Contents

1 Overview

igv.org currently (July 2022) provides 35 common and model organism annotated genomes. Each of these is easily specified and used in igvR

When igvR is initialized communication is established between your R session and your default web browser. Then, in a separate function call, you specifies the genome of interest. igvR then renders the genome browser view and interactive navigation can begin.

2 Demonstration

library(igvR)
igv <- igvR()
setBrowserWindowTitle(igv, "Stock Genomes")
print(sort(getSupportedGenomes(igv)))
ASM294v2 ASM985889v3  bosTau8 bosTau9  canFam3 canFam5  ce11 chm13v1.1
chm13v2.0 danRer10 danRer11 dm3  dm6 dmel_r5.9 galGal6 GCA_003086295.2
gorGor4 gorGor6 hg18 hg19 hg38  hg38_1kg macFas5 mm10 mm39 mm9 panPan2
panTro4 panTro5 panTro6 rn6 rn7 sacCer3 susScr11 tair10
setGenome(igv, "hg38_1Kg")
showGenomicRegion(igv, "APOE")
zoomOut(igv)

3 Display

4 Session Info

sessionInfo()
#> R version 4.3.0 RC (2023-04-13 r84269)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] BiocStyle_2.28.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.31       R6_2.5.1            bookdown_0.33       fastmap_1.1.1       xfun_0.39          
#>  [6] cachem_1.0.7        knitr_1.42          htmltools_0.5.5     rmarkdown_2.21      cli_3.6.1          
#> [11] sass_0.4.5          jquerylib_0.1.4     compiler_4.3.0      highr_0.10          tools_4.3.0        
#> [16] evaluate_0.20       bslib_0.4.2         yaml_2.3.7          BiocManager_1.30.20 jsonlite_1.8.4     
#> [21] rlang_1.1.0