CleanUpRNAseq
This is the released version of CleanUpRNAseq; for the devel version, see CleanUpRNAseq.
Detect and Correct Genomic DNA Contamination in RNA-seq Data
Bioconductor version: Release (3.23)
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")):
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("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 | 1.6.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (2 years) |
| License | GPL-3 |
| Depends | R (>= 4.4.0) |
| Imports | AnnotationFilter, BiocGenerics, Biostrings, BSgenome, DESeq2, edgeR, ensembldb, Seqinfo, 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_1.6.0.tar.gz |
| Windows Binary (x86_64) | CleanUpRNAseq_1.6.0.zip |
| macOS Binary (big-sur-x86_64) | CleanUpRNAseq_1.6.0.tgz |
| macOS Binary (sonoma-arm64) | CleanUpRNAseq_1.6.0.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 |