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CleanUpRNAseq
This is thereleased version of CleanUpRNAseq; for the devel version, seeCleanUpRNAseq.
Detect and Correct Genomic DNA Contamination in RNA-seq Data
Bioconductor version: Release (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("CleanUpRNAseq")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CleanUpRNAseq")For older versions of R, please refer to the appropriateBioconductor 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 | 1.4.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (1 year) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CleanUpRNAseq_1.4.0.tar.gz |
| Windows Binary (x86_64) | CleanUpRNAseq_1.4.0.zip |
| macOS Binary (x86_64) | CleanUpRNAseq_1.4.0.tgz |
| macOS Binary (arm64) | CleanUpRNAseq_1.4.0.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 |