gDNAinRNAseqData
This is the released version of gDNAinRNAseqData; for the devel version, see gDNAinRNAseqData.
RNA-seq data with different levels of gDNA contamination
Bioconductor version: Release (3.23)
Provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.
Author: Robert Castelo [aut, cre]
Maintainer: Robert Castelo <robert.castelo at upf.edu>
citation("gDNAinRNAseqData")):
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("gDNAinRNAseqData")
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("gDNAinRNAseqData")| RNA-seq data with different levels of gDNA contamination | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, ExpressionData, Homo_sapiens_Data, RNASeqData, SequencingData |
| Version | 1.12.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.3) |
| Imports | RCurl, XML, ExperimentHub, BiocGenerics, Rsamtools |
| System Requirements | |
| URL | https://github.com/functionalgenomics/gDNAinRNAseqData |
| Bug Reports | https://github.com/functionalgenomics/gDNAinRNAseqData |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | gDNAx |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gDNAinRNAseqData_1.12.0.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/gDNAinRNAseqData |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/gDNAinRNAseqData |
| Package Short Url | https://bioconductor.org/packages/gDNAinRNAseqData/ |
| Package Downloads Report | Download Stats |