scpdata
This is the development version of scpdata; for the stable release version, see scpdata.
Single-Cell Proteomics Data Package
Bioconductor version: Development (3.24)
The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.
Author: Christophe Vanderaa [aut, cre]
, Laurent Gatto [aut]
, Enes Ayar [dtc]
, Samuel Grégoire [dtc]
Maintainer: Christophe Vanderaa <vanderaa.christophe at gmail.com>
citation("scpdata")):
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("scpdata")
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("scpdata")| Contribution guidelines | HTML | R Script |
| Data Package for Single Cell Proteomics | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, MassSpectrometryData, PackageTypeData, Proteome, ReproducibleResearch, SingleCellData |
| Version | 1.21.0 |
| License | GPL-2 |
| Depends | R (>= 4.2.0), QFeatures, ExperimentHub |
| Imports | utils, AnnotationHub, SingleCellExperiment, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | scp, magrittr, dplyr, knitr, BiocStyle, BiocCheck, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | scp |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scpdata_1.21.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scpdata |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scpdata |
| Package Short Url | https://bioconductor.org/packages/scpdata/ |
| Package Downloads Report | Download Stats |