strandCheckR
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see strandCheckR.
Calculate strandness information of a bam file
Bioconductor version: 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("strandCheckR")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 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_1.22.0.tar.gz |
| Windows Binary (x86_64) | strandCheckR_1.22.0.zip |
| macOS Binary (x86_64) | strandCheckR_1.22.0.tgz |
| macOS Binary (arm64) | strandCheckR_1.22.0.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 3.19 | Source Archive |