This is the development version of CleanUpRNAseq; for the stable release version, see CleanUpRNAseq.
Detect and Correct Genomic DNA Contamination in RNA-seq DataBioconductor version: Development (3.22)
RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.
Author: Haibo Liu [aut, cre] ORCID: 0000-0002-4213-2883 , Kevin O'Connor [ctb], Michelle Kelliher [ctb], Lihua Julie Zhu [aut], Kai Hu [aut]
Maintainer: Haibo Liu <haibo.liu at umassmed.edu>
Citation (from within R, entercitation("CleanUpRNAseq")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CleanUpRNAseq")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("CleanUpRNAseq")Follow Installation instructions to use this package in your R session.
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