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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 |
DOI: | 10.32614/CRAN.package.revert |
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 |
Reference manual: | revert.pdf |
Vignettes: |
Introduction |
Package source: | revert_0.0.1.tar.gz |
Windows binaries: | r-devel: revert_0.0.1.zip, r-release: revert_0.0.1.zip, r-oldrel: revert_0.0.1.zip |
macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
Please use the canonical form https://CRAN.R-project.org/package=revert to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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