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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | R Script |
| Reference Manual |
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 (>= 4.6.0), 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MsBackendParquet_0.99.8.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | MsBackendParquet_0.99.8.tgz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/MsBackendParquet/ |
| Package Short Url | https://bioconductor.org/packages/MsBackendParquet/ |
| Package Downloads Report | Download Stats |