strandCheckR
Calculate strandness information of a bam file
Bioconductor version: 3.24 · Package version: 1.31.0
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 |
| Downloads rank | 472 |
| Source branch | devel |
| biocViews | Alignment, Coverage, ImmunoOncology, QualityControl, RNASeq, Software |
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