strandCheckR

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.

Calculate strandness information of a bam file

Bioconductor version: 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 (!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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software

Version 1.12.0

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

Suggests BiocStyle, knitr, testthat

Linking To

Enhances

Depends On Me

Imports Me

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Links To Me

Build Report 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

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 3.14 Source Archive