README.md

In TomHarrop/oryzr: Work with Oryza sativa gene identifiers

oryzr

Work with Oryza sativa gene identifiers

This R package is for converting between different types of gene identifiers for Oryza sativa L. ssp. japonica cv. Nipponbare genes (MSU, Rap-DB, CSGNL, RefSeq mRNA).

Functions

• LocToGeneName: Convert MSU identifiers to CSGNL gene names and symbols and generate a label for plotting if requested.
• LocToRefSeq: Convert MSU identifiers to Rap-DB identifiers and map them to RefSeq mRNA identifiers.
• SearchByGeneSymbol: Search Rap-DB and oryzabase information by gene symbol and return identifiers for potential matches.
• RapToMsu: Convert Rap-DB identifiers to MSU identifiers.
• GenomicRangeToGeneName: Return information for all of the genes in a genomic region.

Installation

• Requires devtools: install.packages("devtools")
• Install oryzr from GitHub: devtools::install_github("TomHarrop/oryzr")

TomHarrop/oryzr documentation built on May 9, 2019, 4:52 p.m.