CleanUpRNAseq

This is the development version of CleanUpRNAseq; to use it, please install the devel version of Bioconductor.

Detect and Correct Genomic DNA Contamination in RNA-seq Data


Bioconductor version: Development (3.20)

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] , 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, enter citation("CleanUpRNAseq")):

Installation

To install this package, start R (version "4.4") 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.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CleanUpRNAseq")
CleanUpRNAseq: detecting and correcting for DNA contamination\nin RNA-seq data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, QualityControl, Sequencing, Software
Version 0.99.15
In Bioconductor since BioC 3.20 (R-4.4)
License GPL-3
Depends R (>= 4.4.0)
Imports AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, GenomeInfoDb, GenomicRanges, ggplot2, ggrepel, graphics, grDevices, KernSmooth, limma, methods, pheatmap, qsmooth, R6, RColorBrewer, Rsamtools, Rsubread, reshape2, SummarizedExperiment, stats, tximport, utils
System Requirements
URL
Bug Reports https://github.com/haibol2016/CleanUpRNAseq/issues
See More
Suggests BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0)
Linking To
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Depends On Me
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CleanUpRNAseq_0.99.15.tar.gz
Windows Binary CleanUpRNAseq_0.99.15.zip
macOS Binary (x86_64) CleanUpRNAseq_0.99.15.tgz
macOS Binary (arm64) CleanUpRNAseq_0.99.15.tgz
Source Repository git clone https://git.bioconductor.org/packages/CleanUpRNAseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CleanUpRNAseq
Bioc Package Browser https://code.bioconductor.org/browse/CleanUpRNAseq/
Package Short Url https://bioconductor.org/packages/CleanUpRNAseq/
Package Downloads Report Download Stats