ModDNAString alphabet (original) (raw)

References

The alphabets for the modifications used in this package are based on the compilation of DNA modifications by the Hoffman lab (Sood, Viner, and Hoffman 2019). The alphabet was modified to make it compatible for the Modstrings package.

If modifications are missing, let us know.

sessionInfo()

## R version 4.5.0 beta (2025-04-02 r88102)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              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       
## 
## time zone: America/New_York
## tzcode source: system (glibc)
## 
## attached base packages:
## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] Modstrings_1.25.0   Biostrings_2.77.0   GenomeInfoDb_1.45.0
## [4] XVector_0.49.0      IRanges_2.43.0      S4Vectors_0.47.0   
## [7] BiocGenerics_0.55.0 generics_0.1.3      BiocStyle_2.37.0   
## 
## loaded via a namespace (and not attached):
##  [1] crayon_1.5.3            httr_1.4.7              cli_3.6.4              
##  [4] knitr_1.50              rlang_1.1.6             xfun_0.52              
##  [7] stringi_1.8.7           UCSC.utils_1.5.0        jsonlite_2.0.0         
## [10] glue_1.8.0              htmltools_0.5.8.1       sass_0.4.10            
## [13] rmarkdown_2.29          evaluate_1.0.3          jquerylib_0.1.4        
## [16] fastmap_1.2.0           yaml_2.3.10             lifecycle_1.0.4        
## [19] bookdown_0.43           stringr_1.5.1           BiocManager_1.30.25    
## [22] compiler_4.5.0          digest_0.6.37           R6_2.6.1               
## [25] GenomeInfoDbData_1.2.14 magrittr_2.0.3          GenomicRanges_1.61.0   
## [28] bslib_0.9.0             tools_4.5.0             cachem_1.1.0

ModDNAString alphabet (original) (raw)

Contents

References