AnnthomyGILLES / RNA-DNA-seq

Repo hosts scripts for differential expression and variant calling analysis of high throughput sequencing data.

RNA-seq Differential Expression Analysis and Variant Calling

This repository hosts scripts for differential expression and variant calling analysis of high throughput sequencing data.

##cummeRbund cummeRbund: An R package for exploration, analysis, manipulation,and visualization of Cufflinks high-throughput RNA Sequencing data.

##DESeq2 DESeq2: An R package for differential expression analysis. DESEq2 estimates variance-mean dependence in count data (from HTseq-count output) from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

##DNA Variant calling and Annotation
This is a standard GATK and lofreq variant call pipeline with snpEff annotations.