strandCheckR

DOI: 10.18129/B9.bioc.strandCheckR    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.

Calculate strandness information of a bam file

Bioconductor version: 3.8

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 "3.5") and enter:

if (!requireNamespace("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, QualityControl, RNASeq, Software
Version	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 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
LinkingTo
Suggests	BiocStyle, knitr, testthat
SystemRequirements
Enhances
URL
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_1.0.0.tar.gz
Windows Binary	strandCheckR_1.0.0.zip
Mac OS X 10.11 (El Capitan)	strandCheckR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/strandCheckR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/strandCheckR
Package Short Url	http://bioconductor.org/packages/strandCheckR/
Package Downloads Report	Download Stats