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 (3.21)
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], Stevie Pederson [aut]
Maintainer: Thu-Hien To <tothuhien at gmail.com>
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software |
| Version | 1.25.1 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6.5 years) |
| License | GPL (>= 2) |
| Depends | ggplot2 (>= 3.5.0), Rsamtools, S4Vectors |
| Imports | BiocGenerics, dplyr, GenomeInfoDb, GenomicAlignments, GenomicRanges, gridExtra, IRanges, grid, methods, reshape2, rlang, stats, stringr, TxDb.Hsapiens.UCSC.hg38.knownGene, tidyselect |
| System Requirements | |
| URL | https://github.com/UofABioinformaticsHub/strandCheckR |
| Bug Reports | https://github.com/UofABioinformaticsHub/strandCheckR/issues |
See More
| Suggests | BiocStyle, knitr, magrittr, rmarkdown, 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_1.25.1.tar.gz |
| Windows Binary (x86_64) | strandCheckR_1.25.1.zip |
| macOS Binary (x86_64) | strandCheckR_1.25.1.tgz |
| macOS Binary (arm64) | strandCheckR_1.25.1.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 |