1 Citation

If you use DOSE in published research, please cite G. Yu (2015).

G Yu, LG Wang, GR Yan, QY He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609. http://dx.doi.org/10.1093/bioinformatics/btu684.

2 Overview

DOSE provides five methods for measureing semantic similarity among DO terms and genes. It implemented over-representation analysis to associate disease with gene list (e.g. differential expressed genes) and gene set enrichment analysis to associate disease with genome wide expression profiles. The enrichment analyses support Disease Ontology (DO)¹, Network of Cancer Gene (NCG)³ and DisGeNET⁴. In addition, several visualization methods were developed to help interpreting semantic and enrichment results.

3 Vignette Entry

• Semantic similarity analysis
• Disease enrichment analysis
• Disease GSEA analysis

4 Need helps?

If you have questions/issues, please visit DOSE homepage first. Your problems are mostly documented. If you think you found a bug, please follow the guide and provide a reproducible example to be posted on github issue tracker. For questions, please post to Bioconductor support site and tag your post with DOSE.

For Chinese user, you can follow me on WeChat (微信).

5 Session Information

Here is the output of sessionInfo() on the system on which this document was compiled:

## R version 3.5.2 (2018-12-20)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
## 
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] DOSE_3.8.2       BiocStyle_2.10.0
## 
## loaded via a namespace (and not attached):
##  [1] qvalue_2.14.1        tidyselect_0.2.5     fgsea_1.8.0         
##  [4] xfun_0.4             reshape2_1.4.3       purrr_0.2.5         
##  [7] splines_3.5.2        lattice_0.20-38      colorspace_1.4-0    
## [10] htmltools_0.3.6      stats4_3.5.2         yaml_2.2.0          
## [13] blob_1.1.1           rlang_0.3.1          pillar_1.3.1        
## [16] glue_1.3.0           DBI_1.0.0            BiocParallel_1.16.5 
## [19] BiocGenerics_0.28.0  bit64_0.9-7          bindrcpp_0.2.2      
## [22] plyr_1.8.4           bindr_0.1.1          stringr_1.3.1       
## [25] munsell_0.5.0        GOSemSim_2.8.0       gtable_0.2.0        
## [28] memoise_1.1.0        evaluate_0.12        Biobase_2.42.0      
## [31] knitr_1.21           IRanges_2.16.0       parallel_3.5.2      
## [34] AnnotationDbi_1.44.0 Rcpp_1.0.0           scales_1.0.0        
## [37] BiocManager_1.30.4   DO.db_2.9            S4Vectors_0.20.1    
## [40] bit_1.1-14           gridExtra_2.3        fastmatch_1.1-0     
## [43] ggplot2_3.1.0        digest_0.6.18        stringi_1.2.4       
## [46] bookdown_0.9         dplyr_0.7.8          grid_3.5.2          
## [49] tools_3.5.2          magrittr_1.5         lazyeval_0.2.1      
## [52] RSQLite_2.1.1        tibble_2.0.1         crayon_1.3.4        
## [55] GO.db_3.7.0          pkgconfig_2.0.2      Matrix_1.2-15       
## [58] data.table_1.12.0    assertthat_0.2.0     rmarkdown_1.11      
## [61] R6_2.3.0             compiler_3.5.2