Chromatograms
This is the released version of Chromatograms; for the devel version, see Chromatograms.
Infrastructure for Chromatographic Mass Spectrometry Data
Bioconductor version: Release (3.23)
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.
Author: Johannes Rainer [aut]
, Laurent Gatto [aut]
, Philippine Louail [aut, cre] (ORCID:
, fnd: European Union HORIZON-MSCA-2021 project Grant No. 101073062: HUMAN – Harmonising and Unifying Blood Metabolic Analysis Networks)
Maintainer: Philippine Louail <philippine.louail at outlook.com>
citation("Chromatograms")):
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")
BiocManager::install("Chromatograms")
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("Chromatograms")| Creating new `ChromBackend` class for Chromatograms | HTML | R Script |
| Using and understanding a Chromatograms object | HTML | R Script |
| Reference Manual |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| Depends | BiocParallel, ProtGenerics(>= 1.39.2), R (>= 4.5.0) |
| Imports | data.table, methods, S4Vectors, MsCoreUtils(>= 1.7.5), Spectra |
| System Requirements | |
| URL | https://github.com/RforMassSpectrometry/Chromatograms |
| Bug Reports | https://github.com/RforMassSpectrometry/Chromatograms/issues |
See More
| Suggests | msdata(>= 0.19.3), roxygen2, BiocStyle(>= 2.5.19), testthat, knitr (>= 1.1.0), rmarkdown, mzR(>= 2.41.4), MsBackendMetaboLights(>= 1.3.1), pheatmap, vdiffr, IRanges, RColorBrewer |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MsQuality |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | Chromatograms_1.2.0.tar.gz |
| Windows Binary (x86_64) | Chromatograms_1.2.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Chromatograms_1.2.0.tgz |
| macOS Binary (sonoma-arm64) | Chromatograms_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/Chromatograms |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/Chromatograms |
| Bioc Package Browser | https://code.bioconductor.org/browse/Chromatograms/ |
| Package Short Url | https://bioconductor.org/packages/Chromatograms/ |
| Package Downloads Report | Download Stats |