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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 (3.19)

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 "4.4") and enter:


if (!require("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

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 1.21.0
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, rmarkdown
System Requirements
URL https://github.com/UofABioinformaticsHub/strandCheckR
Bug Reports https://github.com/UofABioinformaticsHub/strandCheckR/issues
See More
Suggests BiocStyle, knitr, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package strandCheckR_1.21.0.tar.gz
Windows Binary strandCheckR_1.21.0.zip
macOS Binary (x86_64) strandCheckR_1.21.0.tgz
macOS Binary (arm64) strandCheckR_1.21.0.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