spatialDmelxsim
This is the released version of spatialDmelxsim; for the devel version, see spatialDmelxsim.
Spatial allelic expression counts for fly cross embryo
Bioconductor version: Release (3.23)
Spatial allelic expression counts from Combs & Fraser (2018), compiled into a SummarizedExperiment object. This package contains data of allelic expression counts of spatial slices of a fly embryo, a Drosophila melanogaster x Drosophila simulans cross. See the CITATION file for the data source, and the associated script for how the object was constructed from publicly available data.
Author: Michael Love [aut, cre]
Maintainer: Michael Love <michaelisaiahlove at gmail.com>
citation("spatialDmelxsim")):
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("spatialDmelxsim")
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("spatialDmelxsim")| spatialDmelxsim | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Drosophila_melanogaster_Data, ExperimentData, ExperimentHub, ExpressionData, GEO, RNASeqData, SequencingData |
| Version | 1.18.0 |
| License | GPL-3 |
| Depends | R (>= 4.1), ExperimentHub, SummarizedExperiment |
| Imports | utils |
| System Requirements | |
| URL | https://github.com/mikelove/spatialDmelxsim |
| Bug Reports | https://github.com/mikelove/spatialDmelxsim/issues |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| 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 | spatialDmelxsim_1.18.0.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/spatialDmelxsim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/spatialDmelxsim |
| Package Short Url | https://bioconductor.org/packages/spatialDmelxsim/ |
| Package Downloads Report | Download Stats |