tadar
This is the development version of tadar; for the stable release version, see tadar.
Transcriptome Analysis of Differential Allelic Representation
Bioconductor version: Development (3.21)
This package provides functions to standardise the analysis of Differential Allelic Representation (DAR). DAR compromises the integrity of Differential Expression analysis results as it can bias expression, influencing the classification of genes (or transcripts) as being differentially expressed. DAR analysis results in an easy-to-interpret value between 0 and 1 for each genetic feature of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.
Author: Lachlan Baer [aut, cre] (ORCID:
Maintainer: Lachlan Baer <baerlachlan at gmail.com>
citation("tadar")):
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("tadar")
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("tadar")| DAR analysis | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GenomicVariation, RNASeq, SNP, Sequencing, Software, VariantAnnotation |
| Version | 1.5.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (1 year) |
| License | GPL-3 |
| Depends | GenomicRanges, ggplot2, R (>= 4.4.0) |
| Imports | BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation |
| System Requirements | |
| URL | https://github.com/baerlachlan/tadar |
| Bug Reports | https://github.com/baerlachlan/tadar/issues |
See More
| Suggests | BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse |
| 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 | tadar_1.5.0.tar.gz |
| Windows Binary (x86_64) | tadar_1.5.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/tadar |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tadar |
| Bioc Package Browser | https://code.bioconductor.org/browse/tadar/ |
| Package Short Url | https://bioconductor.org/packages/tadar/ |
| Package Downloads Report | Download Stats |