score 21 stars 1 scripts
Metabonaut - Exploring and Analyzing LC-MS Data
This resource hosts tutorials and end-to-end workflows describing how to analyze LC-MS/MS data, from raw files to annotation, using Bioconductor packages.
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4.38 score 12 stars
MsBackendMassIVE - Retrieve Mass Spectrometry Data from MassIVE
MassIVE is one of the main public repositories for storage of metabolomics experiments. The MsBackendMassIVE package provides functionality to retrieve and represent mass spectrometry (MS) data from MassIVE. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMassIVE package.
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4.04 score 1 starsMsBackendTimsTof - Mass spectrometry Data Backend for Bruker TimsTOF Files
Mass spectrometry (MS) data backend supporting import and export of (ion mobility) MS data from Bruker TimsTOF files. The backend uses the opentimsr package which relies on the proprietory vendor C++ library for raw data access. The backend thus supports import of MS data from the original raw data files.
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3.85 score 7 stars 1 scriptsSpectraStash - Serialize and restore Spectra objects in interoperable file formats
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The SpectraStash package implements the serialization methods from the MsStash package for Spectra objects and its MsBackend classes. A variety of different file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods.
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3.48 scoreSpectraStash - Serialize and restore Spectra objects in interoperable file formats
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The SpectraStash package implements the serialization methods from the MsStash package for Spectra objects and its MsBackend classes. A variety of different file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package are supported. The file type can be defined and configured through a second argument `param` of the save/read methods.
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3.48 scoreMsBackendMetabolomicsWorkbench - Retrieve Mass Spectrometry Data from Metabolomics Workbench
Metabolomics Workbench is one of the main public repositories for storage of metabolomics experiments. The MsBackendMetabolomicsWorkbench package provides functionality to retrieve and represent mass spectrometry (MS) data from Metabolomics Workbench. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetabolomicsWorkbench package.
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3.48 scoreMsBackendMetabolomicsWorkbench - Retrieve Mass Spectrometry Data from Metabolomics Workbench
Metabolomics Workbench is one of the main public repositories for storage of metabolomics experiments. The MsBackendMetabolomicsWorkbench package provides functionality to retrieve and represent mass spectrometry (MS) data from Metabolomics Workbench. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetabolomicsWorkbench package.
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3.48 scoreMsExperimentStash - Serialize and restore MsExperiment objects in interoperable file formats
The serialization mechanism of R allows to save and load R data objects in a binary format, that can however not be read by other programming languages or software. The MsExperimentStash package implements the serialization methods from the MsStash package for MsExperiment objects. Data can be stashed in a variety of file formats and types, including HDF5 and JSON-based formats defined by the Bioconductor *alabaster* package.
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3.18 scoreSpectraVis - Visualising and Exploring Spectra Data
This package defines a set of helper function to visualise and explore mass spectrometry data stored as Spectra objects.
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2.34 score 4 stars 11 scriptsMsBackendMongoDb - NoSQL-based Mass Spectrometry Data Backend
Mass spectrometry (MS) data backend for data storage in NoSQL MongoDB dagabases. Objects from this package expand the data storage and handling infrastructure of the Spectra Bioconductor package. This package adds support to store and retrieve MS data from MongoDB databases.
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2.30 score