README.md

In gdelangel/genomicRTools: Genomic R Tools

genomicRTools

Miscellaneous tools to handle and annotate VCF data from R/Bioconductor. Includes interfaces with VEP API

Specific tools: - Unpack ExAC vcf at a particular gene of interest. Since multi-allelics are such a pain to deal with, tools will split into one row per alt allele. Currently very slow, need to optimize! - Call VEP's API to annotate stuff. Most important use case is to call it using an ENSEMBL tag (ENST) and a hgvs code. Useful if we want to get genomic coordinates from just a clinical mutation report that only contains HGVS mutation codes. - Call VEP to determine gene transcripts and know which one is canonical - Other misc. tools to make dealing with VCF's easier in R

COMING UP: - Process public Clinvar vcf's from R - Improvement in VEP - Deal with dbNSFP files - Package into R library

gdelangel/genomicRTools documentation built on May 16, 2019, 11:14 p.m.