Jiang

MitoSeek. Seeking information like heteroplasmy, structure variants, etc. on Mitochondrial genome from next generation sequencing

pileup2base. Parse samtools pileup file to get how many bases and what kind of bases are called

viewFusion. View fusion event by circos plot

RNASeqDEPipeline. RNA-Seq differential gene expression pipeline

genbank2gtf. Perl

IntronGTF. Make a Intron GTF file from a bed

ATAC. Perl

orolab. CSS

DO.db. Scripts to build up DO.db package based on a obo file

CQScripts. A collection of scripts when I worked at Vanderbilt

knitr. A general-purpose tool for dynamic report generation in R

Personal. Personal code

Temp. Python

miRNA-SNP. The code is to get SNPs located in miRNA/pre-miRNA and their relationship(in loop, upstream of miRNA, downstream of miRNA, seed region or just in the miRNA) miRNA data is from mirBase while dbSNP data is from vcf file

NGScripts. A collection of scripts for NGS data analysis

DOSim. DOSim is developed on DO to 1) measure the similarity between diseases (DO terms), 2) measure the similarity between human genes in terms of diseases, 3) detect DO-driven gene modules and multilayer annotate them on dieases (DO), functions(GO) and pathways(KEGG), 4) conduct DO enrichment analysis, and 5) visualize and describe DO structures and terms. It focuses on the computation of disease similarity and gene similarity. Besides, its module detection and annotation would promote our understanding of the complex pathogenesis of diseases.