CRAN

annovarR 1.0.0

Integrated Framework to Annotate Genetic Variants

Released Jan 9, 2018 by Jianfeng Li

This package cannot yet be used with Renjin it depends on other packages which are not available: AnnotationDbi, BioInstaller 0.3.6, and data.table 1.11.4

Dependencies

data.table 1.11.4 BioInstaller 0.3.6 ngstk 0.2.1 RSQLite futile.logger stringr 1.3.1 RMySQL glue 1.3.0 configr 0.3.3 DBI 1.0.0 stringi vcfR 1.8.0

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' (), 'ANNOVAR' (), 'vcfanno' () and 'AnnotationDbi' (). 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.

Source

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Release History

1.0.0