MsBackendParquet
This is the development version of MsBackendParquet; to use it, please install the devel version of Bioconductor.
Apache Parquet-based Mass Spectrometry Data Backend
Bioconductor version: Development (3.24)
Mass spectrometry (MS) data backend for the Spectra Bioconductor package that stores and retrieves spectra and peak data from on-disk Apache Parquet datasets. Spectra metadata together with m/z and intensity values are stored in a columnar Parquet format that supports compression, dictionary encoding and Hive-style partitioning. Datasets are written with the Apache Arrow R bindings and queried with DuckDB. Spectra variables are held in a bounded in-memory index so that filtering and metadata access are fast while peak data remains on disk.
Author: Ossama Edbali [aut, cre] 
, Ralf Johannes Maria Weber [aut] , BioFAIR UK [fnd] (BioFAIR Pathfinder Project)
Maintainer: Ossama Edbali <o.edbali at bham.ac.uk>
citation("MsBackendParquet")):Ossama Edbali, Ralf Johannes Maria Weber. MsBackendParquet: Apache Parquet-based Mass Spectrometry Data Backend. doi:10.18129/B9.bioc.MsBackendParquet, R package version 0.99.8, https://bioconductor.org/packages/MsBackendParquet.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("MsBackendParquet")For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("MsBackendParquet")| Apache Parquet-based Mass Spectrometry Data Backend | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 0.99.8 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), Spectra (>= 1.16.0) |
| Imports | arrow (>= 14.0.0), BiocParallel, DBI, duckdb (>= 1.2.0), IRanges, jsonlite, methods, MsCoreUtils, ProtGenerics (>= 1.36.0), S4Vectors, stats, tools, utils |
| System Requirements | |
| URL | https://github.com/computational-metabolomics/MsBackendParquet |
| Bug Reports | https://github.com/computational-metabolomics/MsBackendParquet/issues |
See More
| Suggests | BiocStyle, bench, dplyr, knitr, MsDataHub, MsExperiment, mzR, rmarkdown, SpectraQL, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MsBackendParquet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MsBackendParquet |
| Package Short Url | https://bioconductor.org/packages/MsBackendParquet/ |
| Package Downloads Report | Download Stats |