CleanUpRNAseq

This is the development version of CleanUpRNAseq; for the stable release version, see CleanUpRNAseq.

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Bioconductor version: Development (3.21)

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: ), 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 "4.5") 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.

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, QualityControl, Sequencing, Software
Version	1.1.1
In Bioconductor since	BioC 3.20 (R-4.4) (< 6 months)
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

Suggests	BiocStyle, BSgenome.Hsapiens.UCSC.hg38, EnsDb.Hsapiens.v86, ggplotify, knitr, patchwork, R.utils, rmarkdown, testthat (>= 3.0.0)
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	CleanUpRNAseq_1.1.1.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/CleanUpRNAseq
Source Repository (Developer Access)	git clone [email protected]:packages/CleanUpRNAseq
Bioc Package Browser	https://code.bioconductor.org/browse/CleanUpRNAseq/
Package Short Url	https://bioconductor.org/packages/CleanUpRNAseq/
Package Downloads Report	Download Stats