[BioC] rna-seq

saman amini [guest] guest at bioconductor.org
Wed Sep 26 17:03:58 CEST 2012

Hi everybody,

I Have used goseq to take out the enriched GO-terms from my RNA-seq and microarray data and I want to visualize the output from goseq in a network since it is just a list of GO-terms and I cannot see an overview of my result. So my question is what package or software should I use to see a network of regulated GO-terms or pathways.


 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_2.6.12           limma_3.12.3           goseq_1.8.0           
[4] geneLenDataBase_0.99.9 BiasedUrn_1.04        

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.18.3  Biobase_2.16.0        BiocGenerics_0.2.0   
 [4] biomaRt_2.12.0        Biostrings_2.24.1     bitops_1.0-4.1       
 [7] BSgenome_1.24.0       DBI_0.2-5             GenomicFeatures_1.8.3
[10] GenomicRanges_1.8.13  grid_2.15.0           IRanges_1.14.4       
[13] lattice_0.20-10       Matrix_1.0-9          mgcv_1.7-21          
[16] nlme_3.1-104          RCurl_1.91-1          Rsamtools_1.8.6      
[19] RSQLite_0.11.2        rtracklayer_1.16.3    stats4_2.15.0        
[22] tools_2.15.0          XML_3.9-4             zlibbioc_1.2.0  

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