1 Installation and getting started

The crisprVerse is a collection of packages for CRISPR guide RNA (gRNA) design that can easily be installed with the crisprVerse package. This provides a convenient way of downloading and installing all crisprVerse packages with a single R command.

The package can be installed from the Bioconductor devel branch using the following commands in an R session:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(version="devel")
BiocManager::install("crisprVerse")

The core crisprVerse includes the packages that are commonly used for gRNA design, and are attached when you attach the crisprVerse package:

library(crisprVerse)

You can check that all crisprVerse packages are up-to-date with the function crisprVerse_update().

2 Components

The following packages are installed and loaded with the crisprVerse package:

3 Reproducibility

sessionInfo()
## R version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] crisprViz_1.11.1       crisprDesign_1.11.1    crisprScore_1.13.1    
##  [4] crisprScoreData_1.13.0 ExperimentHub_2.99.5   AnnotationHub_3.99.6  
##  [7] BiocFileCache_2.99.6   dbplyr_2.5.1           BiocGenerics_0.55.1   
## [10] generics_0.1.4         crisprBowtie_1.13.1    crisprBase_1.13.0     
## [13] crisprVerse_1.11.0     BiocStyle_2.37.1      
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          rstudioapi_0.17.1          
##   [3] jsonlite_2.0.0              magrittr_2.0.4             
##   [5] GenomicFeatures_1.61.6      farver_2.1.2               
##   [7] rmarkdown_2.30              BiocIO_1.19.0              
##   [9] vctrs_0.6.5                 memoise_2.0.1              
##  [11] Rsamtools_2.25.3            RCurl_1.98-1.17            
##  [13] base64enc_0.1-3             htmltools_0.5.8.1          
##  [15] S4Arrays_1.9.1              progress_1.2.3             
##  [17] curl_7.0.0                  SparseArray_1.9.1          
##  [19] Formula_1.2-5               sass_0.4.10                
##  [21] bslib_0.9.0                 htmlwidgets_1.6.4          
##  [23] basilisk_1.21.5             Gviz_1.53.1                
##  [25] httr2_1.2.1                 cachem_1.1.0               
##  [27] GenomicAlignments_1.45.4    lifecycle_1.0.4            
##  [29] pkgconfig_2.0.3             Matrix_1.7-4               
##  [31] R6_2.6.1                    fastmap_1.2.0              
##  [33] MatrixGenerics_1.21.0       digest_0.6.37              
##  [35] colorspace_2.1-2            AnnotationDbi_1.71.1       
##  [37] S4Vectors_0.47.4            Hmisc_5.2-4                
##  [39] GenomicRanges_1.61.5        RSQLite_2.4.3              
##  [41] filelock_1.0.3              randomForest_4.7-1.2       
##  [43] httr_1.4.7                  abind_1.4-8                
##  [45] compiler_4.5.1              Rbowtie_1.49.0             
##  [47] bit64_4.6.0-1               backports_1.5.0            
##  [49] htmlTable_2.4.3             S7_0.2.0                   
##  [51] BiocParallel_1.43.4         DBI_1.2.3                  
##  [53] biomaRt_2.65.16             rappdirs_0.3.3             
##  [55] DelayedArray_0.35.3         rjson_0.2.23               
##  [57] tools_4.5.1                 foreign_0.8-90             
##  [59] nnet_7.3-20                 glue_1.8.0                 
##  [61] restfulr_0.0.16             grid_4.5.1                 
##  [63] checkmate_2.3.3             cluster_2.1.8.1            
##  [65] gtable_0.3.6                BSgenome_1.77.2            
##  [67] tzdb_0.5.0                  ensembldb_2.33.2           
##  [69] data.table_1.17.8           hms_1.1.3                  
##  [71] XVector_0.49.1              BiocVersion_3.22.0         
##  [73] pillar_1.11.1               stringr_1.5.2              
##  [75] dplyr_1.1.4                 lattice_0.22-7             
##  [77] deldir_2.0-4                rtracklayer_1.69.1         
##  [79] bit_4.6.0                   biovizBase_1.57.1          
##  [81] tidyselect_1.2.1            Biostrings_2.77.2          
##  [83] knitr_1.50                  gridExtra_2.3              
##  [85] bookdown_0.45               ProtGenerics_1.41.0        
##  [87] IRanges_2.43.5              Seqinfo_0.99.2             
##  [89] SummarizedExperiment_1.39.2 stats4_4.5.1               
##  [91] xfun_0.53                   Biobase_2.69.1             
##  [93] matrixStats_1.5.0           stringi_1.8.7              
##  [95] UCSC.utils_1.5.0            lazyeval_0.2.2             
##  [97] yaml_2.3.10                 evaluate_1.0.5             
##  [99] codetools_0.2-20            interp_1.1-6               
## [101] tibble_3.3.0                BiocManager_1.30.26        
## [103] cli_3.6.5                   rpart_4.1.24               
## [105] reticulate_1.43.0           jquerylib_0.1.4            
## [107] dichromat_2.0-0.1           Rcpp_1.1.0                 
## [109] GenomeInfoDb_1.45.12        dir.expiry_1.17.0          
## [111] png_0.1-8                   XML_3.99-0.19              
## [113] parallel_4.5.1              ggplot2_4.0.0              
## [115] readr_2.1.5                 blob_1.2.4                 
## [117] prettyunits_1.2.0           jpeg_0.1-11                
## [119] latticeExtra_0.6-31         AnnotationFilter_1.33.0    
## [121] bitops_1.0-9                txdbmaker_1.5.6            
## [123] VariantAnnotation_1.55.1    scales_1.4.0               
## [125] crayon_1.5.3                rlang_1.1.6                
## [127] KEGGREST_1.49.1