README.md

In dritoshi/genesearchr: Fast full-text and DNA search in NCBI RefSeq, UniProt-KB and genome sequence

genesearchR

This R package can quickly search full-text of NCBI RefSeq, UniProt-KB and whole genome DNA sequence from GGRNA/GGGenome and G-links Web API.

Install

Start R

sudo R

Install packages

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicRanges")

install.packages("devtools")
install.packages("roxygen2")

library(devtools)
install_github("dritoshi/genesearchr")

Usage

library("genesearchr")

## RefSeq
my.hs.gene <- refSeqSearch(query = "NM_001518", species = "hs")
my.mm.gene <- refSeqSearch(query = "homeobox",  species = "mm")

## UniProt-KB
my.gid.gene <- uniprotSearch(query = "GeneID:93986")
my.eco.gene <- uniprotSearch(query = "eco:b2699")

## Genome DNA Sequence
my.mm10.dna <- genomeSearch(query = "TTCATTGACAACATTGCGT", db = "mm10", k = 2)

Search operator

• G-links, UniProt-KB search
• GGRNA, RefSeq search
• GGGenome, Ultrafast sequence search

Licence

MIT

Author

dritoshi

dritoshi/genesearchr documentation built on May 15, 2019, 2:12 p.m.