annovarR: Integrated Framework to Annotate Genetic Variants

The 'annovarR' package provides R functions as well as database resources which offer an integrated framework to annotate genetic variants from genome and transcriptome data. The wrapper functions of 'annovarR' unified the interface of many published annotation tools, such as 'VEP' (<http://asia.ensembl.org/info/docs/tools/vep/index.html>), 'ANNOVAR' (<http://annovar.openbioinformatics.org/>), 'vcfanno' (<https://github.com/brentp/vcfanno>) and 'AnnotationDbi' (<http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html>). It also simplified the use of some of the external annotation tools in R. Besides, massive published genetic variants annotation databases were integrated into 'annovarR'. For example, 'annovarR' provides a newly RNA-seq allele frequency database, BRVar, which built from total 1,285 cases public B-progenitor acute lymphoblastic leukemia (B-ALL) transcriptome data.

Version: 1.0.0
Depends: R (≥ 3.3.0)
Imports: stringr (≥ 1.2.0), configr (≥ 0.2.2), BioInstaller (≥ 0.3.2), ngstk (≥ 0.2.1), DBI (≥ 0.6-1), data.table (≥ 1.10.0), RSQLite (≥ 2.0), futile.logger (≥ 1.4.3), stringi (≥ 1.1.5), RMySQL (≥ 0.10.11), vcfR (≥ 1.6.0), AnnotationDbi, glue, methods
Suggests: testthat, knitr, rmarkdown, org.Hs.eg.db
Published: 2018-01-09
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng at sjtu.edu.cn>
BugReports: https://github.com/JhuangLab/annovarR/issues
License: MIT + file LICENSE
URL: https://github.com/JhuangLab/annovarR
NeedsCompilation: no
Materials: README NEWS ChangeLog
CRAN checks: annovarR results

Downloads:

Reference manual: annovarR.pdf
Vignettes: Databases in annovarR
Introduction to annovarR
Package source: annovarR_1.0.0.tar.gz
Windows binaries: r-devel: annovarR_1.0.0.zip, r-release: annovarR_1.0.0.zip, r-oldrel: annovarR_1.0.0.zip
OS X binaries: r-release: annovarR_1.0.0.tgz, r-oldrel: annovarR_1.0.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=annovarR to link to this page.