strandCheckR

DOI: 10.18129/B9.bioc.strandCheckR    

Calculate strandness information of a bam file

Bioconductor version: Release (3.14)

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 "4.1") 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, ImmunoOncology, QualityControl, RNASeq, Software
Version 1.12.0
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 strandCheckR_1.12.0.tar.gz
Windows Binary strandCheckR_1.12.0.zip
macOS 10.13 (High Sierra) strandCheckR_1.12.0.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 https://bioconductor.org/packages/strandCheckR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive

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