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Bioconductor - strandCheckR (development version)

strandCheckR

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

Calculate strandness information of a bam file

Bioconductor version: Development (3.22)

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")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software Version 1.27.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 years) License GPL (>= 2) Depends ggplot2 (>= 3.5.0), Rsamtools, S4Vectors Imports BiocGenerics, dplyr, GenomeInfoDb, GenomicAlignments, GenomicRanges, gridExtra, IRanges, grid, methods, reshape2, rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene, tidyselect System Requirements URL https://github.com/UofABioinformaticsHub/strandCheckR Bug Reports https://github.com/UofABioinformaticsHub/strandCheckR/issues See More Package Archives

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

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