strandCheckR
Calculate strandness information of a bam file
Bioconductor version: 3.24 · Package version: 1.31.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("strandCheckR")Details
| Maintainer | Thu-Hien To <tothuhien@gmail.com> |
| Author | Thu-Hien To [aut, cre], Stevie Pederson [aut] (ORCID: <https://orcid.org/0000-0001-8197-3303>) |
| License | GPL (>= 2) |
| URL | https://github.com/UofABioinformaticsHub/strandCheckR |
| Bug Reports | https://github.com/UofABioinformaticsHub/strandCheckR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/strandCheckR/ |
Citation
From within R, enter citation("strandCheckR"):
Thu-Hien To, Stevie Pederson. strandCheckR: Calculate strandness information of a bam file. doi:10.18129/B9.bioc.strandCheckR, R package version 1.31.0, https://bioconductor.org/packages/strandCheckR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the 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 (arm64) | strandCheckR_1.31.0.tgz |
| macOS binary (x86_64) | strandCheckR_1.31.0.tgz |
Dependencies
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