mutationtypes: Validate and Convert Mutational Impacts Using Standard Genomic Dictionaries
Check concordance of a vector of mutation impacts with standard dictionaries such as Sequence Ontology (SO) <http://www.sequenceontology.org/>, Mutation Annotation Format (MAF) <https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2/> or Prediction and Annotation of Variant Effects (PAVE) <https://github.com/hartwigmedical/hmftools/tree/master/pave>. It enables conversion between SO/PAVE and MAF terms and selection of the most severe consequence where multiple ampersand (&) delimited impacts are given.
| Version: | 0.0.1 |
| Imports: | assertions, cli, data.table, stats, utils |
| Suggests: | covr, testthat (≥ 3.0.0) |
| Published: | 2023-12-14 |
| DOI: | 10.32614/CRAN.package.mutationtypes |
| Author: | Sam El-Kamand 
[aut, cre],
Children's Cancer Institute Australia [cph] |
| Maintainer: | Sam El-Kamand <sam.elkamand at gmail.com> |
| BugReports: | https://github.com/selkamand/mutationtypes/issues |
| License: | LGPL (≥ 3) |
| URL: | https://github.com/selkamand/mutationtypes |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | mutationtypes results |
Documentation:
| Reference manual: | mutationtypes.html , mutationtypes.pdf |
Downloads:
| Package source: | mutationtypes_0.0.1.tar.gz |
| Windows binaries: | r-devel: mutationtypes_0.0.1.zip, r-release: mutationtypes_0.0.1.zip, r-oldrel: mutationtypes_0.0.1.zip |
| macOS binaries: | r-release (arm64): mutationtypes_0.0.1.tgz, r-oldrel (arm64): mutationtypes_0.0.1.tgz, r-release (x86_64): mutationtypes_0.0.1.tgz, r-oldrel (x86_64): mutationtypes_0.0.1.tgz |
Linking:
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