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 4.3.0 RC (2023-04-13 r84257)
## Platform: x86_64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.6.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## 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_1.2.0       crisprDesign_1.2.0    crisprScore_1.4.0    
##  [4] crisprScoreData_1.4.0 ExperimentHub_2.8.0   AnnotationHub_3.8.0  
##  [7] BiocFileCache_2.8.0   dbplyr_2.3.2          BiocGenerics_0.46.0  
## [10] crisprBowtie_1.4.0    crisprBase_1.4.0      crisprVerse_1.2.0    
## [13] BiocStyle_2.28.0     
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3            rstudioapi_0.14              
##   [3] jsonlite_1.8.5                magrittr_2.0.3               
##   [5] GenomicFeatures_1.52.0        rmarkdown_2.22               
##   [7] BiocIO_1.10.0                 zlibbioc_1.46.0              
##   [9] vctrs_0.6.2                   memoise_2.0.1                
##  [11] Rsamtools_2.16.0              RCurl_1.98-1.12              
##  [13] base64enc_0.1-3               htmltools_0.5.5              
##  [15] S4Arrays_1.0.4                progress_1.2.2               
##  [17] curl_5.0.1                    Formula_1.2-5                
##  [19] sass_0.4.6                    bslib_0.5.0                  
##  [21] htmlwidgets_1.6.2             basilisk_1.12.0              
##  [23] Gviz_1.44.0                   cachem_1.0.8                 
##  [25] GenomicAlignments_1.36.0      mime_0.12                    
##  [27] lifecycle_1.0.3               pkgconfig_2.0.3              
##  [29] Matrix_1.5-4.1                R6_2.5.1                     
##  [31] fastmap_1.1.1                 GenomeInfoDbData_1.2.10      
##  [33] MatrixGenerics_1.12.2         shiny_1.7.4                  
##  [35] digest_0.6.31                 colorspace_2.1-0             
##  [37] AnnotationDbi_1.62.1          S4Vectors_0.38.1             
##  [39] Hmisc_5.1-0                   GenomicRanges_1.52.0         
##  [41] RSQLite_2.3.1                 filelock_1.0.2               
##  [43] randomForest_4.7-1.1          fansi_1.0.4                  
##  [45] httr_1.4.6                    compiler_4.3.0               
##  [47] Rbowtie_1.40.0                bit64_4.0.5                  
##  [49] backports_1.4.1               htmlTable_2.4.1              
##  [51] BiocParallel_1.34.2           DBI_1.1.3                    
##  [53] biomaRt_2.56.1                rappdirs_0.3.3               
##  [55] DelayedArray_0.26.3           rjson_0.2.21                 
##  [57] tools_4.3.0                   foreign_0.8-84               
##  [59] interactiveDisplayBase_1.38.0 httpuv_1.6.11                
##  [61] nnet_7.3-19                   glue_1.6.2                   
##  [63] restfulr_0.0.15               promises_1.2.0.1             
##  [65] grid_4.3.0                    checkmate_2.2.0              
##  [67] cluster_2.1.4                 generics_0.1.3               
##  [69] gtable_0.3.3                  BSgenome_1.68.0              
##  [71] tzdb_0.4.0                    ensembldb_2.24.0             
##  [73] data.table_1.14.8             hms_1.1.3                    
##  [75] xml2_1.3.4                    utf8_1.2.3                   
##  [77] XVector_0.40.0                BiocVersion_3.17.1           
##  [79] pillar_1.9.0                  stringr_1.5.0                
##  [81] later_1.3.1                   dplyr_1.1.2                  
##  [83] lattice_0.21-8                deldir_1.0-9                 
##  [85] rtracklayer_1.60.0            bit_4.0.5                    
##  [87] biovizBase_1.48.0             tidyselect_1.2.0             
##  [89] Biostrings_2.68.1             knitr_1.43                   
##  [91] gridExtra_2.3                 bookdown_0.34                
##  [93] ProtGenerics_1.32.0           IRanges_2.34.0               
##  [95] SummarizedExperiment_1.30.2   stats4_4.3.0                 
##  [97] xfun_0.39                     Biobase_2.60.0               
##  [99] matrixStats_1.0.0             stringi_1.7.12               
## [101] lazyeval_0.2.2                yaml_2.3.7                   
## [103] evaluate_0.21                 codetools_0.2-19             
## [105] interp_1.1-4                  tibble_3.2.1                 
## [107] BiocManager_1.30.21           cli_3.6.1                    
## [109] rpart_4.1.19                  xtable_1.8-4                 
## [111] reticulate_1.30               munsell_0.5.0                
## [113] jquerylib_0.1.4               dichromat_2.0-0.1            
## [115] Rcpp_1.0.10                   GenomeInfoDb_1.36.0          
## [117] dir.expiry_1.8.0              png_0.1-8                    
## [119] XML_3.99-0.14                 parallel_4.3.0               
## [121] ellipsis_0.3.2                ggplot2_3.4.2                
## [123] readr_2.1.4                   blob_1.2.4                   
## [125] basilisk.utils_1.12.1         prettyunits_1.1.1            
## [127] jpeg_0.1-10                   latticeExtra_0.6-30          
## [129] AnnotationFilter_1.24.0       bitops_1.0-7                 
## [131] VariantAnnotation_1.46.0      scales_1.2.1                 
## [133] crayon_1.5.2                  rlang_1.1.1                  
## [135] KEGGREST_1.40.0