[BioC] GenomicFeatures support for UCSC Microbial Genome Browser

Olusegun Oshota [guest] guest at bioconductor.org
Sat Jan 11 12:33:01 CET 2014


I tried using the GenomicFeatures package (R package) to get gene information for Salmonella enterica serovar Typhimurium SL1344 (uid86645) and Campylobacter jejuni (NCTC1168) from the UCSC genome browser,but discovered that UCSC genome browser did not have the two organisms; however, the two organisms are hosted in UCSC Microbial Genome Browser. I wonder if there is any plan to support UCSC Microbial Genome Browser in the nearest future.


 -- output of sessionInfo(): 

R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] rtracklayer_1.20.4     GenomicRanges_1.12.5   IRanges_1.18.2         lumiMouseAll.db_1.20.0 org.Mm.eg.db_2.9.0     RSQLite_0.11.4         DBI_0.2-7             
 [8] annotate_1.38.0        AnnotationDbi_1.22.6   limma_3.16.7           lumi_2.12.0            gplots_2.12.1          DESeq_1.12.0           lattice_0.20-24       
[15] locfit_1.5-9.1         Biobase_2.20.1         BiocGenerics_0.6.0     doMC_1.3.1             iterators_1.0.6        foreach_1.4.1         

loaded via a namespace (and not attached):
 [1] affy_1.38.1           affyio_1.28.0         beanplot_1.1          BiocInstaller_1.10.3  Biostrings_2.28.0     bitops_1.0-6          BSgenome_1.28.0      
 [8] caTools_1.16          codetools_0.2-8       colorspace_1.2-2      compiler_3.0.2        gdata_2.13.2          genefilter_1.42.0     geneplotter_1.38.0   
[15] grid_3.0.2            gtools_3.1.0          illuminaio_0.2.0      KernSmooth_2.23-10    MASS_7.3-29           Matrix_1.1-1.1        matrixStats_0.8.5    
[22] mclust_4.2            methylumi_2.6.1       mgcv_1.7-27           minfi_1.6.0           multtest_2.16.0       nleqslv_2.0           nlme_3.1-113         
[29] nor1mix_1.1-4         preprocessCore_1.22.0 RColorBrewer_1.0-5    RCurl_1.95-4.1        reshape_0.8.4         R.methodsS3_1.5.2     Rsamtools_1.12.4     
[36] siggenes_1.34.0       splines_3.0.2         stats4_3.0.2          survival_2.37-4       tools_3.0.2           XML_3.98-1.1          xtable_1.7-1         
[43] zlibbioc_1.6.0 

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