ProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Last updated 2 months ago

bioconductor-packagebioconductormass-spectrometrymetabolomicsproteomics

7 stars 7.58 score 0 dependencies 180 dependents

ProtGenerics - Generic infrastructure for Bioconductor mass spectrometry packages

S4 generic functions and classes needed by Bioconductor proteomics packages.

Last updated 2 months ago

infrastructureproteomicsmassspectrometry

7 stars 7.56 score 0 dependencies 180 dependents

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.

Last updated 6 days ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometry

35 stars 6.21 score 20 dependencies 29 dependents

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.

Last updated 8 hours ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometryutils

16 stars 5.54 score 6 dependencies 61 dependents

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.

Last updated 2 months ago

infrastructureproteomicsmassspectrometrymetabolomics

16 stars 5.51 score 6 dependencies 62 dependents

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.

Last updated 7 hours ago

infrastructuremassspectrometryproteomicsmetabolomicsbioconductormass-spectrometry

24 stars 5.06 score 98 dependencies 43 dependents

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.

Last updated 3 months ago

infrastructuremassspectrometryproteomicsmetabolomics

24 stars 5.06 score 98 dependencies 45 dependents

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.

Last updated 6 days ago

infrastructureproteomicsmassspectrometrymetabolomicsbioconductormass-spectrometry

35 stars 4.79 score 20 dependencies 29 dependents

PSMatch - 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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometry

3 stars 4.31 score 107 dependencies 36 dependents

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.

Last updated 5 months ago

infrastructuremetabolomicsmassspectrometrymass-spectrometry

7 stars 4.29 score 16 dependencies 30 dependents

PSMatch - 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.

Last updated 6 months ago

infrastructureproteomicsmassspectrometrymass-spectrometrypeptide-spectrum-matches

3 stars 4.28 score 107 dependencies 34 dependents

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.

Last updated 5 months ago

infrastructuremetabolomicsmassspectrometrymass-spectrometry

7 stars 4.23 score 16 dependencies 30 dependents

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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

5 stars 3.14 score 110 dependencies 15 dependents

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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometrymetabolomicsexperimentaldesigndataimport

5 stars 3.08 score 110 dependencies 13 dependents

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.

Last updated 5 months ago

infrastructuremassspectrometrymetabolomics

7 stars 2.94 score 34 dependencies 13 dependents

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.

Last updated 1 years ago

infrastructuremassspectrometrymetabolomics

7 stars 2.86 score 34 dependencies 11 dependents

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.

Last updated 2 months ago

massspectrometrymetabolomicsannotationdatabasesmass-spectrometry

16 stars 2.57 score 110 dependencies 1 dependents

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.

Last updated 2 months ago

massspectrometrymetabolomicsannotation

16 stars 2.38 score 110 dependencies 1 dependents

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.

Last updated 4 months ago

infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry

14 stars 2.38 score 135 dependencies

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.

Last updated 4 months ago

infrastructuremetabolomicsmassspectrometryannotationmass-spectromtry

14 stars 2.18 score 135 dependencies

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.

Last updated 5 months ago

bioconductor-packageinfrastructuremass-spectrometry

5 stars 1.75 score 21 dependencies 1 dependents

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.

Last updated 7 months ago

bioconductor-package

4 stars 1.69 score 21 dependencies 1 dependents

RforMassSpectrometry - 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.

Last updated 9 months ago

15 stars 1.64 score 112 dependencies

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.

Last updated 6 months ago

bioconductor-package

4 stars 1.58 score 34 dependencies

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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimportmass-spectrometry

5 stars 1.51 score 21 dependencies 1 dependents

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.

Last updated 5 months ago

infrastructureproteomicsmassspectrometrymetabolomicsdataimport

4 stars 1.45 score 21 dependencies 1 dependents

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.

Last updated 7 months ago

bioconductor-packagemassbankspectra

3 stars 1.38 score 22 dependencies

SpectriPy - Integrating Spectra with Python's matchms

The SpectriPy package allows integration of Python-based MS analysis code with the Spectra package. Spectra objects can be converted into Python's matchms Spectrum objects. In addition, SpectriPy integrates and wraps the similarity scoring functions from the matchms package into R.

Last updated 1 years ago

infrastructuremass-spectrometrypython

9 stars 1.38 score 36 dependencies

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.

Last updated 5 months ago

infrastructuremassspectrometrymetabolomicsdataimportproteomics

4 stars 1.31 score 34 dependencies

MsDataHub - 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.

Last updated 5 months ago

bioconductor-packagebioconductordatamass-spectrometrymetabolomicsproteomics

1 stars 1.24 score 60 dependencies

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.

Last updated 14 days ago

7 stars 1.16 score 21 dependencies

MsIO - Serializing and restoring/importing 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 MsIO package supports 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 export/import methods.

Last updated 14 days ago

mass-spectrometrymetabolomicsproteomics

2 stars 1.08 score 17 dependencies

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.

Last updated 5 months ago

infrastructuremassspectrometrymetabolomicsdataimportmassbankspectra

3 stars 1.08 score 22 dependencies

MsDataHub - 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.

Last updated 5 months ago

experimenthubsoftwaremassspectrometryproteomicsmetabolomicsbioconductordatamass-spectrometry

1 stars 0.91 score 60 dependencies

Chromatograms - Infrastructure for Chromatographic Mass Spectrometry Data

The Chromatograms packages defines a 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.

Last updated 16 days ago

1 stars 0.71 score 9 dependencies

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.

Last updated 8 days ago

infrastructuremassspectrometrymetabolomicsdataimportproteomicsmass-spectrometrymetabolomics-data

1 stars 0.49 score 60 dependencies

SpectraVis - Visualising and Exploring Spectra Data

This package defines a set of helper function to visualise and explore mass spectrometry data stored as Spectra objects.

Last updated 2 years ago

bioconductormass-spectrometrymetabolomicsproteomicsspectravisualisation

4 stars 0.61 score 115 dependencies

MsQuantitation - Mass Spectrometry Quantitation

This package quantitates raw mass spectrometry data contained in Spectra objects into QFeaures instances.

Last updated 2 years ago

3 stars 0.36 score 109 dependencies