CleanUpRNAseq
Detect and Correct Genomic DNA Contamination in RNA-seq Data
Bioconductor version: Release (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")
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 | 1.0.0 |
| 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 |
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_1.0.0.tar.gz |
| Windows Binary (x86_64) | CleanUpRNAseq_1.0.0.zip |
| macOS Binary (x86_64) | CleanUpRNAseq_1.0.0.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 |