SeqGSEA: Gene Set Enrichment Analysis of RNA-Seq Data

[master_shake]

Using EasyRNASeq for SeqGSEA

The latest vignette claims one can use easyRNAseq for read counts. Using easyRNAseq, should one count exons, or genes? Also, how should the file be outputted, as a summarized experiment? A count table? Normalized values for DESeq?

[Xi Wang]

The package SeqGSEA started with R version 3.0.0. Perhaps you need to install the latest release of R. If you are not happy with the latest R, and if you are based on Linux platform, you can download the tar ball of the package at

http://www.bioconductor.org/packages/release/bioc/src/contrib/SeqGSEA_1.0.2.tar.gz

and type 'R CMD INSTALL SeqGSEA_1.0.2.tar.gz' to install.

Cheers
Xi

[wilson90]

I am sorry, but it is not available for R version 2.15.1. Is it still available?

[Xi Wang]

Could you offer an example and describe how to use this package for RNA-seq data analysis?

Thanks for your message. I have included an example in Section 6 in the package's vignette available at http://bioconductor.org/packages/rel...oc/SeqGSEA.pdf

Any further questions or comments please feel free to let me know. Thanks.

[xkcao]

Could you offer an example and describe how to use this package for RNA-seq data analysis?

[Xi Wang]

I am glad to introduce to you guys a new Bioconductor package, SeqGSEA, developed by our group. The detailed description of this package is:

SeqGSEA: Gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. Using negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Statistical significance of each gene set investigated is reached by subject permutation. Based on the permutation, statistical significance regarding to each gene's differential expression and splicing can also be achieved , respectively.

The package can be accessed at the URL:

http://bioconductor.org/packages/rel...l/SeqGSEA.html

Should you have any questions, comments, or suggestions, please feel free to email me at (xi.wang (at) newcastle.edu.au). Thanks.