strandCheckR

DOI: 10.18129/B9.bioc.strandCheckR  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.

Calculate strandness information of a bam file

Bioconductor version: 3.17

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 gmail.com>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	An Introduction To strandCheckR
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software
Version	1.18.0
In Bioconductor since	BioC 3.8 (R-3.5) (5 years)
License	GPL (>= 2)
Depends
Imports	dplyr, magrittr, GenomeInfoDb, GenomicAlignments, GenomicRanges, IRanges, Rsamtools, S4Vectors, grid, BiocGenerics, ggplot2, reshape2, stats, gridExtra, TxDb.Hsapiens.UCSC.hg38.knownGene, methods, stringr, rmarkdown
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL	https://github.com/UofABioinformaticsHub/strandCheckR
BugReports	https://github.com/UofABioinformaticsHub/strandCheckR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	strandCheckR_1.18.0.tar.gz
Windows Binary	strandCheckR_1.18.0.zip
macOS Binary (x86_64)	strandCheckR_1.18.0.tgz
macOS Binary (arm64)	strandCheckR_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/strandCheckR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/strandCheckR
Bioc Package Browser	https://code.bioconductor.org/browse/strandCheckR/
Package Short Url	https://bioconductor.org/packages/strandCheckR/
Package Downloads Report	Download Stats