Package: revert 0.0.1

Hui Xiao

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.

Authors:Hui Xiao [aut, cre], Adam Mills [aut], John Alexander [ctb], Stephen Pettitt [aut], Syed Haider [aut]

revert_0.0.1.tar.gz
revert_0.0.1.tar.gz(r-4.5-noble)revert_0.0.1.tar.gz(r-4.4-noble)
revert_0.0.1.tgz(r-4.4-emscripten)revert_0.0.1.tgz(r-4.3-emscripten)
revert.pdf |revert.html
revert/json (API)
NEWS

# Install 'revert' in R:
install.packages('revert', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 93 downloads 1 exports 52 dependencies

Last updated 12 months agofrom:81e0144f70. Checks:OK: 1 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-linuxWARNINGOct 31 2024

Exports:getReversions

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomeBSgenome.Hsapiens.UCSC.hg38codetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

revert

Rendered fromIntroduction.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-11-24
Started: 2023-11-24