homosapienDEE2CellScore
This is the released version of homosapienDEE2CellScore; for the devel version, see homosapienDEE2CellScore.
Example Data Package for CellScore
Bioconductor version: Release (3.23)
This is a data package for normalised homosapien data downloaded from DEE2. The package both downloads, normalises, and filters the data, and provides a way to access the data from a canonical store without needing local processing. This package was built as a way to generate and store canonical test data for CellScore.
Author: Justin Marsh [aut, cre]
Maintainer: Justin Marsh <j.marsh at auckland.ac.nz>
citation("homosapienDEE2CellScore")):
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("homosapienDEE2CellScore")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, Genome, RNASeqData |
| Version | 1.8.0 |
| License | GPL (>= 3) |
| Depends | |
| Imports | Rtsne (>= 0.15), utils (>= 3.5.0), ExperimentHub, BiocGenerics, DESeq2, S4Vectors, SummarizedExperiment, getDEE2, MatrixGenerics |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/flaviusb/homosapienDEE2CellScore/issues |
See More
| Suggests | knitr, rmarkdown, devtools, Biobase(>= 2.39.1), BiocManager, AnnotationHubData, ExperimentHubData, AnnotationHub, CellScore (>= 1.21.4) |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/homosapienDEE2CellScore |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/homosapienDEE2CellScore |
| Package Short Url | https://bioconductor.org/packages/homosapienDEE2CellScore/ |
| Package Downloads Report | Download Stats |