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 (3.15)

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 <tothuhien at gmail.com>, Steve Pederson <stephen.pederson at adelaide.edu.au>

Maintainer: Thu-Hien To <tothuhien at gmail.com>

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

Installation

To install this package, start R (version "4.2") and enter:

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software
Version 1.13.0
In Bioconductor since BioC 3.8 (R-3.5) (3 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
Windows Binary
macOS 10.13 (High Sierra)
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 https://bioconductor.org/packages/strandCheckR/
Package Downloads Report Download Stats

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