LRcellTypeMarkers
This is the released version of LRcellTypeMarkers; for the devel version, see LRcellTypeMarkers.
Marker gene information for LRcell R Bioconductor package
Bioconductor version: Release (3.23)
This is an external ExperimentData package for LRcell. This data package contains the gene enrichment scores calculated from scRNA-seq dataset which indicates the gene enrichment of each cell type in certain brain region. LRcell package is used to identify specific sub-cell types that drives the changes observed in a bulk RNA-seq differential gene expression experiment. For more details, please visit: https://github.com/marvinquiet/LRcell.
Maintainer: Wenjing Ma <wenjing.ma at emory.edu>
citation("LRcellTypeMarkers")):
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("LRcellTypeMarkers")
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("LRcellTypeMarkers")| LRcellTypeMarkers: Marker gene information for LRcell R Bioconductor package using Bioconductor's ExperimentHub | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, PackageTypeData, RNASeqData, SingleCellData |
| Version | 1.20.0 |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | ExperimentHub |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/marvinquiet/LRcellTypeMarkers/issues |
See More
| Suggests | LRcell, BiocStyle, knitr, rmarkdown, roxygen2, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | LRcell |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | LRcellTypeMarkers_1.20.0.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/LRcellTypeMarkers |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/LRcellTypeMarkers |
| Package Short Url | https://bioconductor.org/packages/LRcellTypeMarkers/ |
| Package Downloads Report | Download Stats |