revert: Reversion Mutation Identifier for Sequencing Data

A tool for detecting reversions for a given pathogenic mutation from next-generation DNA sequencing data. It analyses reads aligned to the locus of the pathogenic mutation and reports reversion events where secondary mutations have restored or undone the deleterious effect of the original pathogenic mutation, e.g., secondary indels complement to a frameshift pathogenic mutation converting the orignal frameshift mutation into inframe mutaions, deletions or SNVs that replaced the original pathogenic mutation restoring the open reading frame, SNVs changing the stop codon caused by the original nonsense SNV into an amino acid, etc.

Version: 0.0.1
Imports: IRanges, GenomicRanges, Biostrings, Rsamtools, BSgenome, BSgenome.Hsapiens.UCSC.hg38
Suggests: knitr, rmarkdown, futile.logger
Published: 2023-11-23
Author: Hui Xiao [aut, cre], Adam Mills [aut], John Alexander [ctb], Stephen Pettitt [aut], Syed Haider [aut]
Maintainer: Hui Xiao <hui.xiao at icr.ac.uk>
License: GPL-2
NeedsCompilation: no
SystemRequirements: R >= 4.1.0, SAMtools >= 1.11
Materials: NEWS
CRAN checks: revert results

Documentation:

Reference manual: revert.pdf
Vignettes: Introduction

Downloads:

Package source: revert_0.0.1.tar.gz
Windows binaries: r-prerel: revert_0.0.1.zip, r-release: revert_0.0.1.zip, r-oldrel: revert_0.0.1.zip
macOS binaries: r-prerel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): not available, r-prerel (x86_64): not available, r-release (x86_64): not available

Linking:

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