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This is the development version of strandCheckR; for the stable release version, see strandCheckR.

Calculate strandness information of a bam file

Bioconductor version: Development (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

An Introduction To strandCheckR HTML R Script
Reference Manual PDF


biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software
Version 1.23.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
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, rmarkdown
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Follow Installation instructions to use this package in your R session.

Source Package strandCheckR_1.23.0.tar.gz
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macOS Binary (x86_64) strandCheckR_1.23.0.tgz
macOS Binary (arm64) strandCheckR_1.23.0.tgz
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Source Repository (Developer Access) git clone
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