tadar

DOI: 10.18129/B9.bioc.tadar  

Transcriptome Analysis of Differential Allelic Representation

Bioconductor version: Release (3.18)

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] , Stevie Pederson [aut]

Maintainer: Lachlan Baer <baerlachlan at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	DAR analysis
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, GenomicVariation, RNASeq, SNP, Sequencing, Software, VariantAnnotation
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	GPL-3
Depends	GenomicRanges, ggplot2, R (>= 4.3.0)
Imports	BiocGenerics, GenomeInfoDb, Gviz, IRanges, MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats, VariantAnnotation
LinkingTo
Suggests	BiocStyle, covr, knitr, limma, rmarkdown, testthat (>= 3.0.0), tidyverse
SystemRequirements
Enhances
URL	https://github.com/baerlachlan/tadar
BugReports	https://github.com/baerlachlan/tadar/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	tadar_1.0.0.tar.gz
Windows Binary	tadar_1.0.0.zip
macOS Binary (x86_64)	tadar_1.0.0.tgz
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
Old Source Packages for BioC 3.18	Source Archive