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 Under development (unstable) (2024-11-20 r87352)
## Platform: x86_64-apple-darwin20
## Running under: macOS Monterey 12.7.6
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## 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_1.9.0        crisprDesign_1.9.0     crisprScore_1.11.0    
##  [4] crisprScoreData_1.11.0 ExperimentHub_2.15.0   AnnotationHub_3.15.0  
##  [7] BiocFileCache_2.15.0   dbplyr_2.5.0           BiocGenerics_0.53.3   
## [10] generics_0.1.3         crisprBowtie_1.11.0    crisprBase_1.11.0     
## [13] crisprVerse_1.9.0      BiocStyle_2.35.0      
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          rstudioapi_0.17.1          
##   [3] jsonlite_1.8.9              magrittr_2.0.3             
##   [5] GenomicFeatures_1.59.1      rmarkdown_2.29             
##   [7] BiocIO_1.17.1               zlibbioc_1.53.0            
##   [9] vctrs_0.6.5                 memoise_2.0.1              
##  [11] Rsamtools_2.23.0            RCurl_1.98-1.16            
##  [13] base64enc_0.1-3             htmltools_0.5.8.1          
##  [15] S4Arrays_1.7.1              progress_1.2.3             
##  [17] curl_6.0.1                  SparseArray_1.7.2          
##  [19] Formula_1.2-5               sass_0.4.9                 
##  [21] bslib_0.8.0                 htmlwidgets_1.6.4          
##  [23] basilisk_1.19.0             Gviz_1.51.0                
##  [25] httr2_1.0.6                 cachem_1.1.0               
##  [27] GenomicAlignments_1.43.0    lifecycle_1.0.4            
##  [29] pkgconfig_2.0.3             Matrix_1.7-1               
##  [31] R6_2.5.1                    fastmap_1.2.0              
##  [33] GenomeInfoDbData_1.2.13     MatrixGenerics_1.19.0      
##  [35] digest_0.6.37               colorspace_2.1-1           
##  [37] AnnotationDbi_1.69.0        S4Vectors_0.45.2           
##  [39] Hmisc_5.2-0                 GenomicRanges_1.59.1       
##  [41] RSQLite_2.3.8               filelock_1.0.3             
##  [43] randomForest_4.7-1.2        fansi_1.0.6                
##  [45] httr_1.4.7                  abind_1.4-8                
##  [47] compiler_4.5.0              Rbowtie_1.47.0             
##  [49] bit64_4.5.2                 backports_1.5.0            
##  [51] htmlTable_2.4.3             BiocParallel_1.41.0        
##  [53] DBI_1.2.3                   biomaRt_2.63.0             
##  [55] rappdirs_0.3.3              DelayedArray_0.33.2        
##  [57] rjson_0.2.23                tools_4.5.0                
##  [59] foreign_0.8-87              nnet_7.3-19                
##  [61] glue_1.8.0                  restfulr_0.0.15            
##  [63] grid_4.5.0                  checkmate_2.3.2            
##  [65] cluster_2.1.6               gtable_0.3.6               
##  [67] BSgenome_1.75.0             tzdb_0.4.0                 
##  [69] ensembldb_2.31.0            data.table_1.16.2          
##  [71] hms_1.1.3                   xml2_1.3.6                 
##  [73] utf8_1.2.4                  XVector_0.47.0             
##  [75] BiocVersion_3.21.1          pillar_1.9.0               
##  [77] stringr_1.5.1               dplyr_1.1.4                
##  [79] lattice_0.22-6              deldir_2.0-4               
##  [81] rtracklayer_1.67.0          bit_4.5.0                  
##  [83] biovizBase_1.55.0           tidyselect_1.2.1           
##  [85] Biostrings_2.75.1           knitr_1.49                 
##  [87] gridExtra_2.3               bookdown_0.41              
##  [89] ProtGenerics_1.39.0         IRanges_2.41.1             
##  [91] SummarizedExperiment_1.37.0 stats4_4.5.0               
##  [93] xfun_0.49                   Biobase_2.67.0             
##  [95] matrixStats_1.4.1           stringi_1.8.4              
##  [97] UCSC.utils_1.3.0            lazyeval_0.2.2             
##  [99] yaml_2.3.10                 evaluate_1.0.1             
## [101] codetools_0.2-20            interp_1.1-6               
## [103] tibble_3.2.1                BiocManager_1.30.25        
## [105] cli_3.6.3                   rpart_4.1.23               
## [107] reticulate_1.40.0           munsell_0.5.1              
## [109] jquerylib_0.1.4             dichromat_2.0-0.1          
## [111] Rcpp_1.0.13-1               GenomeInfoDb_1.43.1        
## [113] dir.expiry_1.15.0           png_0.1-8                  
## [115] XML_3.99-0.17               parallel_4.5.0             
## [117] ggplot2_3.5.1               readr_2.1.5                
## [119] blob_1.2.4                  basilisk.utils_1.19.0      
## [121] prettyunits_1.2.0           jpeg_0.1-10                
## [123] latticeExtra_0.6-30         AnnotationFilter_1.31.0    
## [125] bitops_1.0-9                txdbmaker_1.3.1            
## [127] VariantAnnotation_1.53.0    scales_1.3.0               
## [129] crayon_1.5.3                rlang_1.1.4                
## [131] KEGGREST_1.47.0