[BioC] New package to identify differentially expressed genes from RNA-seq data

Naomi Altman naomi at stat.psu.edu
Wed Oct 14 22:18:20 CEST 2009

I could not find this package on bioconductor.org.   Thanks to rules 
about software downloads here, it will take a while for me to get R 
2.10.0, and I would like to have
a look at the documentation in the meantime.  Where could I find it?


At 09:15 AM 10/14/2009, Likun Wang wrote:
>Hi all,
>     We present a new R package DEGseq for identifying differentially
>expressed genes from RNA-seq data.The input of DEGseq is uniquely mapped
>reads from RNA-seq data with a gene annotation of the corresponding genome,
>or gene (or transcript isoform) expression values provided by other
>programs. The output of DEGseq includes a text file and an XHTML summary
>page. The text file contains the expression values for the samples, a
>P-value and two kinds of Q-values for each gene to denote its expression
>difference between libraries. Two novel MA-plot based methods along with
>some existing methods have been integrated into it.
>     You may access it through the commands:
>  > source("http://bioconductor.org/biocLite.R")   # R >= 2.10.0
>  > biocLite("DEGseq")
>     Comments, questions, etc, are all welcome.
>      Best regards
>         [[alternative HTML version deleted]]
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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