Here, I list all the used annotation in my previous publication:
- VIP: Very Important Pharmacogenes: N=66
- InnateDB: All immmnue system related genes list N=4723
- FDR drug marker: Pharmacogenomic Biomarkers in Drug Labeling
- FDR:FDA_approved_drugtarget: 460 FDA_approved_drugtarget
Step by step to prepare your db folder (hg38):
wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cytoBand.txt.gz -O cytoBand.hg38.bed.gz
wget http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/cpgIslandExt.txt.gz -O cpgIsland.hg38.bed.gz
wget https://raw.githubusercontent.com/Shicheng-Guo/miRNA-RA/master/db/hsa.gff.hg19.bed -O hsa.gff3.hg38.bed
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver -O liftOver
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz -O hg18ToHg19.over.chain.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz -O hg19ToHg38.over.chain.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz -O hg38ToHg19.over.chain.gz
wget https://raw.githubusercontent.com/Shicheng-Guo/GscRbasement/master/manhattan.qqplot.R -O manhattan.plot.R
wget https://raw.githubusercontent.com/Shicheng-Guo/Gscutility/master/localhit.pl -O localhit.pl
wget https://raw.githubusercontent.com/Shicheng-Guo/rheumatoidarthritis/master/R/make.fancy.locus.plot.unix.R -O make.fancy.locus.plot.unix.R
