[BioC] any package to do gene expression value estimation

[Martin Morgan]

On 10/24/2011 11:27 AM, wang peter wrote:
> dear all:
>
> i used all the RNA-seq data to assemble the transcripsome.
> but anyone  R package or software can map data of each sample to the the
> transcripsome
> and also estimate gene expression value

Hi -- your question is quite vague. Alignment via Rsubread / 
Biostrings::matchPDict / third party. Count overlaps via GenomicRanges 
readGappedAlignments, countOverlaps, summarizeExperiment (in 'devel'). 
Differential representation via edgeR, DESeq, DEXSeq and others at

http://bioconductor.org/packages/release/BiocViews.html#___RNAseq

Hope that helps,

Martin

>
> thank you
> shan gao
>
> 	[[alternative HTML version deleted]]
>
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