DOI: 10.18129/B9.bioc.strandCheckR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.

Calculate strandness information of a bam file

Bioconductor version: 3.9

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

Author: Thu-Hien To [aut, cre], Steve Pederson [aut]

Maintainer: Thu-Hien To <tothuhien at>

Citation (from within R, enter citation("strandCheckR")):


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



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biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (1 year)
License GPL (>= 2)
Imports dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr
Suggests BiocStyle, knitr, testthat
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Source Package strandCheckR_1.2.0.tar.gz
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Mac OS X 10.11 (El Capitan) strandCheckR_1.2.0.tgz
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