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 (3.24)
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>
citation("strandCheckR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | GPL (>= 2) |
| Depends | ggplot2 (>= 4.0.0), Rsamtools, S4Vectors |
| Imports | BiocGenerics, dplyr, Seqinfo, 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_1.31.0.tar.gz |
| Windows Binary (x86_64) | strandCheckR_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | strandCheckR_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | strandCheckR_1.31.0.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 |