strandCheckR

DOI: 10.18129/B9.bioc.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 (3.9)

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>

Citation (from within R, enter citation("strandCheckR")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("strandCheckR", version = "3.9")

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 1.1.0
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_1.1.0.tar.gz
Windows Binary strandCheckR_1.1.0.zip
Mac OS X 10.11 (El Capitan) strandCheckR_1.1.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: