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("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 | ||
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 | |
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_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 |