ICETEA : Integrating Cap Enrichment with Transcript Expression Analysis

The ICETEA R package is built to work with the newly developed transcript 5' profiling techniques, such as RAMPAGE and MAPCap.

The package can be used for data processing, detection of TSS enrichments, as well as differential TSS detection between two group of samples.
Functions for :

1. Read demultiplexing.
2. Mapping
3. Removal of PCR duplicates using UMIs and mapping position of reads in genomic bins.
4. New TSS detection method that considers biological replicates.
5. Differential TSS detection using an RNAseq-like approach.
6. Annotation of detected TSS.
7. QC plots
8. Other helper functions.


icetea v1.7 
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Changes:

* Additional option to use either 3' or center of the reads when doing TSS calling. This would be useful for protocols like iCLiP etc. Default is to use 5' site (for CAGE-like protocols)
