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)
## Warning: replacing previous import 'utils::findMatches' by
## 'S4Vectors::findMatches' when loading 'AnnotationDbi'

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 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so 
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## 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_1.2.0       crisprDesign_1.2.0    crisprScore_1.4.0    
##  [4] crisprScoreData_1.3.0 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_1.8.4                magrittr_2.0.3               
##   [5] GenomicFeatures_1.52.0        rmarkdown_2.21               
##   [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] progress_1.2.2                curl_5.0.0                   
##  [17] Formula_1.2-5                 sass_0.4.5                   
##  [19] bslib_0.4.2                   htmlwidgets_1.6.2            
##  [21] basilisk_1.12.0               Gviz_1.44.0                  
##  [23] cachem_1.0.7                  GenomicAlignments_1.36.0     
##  [25] mime_0.12                     lifecycle_1.0.3              
##  [27] pkgconfig_2.0.3               Matrix_1.5-4                 
##  [29] R6_2.5.1                      fastmap_1.1.1                
##  [31] GenomeInfoDbData_1.2.10       MatrixGenerics_1.12.0        
##  [33] shiny_1.7.4                   digest_0.6.31                
##  [35] colorspace_2.1-0              AnnotationDbi_1.62.0         
##  [37] S4Vectors_0.38.0              Hmisc_5.0-1                  
##  [39] GenomicRanges_1.52.0          RSQLite_2.3.1                
##  [41] filelock_1.0.2                randomForest_4.7-1.1         
##  [43] fansi_1.0.4                   httr_1.4.5                   
##  [45] compiler_4.3.0                Rbowtie_1.40.0               
##  [47] bit64_4.0.5                   backports_1.4.1              
##  [49] htmlTable_2.4.1               BiocParallel_1.34.0          
##  [51] DBI_1.1.3                     biomaRt_2.56.0               
##  [53] rappdirs_0.3.3                DelayedArray_0.26.0          
##  [55] rjson_0.2.21                  tools_4.3.0                  
##  [57] foreign_0.8-84                interactiveDisplayBase_1.38.0
##  [59] httpuv_1.6.9                  nnet_7.3-18                  
##  [61] glue_1.6.2                    restfulr_0.0.15              
##  [63] promises_1.2.0.1              grid_4.3.0                   
##  [65] checkmate_2.1.0               cluster_2.1.4                
##  [67] generics_0.1.3                gtable_0.3.3                 
##  [69] BSgenome_1.68.0               tzdb_0.3.0                   
##  [71] ensembldb_2.24.0              data.table_1.14.8            
##  [73] hms_1.1.3                     xml2_1.3.3                   
##  [75] utf8_1.2.3                    XVector_0.40.0               
##  [77] BiocVersion_3.17.1            pillar_1.9.0                 
##  [79] stringr_1.5.0                 later_1.3.0                  
##  [81] dplyr_1.1.2                   lattice_0.21-8               
##  [83] deldir_1.0-6                  rtracklayer_1.60.0           
##  [85] bit_4.0.5                     biovizBase_1.48.0            
##  [87] tidyselect_1.2.0              Biostrings_2.68.0            
##  [89] knitr_1.42                    gridExtra_2.3                
##  [91] bookdown_0.33                 ProtGenerics_1.32.0          
##  [93] IRanges_2.34.0                SummarizedExperiment_1.30.0  
##  [95] stats4_4.3.0                  xfun_0.39                    
##  [97] Biobase_2.60.0                matrixStats_0.63.0           
##  [99] stringi_1.7.12                lazyeval_0.2.2               
## [101] yaml_2.3.7                    evaluate_0.20                
## [103] codetools_0.2-19              interp_1.1-4                 
## [105] tibble_3.2.1                  BiocManager_1.30.20          
## [107] cli_3.6.1                     rpart_4.1.19                 
## [109] xtable_1.8-4                  reticulate_1.28              
## [111] munsell_0.5.0                 jquerylib_0.1.4              
## [113] dichromat_2.0-0.1             Rcpp_1.0.10                  
## [115] GenomeInfoDb_1.36.0           dir.expiry_1.8.0             
## [117] png_0.1-8                     XML_3.99-0.14                
## [119] parallel_4.3.0                ellipsis_0.3.2               
## [121] ggplot2_3.4.2                 readr_2.1.4                  
## [123] blob_1.2.4                    basilisk.utils_1.12.0        
## [125] prettyunits_1.1.1             jpeg_0.1-10                  
## [127] latticeExtra_0.6-30           AnnotationFilter_1.24.0      
## [129] bitops_1.0-7                  VariantAnnotation_1.46.0     
## [131] scales_1.2.1                  crayon_1.5.2                 
## [133] rlang_1.1.0                   KEGGREST_1.40.0