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strandCheckR

This is the released version of strandCheckR; for the devel version, see strandCheckR.

All versions

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

DOI: 10.18129/B9.bioc.strandCheckR

Bioconductor version: Release (3.23)

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] ORCID: 0000-0001-8197-3303

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.

Documentation

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

browseVignettes("strandCheckR")

Details

Package Archives

Follow Installation instructions to use this package in your R session.