QFeatures
This is the development version of QFeatures; for the stable release version, see QFeatures.
Quantitative features for mass spectrometry data
Bioconductor version: Development (3.24)
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.
Author: Laurent Gatto [aut, cre]
, Christophe Vanderaa [aut]
, Karolína Kryštofová [ctb]
, Léopold Guyot [ctb]
Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>
citation("QFeatures")):
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("QFeatures")
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("QFeatures")| Data visualization from a QFeatures object | HTML | R Script |
| Imputation | HTML | R Script |
| Load data using readQFeatures() | HTML | R Script |
| Processing quantitative proteomics data with QFeatures | HTML | R Script |
| Quantitative features for mass spectrometry data | HTML | R Script |
| readQFeatures() input format | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Infrastructure, MassSpectrometry, Metabolomics, Proteomics, Software |
| Version | 1.23.1 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1), MultiAssayExperiment(>= 1.33.6) |
| Imports | methods, stats, utils, S4Vectors, IRanges, SummarizedExperiment, BiocGenerics(>= 0.53.4), ProtGenerics(>= 1.35.1), AnnotationFilter, lazyeval, Biobase, MsCoreUtils(>= 1.25.3), igraph, grDevices, plotly, tidyr, dplyr, tidyselect, reshape2 |
| System Requirements | |
| URL | https://rformassspectrometry.github.io/QFeatures |
| Bug Reports | https://github.com/rformassspectrometry/QFeatures/issues |
See More
| Suggests | SingleCellExperiment, MsDataHub(>= 1.11.5), arrow, Matrix, HDF5Array, ggplot2, gplots, limma, DT, shiny, shinydashboard, testthat, knitr, BiocStyle, rmarkdown, vsn, preprocessCore, matrixStats, imputeLCMD, pcaMethods, impute, norm, ComplexHeatmap |
| Linking To | |
| Enhances | |
| Depends On Me | hdxmsqc, msqrob2, scp, scpdata |
| Imports Me | MetaboAnnotation, MsExperiment, mspms, omicsGMF, proBatch, PSMatch |
| Suggests Me | MsDataHub |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | QFeatures_1.23.1.tar.gz |
| Windows Binary (x86_64) | QFeatures_1.23.1.zip |
| macOS Binary (big-sur-x86_64) | QFeatures_1.23.1.tgz |
| macOS Binary (sonoma-arm64) | QFeatures_1.23.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/QFeatures |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QFeatures |
| Bioc Package Browser | https://code.bioconductor.org/browse/QFeatures/ |
| Package Short Url | https://bioconductor.org/packages/QFeatures/ |
| Package Downloads Report | Download Stats |