1) Deal with stranded RNA-Seq
Have a look at the HistoneChIPseq package for the implementation

2) Deal with GenomicFeatures

## using different annotation (makeTranscriptDB)
library(GenomicFeatures)
hg19.tx <- makeTranscriptDbFromUCSC(
                                    genome="hg19",
                                    tablename="refGene")

## easyRNASeq can deal with GRangesList object, so no need to modify it much, i.e. no need to convert it to a RangedData
gAnnot <- exons(hg19.tx)

## REMEMBER we can fetch it this way
## exons(hg19.tx,columns=c("gene_id","tx_id","exon_id"))
## we need to adapt the GRanges then; i.e. multiply by gene and transcripts...

## NOTE that exon have integer ID, as well as the tx_id

## change the metadata column name to suit easyRNASeq
colnames(elementMetadata(gAnnot)) <- "exon"

## finally turn it into a GRangesList
gAnnot <- split(gAnnot,seqnames(gAnnot))

3) Integrate the DEXSeq object generation
## create the disjoin exon
## report both the disjoin exon count and the new annotation

4) clarify the vignette (email from Gordon Assaf, paired end, detail more the geneModels) and rework the Rd (clean them up, use describe instead of itemize, etc.)

5) Add Simon's data

6) Offer the possibility to define your own organism name conversion, akine to the srFilter

7) rework geneModels to use the disjoin function / add a geneModel switch to the annotation (add geneModels functionality to return and modify the created gene models)

8) deprecate the summarization

9) group the parameter a la scanbamWhat

10) lookup all the TODOs in the code

11) From Simon, to filter reads: "NH:i:n" with n>1. However, not all aligner use the NH tag properly, so this is not a full solution. Another possibility is to discard everything with mapping quality below 10, because non-uniquly mapped reads should have a MAPQ<3.

12) Check the possibility to split BAM files

13) Chek the possibility to stream BAM files

14) Develop fragment counting

15) Add a use case to clean up annotations against double counting.

16) check that for easyRNASeq: http://bioinformatics.oxfordjournals.org/content/28/7/1021.full

17) Remove/Hide the readLength argument once we have introduced variable read length reads. Change the vignette then.

18) check if countBam is not faster for both bam and gappedAlignments to get the library size

19) deal with paired end data

20) the count should default to "exons", not "features"

21) check richard's email about the H. sapiens use case.

22) Add support for SummarizedExperiments

23) Check that the double quotes are removed from textual context attribute when loading a gtf