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().
The following packages are installed and loaded with the crisprVerse package:
GuideSet objects.sessionInfo()## R version 4.5.1 Patched (2025-08-23 r88802)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.22-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## 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_1.12.0 crisprDesign_1.12.0 crisprScore_1.14.0
## [4] crisprScoreData_1.13.0 ExperimentHub_3.0.0 AnnotationHub_4.0.0
## [7] BiocFileCache_3.0.0 dbplyr_2.5.1 BiocGenerics_0.56.0
## [10] generics_0.1.4 crisprBowtie_1.14.0 crisprBase_1.14.0
## [13] crisprVerse_1.12.0 BiocStyle_2.38.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] jsonlite_2.0.0 magrittr_2.0.4
## [5] GenomicFeatures_1.62.0 farver_2.1.2
## [7] rmarkdown_2.30 BiocIO_1.20.0
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.26.0 RCurl_1.98-1.17
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.10.0 progress_1.2.3
## [17] curl_7.0.0 SparseArray_1.10.0
## [19] Formula_1.2-5 sass_0.4.10
## [21] bslib_0.9.0 htmlwidgets_1.6.4
## [23] basilisk_1.22.0 Gviz_1.54.0
## [25] httr2_1.2.1 cachem_1.1.0
## [27] GenomicAlignments_1.46.0 lifecycle_1.0.4
## [29] pkgconfig_2.0.3 Matrix_1.7-4
## [31] R6_2.6.1 fastmap_1.2.0
## [33] MatrixGenerics_1.22.0 digest_0.6.37
## [35] colorspace_2.1-2 AnnotationDbi_1.72.0
## [37] S4Vectors_0.48.0 Hmisc_5.2-4
## [39] GenomicRanges_1.62.0 RSQLite_2.4.3
## [41] filelock_1.0.3 randomForest_4.7-1.2
## [43] httr_1.4.7 abind_1.4-8
## [45] compiler_4.5.1 Rbowtie_1.50.0
## [47] bit64_4.6.0-1 backports_1.5.0
## [49] htmlTable_2.4.3 S7_0.2.0
## [51] BiocParallel_1.44.0 DBI_1.2.3
## [53] biomaRt_2.66.0 rappdirs_0.3.3
## [55] DelayedArray_0.36.0 rjson_0.2.23
## [57] tools_4.5.1 foreign_0.8-90
## [59] nnet_7.3-20 glue_1.8.0
## [61] restfulr_0.0.16 grid_4.5.1
## [63] checkmate_2.3.3 cluster_2.1.8.1
## [65] gtable_0.3.6 BSgenome_1.78.0
## [67] tzdb_0.5.0 ensembldb_2.34.0
## [69] data.table_1.17.8 hms_1.1.4
## [71] XVector_0.50.0 BiocVersion_3.22.0
## [73] pillar_1.11.1 stringr_1.5.2
## [75] dplyr_1.1.4 lattice_0.22-7
## [77] deldir_2.0-4 rtracklayer_1.70.0
## [79] bit_4.6.0 biovizBase_1.58.0
## [81] tidyselect_1.2.1 Biostrings_2.78.0
## [83] knitr_1.50 gridExtra_2.3
## [85] bookdown_0.45 ProtGenerics_1.42.0
## [87] IRanges_2.44.0 Seqinfo_1.0.0
## [89] SummarizedExperiment_1.40.0 stats4_4.5.1
## [91] xfun_0.53 Biobase_2.70.0
## [93] matrixStats_1.5.0 stringi_1.8.7
## [95] UCSC.utils_1.6.0 lazyeval_0.2.2
## [97] yaml_2.3.10 evaluate_1.0.5
## [99] codetools_0.2-20 cigarillo_1.0.0
## [101] interp_1.1-6 tibble_3.3.0
## [103] BiocManager_1.30.26 cli_3.6.5
## [105] rpart_4.1.24 reticulate_1.44.0
## [107] jquerylib_0.1.4 dichromat_2.0-0.1
## [109] Rcpp_1.1.0 GenomeInfoDb_1.46.0
## [111] dir.expiry_1.18.0 png_0.1-8
## [113] XML_3.99-0.19 parallel_4.5.1
## [115] ggplot2_4.0.0 readr_2.1.5
## [117] blob_1.2.4 prettyunits_1.2.0
## [119] jpeg_0.1-11 latticeExtra_0.6-31
## [121] AnnotationFilter_1.34.0 bitops_1.0-9
## [123] txdbmaker_1.6.0 VariantAnnotation_1.56.0
## [125] scales_1.4.0 crayon_1.5.3
## [127] rlang_1.1.6 KEGGREST_1.50.0