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 Under development (unstable) (2025-10-20 r88955)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.23-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_1.13.0 crisprDesign_1.13.5 crisprScore_1.15.2
## [4] crisprScoreData_1.15.0 ExperimentHub_3.1.0 AnnotationHub_4.1.0
## [7] BiocFileCache_3.1.0 dbplyr_2.5.1 BiocGenerics_0.57.0
## [10] generics_0.1.4 crisprBowtie_1.15.0 crisprBase_1.15.0
## [13] crisprVerse_1.13.1 BiocStyle_2.39.0
##
## 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_1.63.1 farver_2.1.2
## [7] rmarkdown_2.30 BiocIO_1.21.0
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.27.0 RCurl_1.98-1.17
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.11.0 progress_1.2.3
## [17] curl_7.0.0 SparseArray_1.11.4
## [19] Formula_1.2-5 sass_0.4.10
## [21] bslib_0.9.0 htmlwidgets_1.6.4
## [23] Gviz_1.55.0 httr2_1.2.1
## [25] cachem_1.1.0 GenomicAlignments_1.47.0
## [27] lifecycle_1.0.4 pkgconfig_2.0.3
## [29] Matrix_1.7-4 R6_2.6.1
## [31] fastmap_1.2.0 MatrixGenerics_1.23.0
## [33] digest_0.6.39 colorspace_2.1-2
## [35] AnnotationDbi_1.73.0 S4Vectors_0.49.0
## [37] Hmisc_5.2-4 GenomicRanges_1.63.0
## [39] RSQLite_2.4.4 filelock_1.0.3
## [41] randomForest_4.7-1.2 httr_1.4.7
## [43] abind_1.4-8 compiler_4.6.0
## [45] Rbowtie_1.51.0 bit64_4.6.0-1
## [47] htmlTable_2.4.3 S7_0.2.1
## [49] backports_1.5.0 BiocParallel_1.45.0
## [51] DBI_1.2.3 biomaRt_2.67.0
## [53] rappdirs_0.3.3 DelayedArray_0.37.0
## [55] rjson_0.2.23 tools_4.6.0
## [57] foreign_0.8-90 nnet_7.3-20
## [59] glue_1.8.0 restfulr_0.0.16
## [61] grid_4.6.0 checkmate_2.3.3
## [63] cluster_2.1.8.1 gtable_0.3.6
## [65] BSgenome_1.79.1 tzdb_0.5.0
## [67] ensembldb_2.35.0 data.table_1.17.8
## [69] hms_1.1.4 XVector_0.51.0
## [71] BiocVersion_3.23.1 pillar_1.11.1
## [73] stringr_1.6.0 dplyr_1.1.4
## [75] lattice_0.22-7 deldir_2.0-4
## [77] rtracklayer_1.71.0 bit_4.6.0
## [79] biovizBase_1.59.0 tidyselect_1.2.1
## [81] Biostrings_2.79.2 knitr_1.50
## [83] gridExtra_2.3 bookdown_0.45
## [85] ProtGenerics_1.43.0 IRanges_2.45.0
## [87] Seqinfo_1.1.0 SummarizedExperiment_1.41.0
## [89] stats4_4.6.0 xfun_0.54
## [91] Biobase_2.71.0 matrixStats_1.5.0
## [93] stringi_1.8.7 UCSC.utils_1.7.0
## [95] lazyeval_0.2.2 yaml_2.3.10
## [97] evaluate_1.0.5 codetools_0.2-20
## [99] cigarillo_1.1.0 interp_1.1-6
## [101] tibble_3.3.0 BiocManager_1.30.27
## [103] cli_3.6.5 rpart_4.1.24
## [105] reticulate_1.44.1 jquerylib_0.1.4
## [107] dichromat_2.0-0.1 Rcpp_1.1.0
## [109] GenomeInfoDb_1.47.0 png_0.1-8
## [111] XML_3.99-0.20 parallel_4.6.0
## [113] ggplot2_4.0.1 readr_2.1.6
## [115] blob_1.2.4 prettyunits_1.2.0
## [117] jpeg_0.1-11 latticeExtra_0.6-31
## [119] AnnotationFilter_1.35.0 bitops_1.0-9
## [121] txdbmaker_1.7.1 VariantAnnotation_1.57.0
## [123] scales_1.4.0 crayon_1.5.3
## [125] rlang_1.1.6 KEGGREST_1.51.1