strandCheckR
This is the released version of strandCheckR; for the devel version, see strandCheckR.
All Bioconductor versions of strandCheckR
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8
Calculate strandness information of a bam file
Bioconductor version: 3.23 · Package version: 1.30.0
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], Stevie Pederson [aut] 
Maintainer: Thu-Hien To <tothuhien at gmail.com>
Citation
From within R, enter citation("strandCheckR"):
Thu-Hien To, Stevie Pederson. strandCheckR: Calculate strandness information of a bam file. doi:10.18129/B9.bioc.strandCheckR, R package version 1.30.0, https://bioconductor.org/packages/strandCheckR.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("strandCheckR")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.30.0 |
| License | GPL (>= 2) |
| URL | https://github.com/UofABioinformaticsHub/strandCheckR |
| Bug Reports | https://github.com/UofABioinformaticsHub/strandCheckR/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| Downloads rank | 1240 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/strandCheckR/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("strandCheckR")| An Introduction To strandCheckR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | strandCheckR_1.30.0.tar.gz |
| Windows binary (x86_64) | strandCheckR_1.30.0.zip |
| macOS binary (arm64) | strandCheckR_1.30.0.tgz |
| macOS binary (x86_64) | strandCheckR_1.30.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/strandCheckR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/strandCheckR |
| Package Downloads Report | Download Stats |
Dependencies
Depends: ggplot2 (>= 4.0.0), Rsamtools, S4Vectors
Imports: BiocGenerics, dplyr, Seqinfo, GenomicAlignments, GenomicRanges, gridExtra, IRanges, grid, methods, reshape2, rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene, tidyselect