strandCheckR

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.

Calculate strandness information of a bam file


Bioconductor version: 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 (version "3.6") 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")
An Introduction To strandCheckR HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (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
System Requirements
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Suggests BiocStyle, knitr, testthat
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Build Report Build Report

Package Archives

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

Source Package strandCheckR_1.2.0.tar.gz
Windows Binary strandCheckR_1.2.0.zip
Mac OS X 10.11 (El Capitan) strandCheckR_1.2.0.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
Old Source Packages for BioC 3.9 Source Archive