riverlee/MitoSeek

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Language
Perl
Created almost 12 years ago
Updated almost 6 years ago

riverlee/MitoSeek

riverlee

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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

IntronGTF

Make a Intron GTF file from a bed

genbank2gtf

ATAC

orolab

CQScripts

A collection of scripts when I worked at Vanderbilt

DO.db

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

Temp

Personal

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.

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