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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.19-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_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [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_1.6.0       crisprDesign_1.6.0    crisprScore_1.8.0    
##  [4] crisprScoreData_1.7.0 ExperimentHub_2.12.0  AnnotationHub_3.12.0 
##  [7] BiocFileCache_2.12.0  dbplyr_2.5.0          BiocGenerics_0.50.0  
## [10] crisprBowtie_1.8.0    crisprBase_1.8.0      crisprVerse_1.6.0    
## [13] BiocStyle_2.32.0     
## 
## loaded via a namespace (and not attached):
##   [1] RColorBrewer_1.1-3          rstudioapi_0.16.0          
##   [3] jsonlite_1.8.8              magrittr_2.0.3             
##   [5] GenomicFeatures_1.56.0      rmarkdown_2.26             
##   [7] BiocIO_1.14.0               zlibbioc_1.50.0            
##   [9] vctrs_0.6.5                 memoise_2.0.1              
##  [11] Rsamtools_2.20.0            RCurl_1.98-1.14            
##  [13] base64enc_0.1-3             htmltools_0.5.8.1          
##  [15] S4Arrays_1.4.0              progress_1.2.3             
##  [17] curl_5.2.1                  SparseArray_1.4.0          
##  [19] Formula_1.2-5               sass_0.4.9                 
##  [21] bslib_0.7.0                 htmlwidgets_1.6.4          
##  [23] basilisk_1.16.0             Gviz_1.48.0                
##  [25] httr2_1.0.1                 cachem_1.0.8               
##  [27] GenomicAlignments_1.40.0    lifecycle_1.0.4            
##  [29] pkgconfig_2.0.3             Matrix_1.7-0               
##  [31] R6_2.5.1                    fastmap_1.1.1              
##  [33] GenomeInfoDbData_1.2.12     MatrixGenerics_1.16.0      
##  [35] digest_0.6.35               colorspace_2.1-0           
##  [37] AnnotationDbi_1.66.0        S4Vectors_0.42.0           
##  [39] Hmisc_5.1-2                 GenomicRanges_1.56.0       
##  [41] RSQLite_2.3.6               filelock_1.0.3             
##  [43] randomForest_4.7-1.1        fansi_1.0.6                
##  [45] httr_1.4.7                  abind_1.4-5                
##  [47] compiler_4.4.0              Rbowtie_1.44.0             
##  [49] bit64_4.0.5                 backports_1.4.1            
##  [51] htmlTable_2.4.2             BiocParallel_1.38.0        
##  [53] DBI_1.2.2                   biomaRt_2.60.0             
##  [55] rappdirs_0.3.3              DelayedArray_0.30.0        
##  [57] rjson_0.2.21                tools_4.4.0                
##  [59] foreign_0.8-86              nnet_7.3-19                
##  [61] glue_1.7.0                  restfulr_0.0.15            
##  [63] grid_4.4.0                  checkmate_2.3.1            
##  [65] cluster_2.1.6               generics_0.1.3             
##  [67] gtable_0.3.5                BSgenome_1.72.0            
##  [69] tzdb_0.4.0                  ensembldb_2.28.0           
##  [71] data.table_1.15.4           hms_1.1.3                  
##  [73] xml2_1.3.6                  utf8_1.2.4                 
##  [75] XVector_0.44.0              BiocVersion_3.19.1         
##  [77] pillar_1.9.0                stringr_1.5.1              
##  [79] dplyr_1.1.4                 lattice_0.22-6             
##  [81] deldir_2.0-4                rtracklayer_1.64.0         
##  [83] bit_4.0.5                   biovizBase_1.52.0          
##  [85] tidyselect_1.2.1            Biostrings_2.72.0          
##  [87] knitr_1.46                  gridExtra_2.3              
##  [89] bookdown_0.39               ProtGenerics_1.36.0        
##  [91] IRanges_2.38.0              SummarizedExperiment_1.34.0
##  [93] stats4_4.4.0                xfun_0.43                  
##  [95] Biobase_2.64.0              matrixStats_1.3.0          
##  [97] stringi_1.8.3               UCSC.utils_1.0.0           
##  [99] lazyeval_0.2.2              yaml_2.3.8                 
## [101] evaluate_0.23               codetools_0.2-20           
## [103] interp_1.1-6                tibble_3.2.1               
## [105] BiocManager_1.30.22         cli_3.6.2                  
## [107] rpart_4.1.23                reticulate_1.36.1          
## [109] munsell_0.5.1               jquerylib_0.1.4            
## [111] dichromat_2.0-0.1           Rcpp_1.0.12                
## [113] GenomeInfoDb_1.40.0         dir.expiry_1.12.0          
## [115] png_0.1-8                   XML_3.99-0.16.1            
## [117] parallel_4.4.0              ggplot2_3.5.1              
## [119] readr_2.1.5                 blob_1.2.4                 
## [121] basilisk.utils_1.16.0       prettyunits_1.2.0          
## [123] jpeg_0.1-10                 latticeExtra_0.6-30        
## [125] AnnotationFilter_1.28.0     bitops_1.0-7               
## [127] txdbmaker_1.0.0             VariantAnnotation_1.50.0   
## [129] scales_1.3.0                crayon_1.5.2               
## [131] rlang_1.1.3                 KEGGREST_1.44.0