igvR 1.25.0
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.
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)
sessionInfo()
#> R version 4.4.0 RC (2024-04-16 r86468)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 22.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.20-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_2.33.0
#>
#> loaded via a namespace (and not attached):
#> [1] digest_0.6.35 R6_2.5.1 bookdown_0.39 fastmap_1.1.1 xfun_0.43
#> [6] cachem_1.0.8 knitr_1.46 htmltools_0.5.8.1 rmarkdown_2.26 lifecycle_1.0.4
#> [11] cli_3.6.2 sass_0.4.9 jquerylib_0.1.4 compiler_4.4.0 highr_0.10
#> [16] tools_4.4.0 evaluate_0.23 bslib_0.7.0 yaml_2.3.8 BiocManager_1.30.22
#> [21] jsonlite_1.8.8 rlang_1.1.3