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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>

Citation (from within R, enter citation("tadar")):

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")
DAR analysis HTML R Script
Reference Manual PDF
NEWS Text

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
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
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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