ESCC RNA seq using Galaxy and R

Galaxy Tools used :-

1. NCBI Fastq download
2. FastQC quality report
3. Alignment using BowTie2
4. Count Matrix using HTseq-count

R libraries used :-

1. DESeq for differential gene expression
2. org.Hs.eg.db to change Ensemble ID to gene symbol
3. edgeR for calculating various parameter from count matrix
4. RColorBrewer, gplot, pheatmap for graphs and heatmap generation
5. GOfuncR, Homo.sapiens for gene ontology

ESCC human esophageal squamous cell carcinoma, exploratory data analysis on RNA seq data
Data available on NCBI GEO ID: GSE29968
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE29968