ensembldb - Utilities to create and use Ensembl-based annotation databases
The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.
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geneticsannotationdatasequencingcoverageannotationbioconductorbioconductor-packagesensembl
14.29 score 36 stars 115 dependents 1.7k scripts 20k 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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10.44 score 9 stars 80 dependents 108 scripts 4.3k downloads
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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massspectrometrymetabolomicsannotationdatabasesmass-spectrometry
8.83 score 19 stars 3 dependents 98 scripts 1.0k downloads
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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8.35 score 7 stars 15 dependents 51 scripts 3.5k downloads
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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7.97 score 13 stars 61 scripts 198 downloads
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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7.85 score 21 stars 1 dependents 75 scripts 621 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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6.69 score 5 stars 2 dependents 41 scripts 750 downloads
RmzTabM - R API for the mzTab-M Reference Implementation
The RmzTabM package provides functions to read and write files in the HUPO-PSI mzTab-M file format for reporting of results from metabolomics and lipidomics experiments. This package represents the reference implementation for mzTab-M import/export for R. Core, low level functions allow to format and parse the individual sections of the mzTab-M format. These functions are designed to be re-used by other packages implementing import/export of results in mzTab-M.
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5.91 score 3 stars 16 scripts 470 downloads
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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5.68 score 4 stars 34 scripts 462 downloads
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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5.52 score 2 stars 358 downloads
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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5.48 score 10 stars 15 scripts 255 downloadsMsStash - 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 1 stars 3 dependents 404 downloadsFamAgg - Pedigree Analysis and Familial Aggregation
Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.
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geneticspedigree
5.26 score 1 stars 5 scripts 490 downloads
SpectraStash - 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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4.70 score 117 downloadsMsBackendTimsTof - 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 without needing to convert them to an open format.
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4.32 score 7 stars
MsExperimentStash - Save 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. The package provides also functionality to read a full MS experiment, including MS data and experimental metadata information, from the MetaboLights repository.
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3.48 score
MsExperimentStash - Save 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. The package provides also functionality to read a full MS experiment, including MS data and experimental metadata information, from the MetaboLights repository.
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3.40 scoreAHMassBank - MassBank Annotation Resources for AnnotationHub
Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds' ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.
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massspectrometryannotationhubsoftware
3.30 score 1 stars 5 scripts 323 downloadsMsBackendMongoDb - 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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infrastructuremassspectrometrymetabolomicsdataimportproteomics
2.30 score