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 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: America/New_York
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] crisprViz_1.11.0       crisprDesign_1.11.0    crisprScore_1.13.0    
##  [4] crisprScoreData_1.13.0 ExperimentHub_2.99.0   AnnotationHub_3.99.0  
##  [7] BiocFileCache_2.99.0   dbplyr_2.5.0           BiocGenerics_0.55.0   
## [10] generics_0.1.3         crisprBowtie_1.13.0    crisprBase_1.13.0     
## [13] crisprVerse_1.11.0     BiocStyle_2.37.0      
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          rstudioapi_0.17.1          
##   [3] jsonlite_2.0.0              magrittr_2.0.3             
##   [5] GenomicFeatures_1.61.0      farver_2.1.2               
##   [7] rmarkdown_2.29              BiocIO_1.19.0              
##   [9] vctrs_0.6.5                 memoise_2.0.1              
##  [11] Rsamtools_2.25.0            RCurl_1.98-1.17            
##  [13] base64enc_0.1-3             htmltools_0.5.8.1          
##  [15] S4Arrays_1.9.0              progress_1.2.3             
##  [17] curl_6.2.2                  SparseArray_1.9.0          
##  [19] Formula_1.2-5               sass_0.4.10                
##  [21] bslib_0.9.0                 htmlwidgets_1.6.4          
##  [23] basilisk_1.21.0             Gviz_1.53.0                
##  [25] httr2_1.1.2                 cachem_1.1.0               
##  [27] GenomicAlignments_1.45.0    lifecycle_1.0.4            
##  [29] pkgconfig_2.0.3             Matrix_1.7-3               
##  [31] R6_2.6.1                    fastmap_1.2.0              
##  [33] GenomeInfoDbData_1.2.14     MatrixGenerics_1.21.0      
##  [35] digest_0.6.37               colorspace_2.1-1           
##  [37] AnnotationDbi_1.71.0        S4Vectors_0.47.0           
##  [39] Hmisc_5.2-3                 GenomicRanges_1.61.0       
##  [41] RSQLite_2.3.9               filelock_1.0.3             
##  [43] randomForest_4.7-1.2        httr_1.4.7                 
##  [45] abind_1.4-8                 compiler_4.5.0             
##  [47] Rbowtie_1.49.0              bit64_4.6.0-1              
##  [49] backports_1.5.0             htmlTable_2.4.3            
##  [51] BiocParallel_1.43.0         DBI_1.2.3                  
##  [53] biomaRt_2.65.0              rappdirs_0.3.3             
##  [55] DelayedArray_0.35.1         rjson_0.2.23               
##  [57] tools_4.5.0                 foreign_0.8-90             
##  [59] nnet_7.3-20                 glue_1.8.0                 
##  [61] restfulr_0.0.15             grid_4.5.0                 
##  [63] checkmate_2.3.2             cluster_2.1.8.1            
##  [65] gtable_0.3.6                BSgenome_1.77.0            
##  [67] tzdb_0.5.0                  ensembldb_2.33.0           
##  [69] data.table_1.17.0           hms_1.1.3                  
##  [71] xml2_1.3.8                  XVector_0.49.0             
##  [73] BiocVersion_3.22.0          pillar_1.10.2              
##  [75] stringr_1.5.1               dplyr_1.1.4                
##  [77] lattice_0.22-7              deldir_2.0-4               
##  [79] rtracklayer_1.69.0          bit_4.6.0                  
##  [81] biovizBase_1.57.0           tidyselect_1.2.1           
##  [83] Biostrings_2.77.0           knitr_1.50                 
##  [85] gridExtra_2.3               bookdown_0.43              
##  [87] ProtGenerics_1.41.0         IRanges_2.43.0             
##  [89] SummarizedExperiment_1.39.0 stats4_4.5.0               
##  [91] xfun_0.52                   Biobase_2.69.0             
##  [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_1.0.3             
##  [99] codetools_0.2-20            interp_1.1-6               
## [101] tibble_3.2.1                BiocManager_1.30.25        
## [103] cli_3.6.5                   rpart_4.1.24               
## [105] reticulate_1.42.0           jquerylib_0.1.4            
## [107] dichromat_2.0-0.1           Rcpp_1.0.14                
## [109] GenomeInfoDb_1.45.0         dir.expiry_1.17.0          
## [111] png_0.1-8                   XML_3.99-0.18              
## [113] parallel_4.5.0              ggplot2_3.5.2              
## [115] readr_2.1.5                 blob_1.2.4                 
## [117] basilisk.utils_1.21.0       prettyunits_1.2.0          
## [119] jpeg_0.1-11                 latticeExtra_0.6-30        
## [121] AnnotationFilter_1.33.0     bitops_1.0-9               
## [123] txdbmaker_1.5.0             VariantAnnotation_1.55.0   
## [125] scales_1.4.0                crayon_1.5.3               
## [127] rlang_1.1.6                 KEGGREST_1.49.0