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:
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.## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so; LAPACK version 3.12.0
##
## 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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.15.0 crisprDesign_1.15.7 crisprScore_1.17.0
## [4] crisprScoreData_1.17.0 ExperimentHub_3.3.1 AnnotationHub_4.3.2
## [7] BiocFileCache_3.3.0 dbplyr_2.6.0 BiocGenerics_0.59.10
## [10] generics_0.1.4 crisprBowtie_1.17.0 crisprBase_1.17.0
## [13] crisprVerse_1.15.0 BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.19.0
## [3] sys_3.4.3 jsonlite_2.0.0
## [5] magrittr_2.0.5 GenomicFeatures_1.65.0
## [7] farver_2.1.2 rmarkdown_2.31
## [9] BiocIO_1.23.3 vctrs_0.7.3
## [11] memoise_2.0.1 Rsamtools_2.29.0
## [13] RCurl_1.98-1.19 base64enc_0.1-6
## [15] htmltools_0.5.9 S4Arrays_1.13.0
## [17] BiocBaseUtils_1.15.1 progress_1.2.3
## [19] curl_7.1.0 SparseArray_1.13.2
## [21] Formula_1.2-5 sass_0.4.10
## [23] bslib_0.11.0 htmlwidgets_1.6.4
## [25] Gviz_1.57.0 httr2_1.2.3
## [27] cachem_1.1.0 buildtools_1.0.0
## [29] GenomicAlignments_1.49.1 lifecycle_1.0.5
## [31] pkgconfig_2.0.3 Matrix_1.7-5
## [33] R6_2.6.1 fastmap_1.2.0
## [35] MatrixGenerics_1.25.0 digest_0.6.39
## [37] colorspace_2.1-2 AnnotationDbi_1.75.0
## [39] S4Vectors_0.51.5 Hmisc_5.2-6
## [41] GenomicRanges_1.65.1 RSQLite_3.53.3
## [43] filelock_1.0.3 randomForest_4.7-1.2
## [45] httr_1.4.8 abind_1.4-8
## [47] compiler_4.6.1 Rbowtie_1.53.0
## [49] bit64_4.8.2 backports_1.5.1
## [51] htmlTable_2.5.0 S7_0.2.2
## [53] BiocParallel_1.47.0 DBI_1.3.0
## [55] biomaRt_2.69.0 rappdirs_0.3.4
## [57] DelayedArray_0.39.3 rjson_0.2.23
## [59] tools_4.6.1 foreign_0.8-91
## [61] otel_0.2.0 nnet_7.3-20
## [63] glue_1.8.1 restfulr_0.0.17
## [65] grid_4.6.1 checkmate_2.3.4
## [67] cluster_2.1.8.2 gtable_0.3.6
## [69] BSgenome_1.81.0 tzdb_0.5.0
## [71] ensembldb_2.37.3 data.table_1.18.4
## [73] hms_1.1.4 XVector_0.53.0
## [75] BiocVersion_3.24.0 pillar_1.11.1
## [77] stringr_1.6.0 dplyr_1.2.1
## [79] lattice_0.22-9 deldir_2.0-4
## [81] rtracklayer_1.73.0 bit_4.6.0
## [83] biovizBase_1.61.0 tidyselect_1.2.1
## [85] maketools_1.3.2 Biostrings_2.81.5
## [87] knitr_1.51 gridExtra_2.3.1
## [89] ProtGenerics_1.45.0 IRanges_2.47.2
## [91] Seqinfo_1.3.0 SummarizedExperiment_1.43.0
## [93] stats4_4.6.1 xfun_0.60
## [95] Biobase_2.73.1 matrixStats_1.5.0
## [97] stringi_1.8.7 UCSC.utils_1.9.0
## [99] lazyeval_0.2.3 yaml_2.3.12
## [101] evaluate_1.0.5 codetools_0.2-20
## [103] cigarillo_1.3.0 interp_1.1-6
## [105] tibble_3.3.1 BiocManager_1.30.27
## [107] cli_3.6.6 rpart_4.1.27
## [109] reticulate_1.46.0 jquerylib_0.1.4
## [111] dichromat_2.0-0.1 Rcpp_1.1.2
## [113] GenomeInfoDb_1.49.1 png_0.1-9
## [115] XML_3.99-0.23 parallel_4.6.1
## [117] ggplot2_4.0.3 readr_2.2.0
## [119] blob_1.3.0 prettyunits_1.2.0
## [121] jpeg_0.1-11 latticeExtra_0.6-31
## [123] AnnotationFilter_1.37.0 bitops_1.0-9
## [125] txdbmaker_1.9.0 VariantAnnotation_1.59.0
## [127] scales_1.4.0 crayon_1.5.3
## [129] rlang_1.3.0 KEGGREST_1.53.5