TODO.txt

TODO List for Robin
===================


- 	integration of tiling array support using the code to be written/ported to R by
	Liam Childs
	
- 	Configurability of PCA plot (asked for by John and Mark) - ability to plot PCs upt to PC5 against PC6 and Show a 
	scree plot to give an overview on the distribution of variances explained by ordered
	PCs.
	
- 	Integration of RNA-Seq analysis. Unsure at what point of the RNA-Seq pipeline we can
	enter the business. Just implementing an interface for packages like edgeR would be
	a rather thin solution but require a lot of prior manual work from the user. Integrating
	moe steps like
		
		- raw read quality checking (different for different platforms)
		- quality-based preprocessing and filtering of reads (not so extremely platform-dependent)
		- mapping to user-provided target genome (FASTA) and inferrence of coverage vector
		- normalization
		- statistical analysis of differential expression (again egdeR and the like)
			
	would be nicer