This is walk through for a basic sequencing analysis pipelines. This Repository contains Walkthrus using....
- E-utils and the SRA toolkit from the Linux command line
- How to use various packages in R.
- DEXseq for differnetial expresion of transcripts
- Limma, Minifi and Bumphunter for looking at Methylation data from the illumina 450. With the package Minifi you'll find conectivity to GEO as well as TCGA