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 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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-r0.3.26.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=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: Etc/UTC
## 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_1.14.0 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] sys_3.4.3 jsonlite_2.0.0
## [5] magrittr_2.0.4 GenomicFeatures_1.62.0
## [7] farver_2.1.2 rmarkdown_2.30
## [9] BiocIO_1.20.0 vctrs_0.6.5
## [11] memoise_2.0.1 Rsamtools_2.26.0
## [13] RCurl_1.98-1.17 base64enc_0.1-3
## [15] htmltools_0.5.8.1 S4Arrays_1.10.0
## [17] progress_1.2.3 curl_7.0.0
## [19] SparseArray_1.10.1 Formula_1.2-5
## [21] sass_0.4.10 bslib_0.9.0
## [23] htmlwidgets_1.6.4 basilisk_1.22.0
## [25] Gviz_1.54.0 httr2_1.2.1
## [27] cachem_1.1.0 buildtools_1.0.0
## [29] GenomicAlignments_1.46.0 lifecycle_1.0.4
## [31] pkgconfig_2.0.3 Matrix_1.7-4
## [33] R6_2.6.1 fastmap_1.2.0
## [35] MatrixGenerics_1.22.0 digest_0.6.38
## [37] colorspace_2.1-2 AnnotationDbi_1.72.0
## [39] S4Vectors_0.48.0 Hmisc_5.2-4
## [41] GenomicRanges_1.62.0 RSQLite_2.4.4
## [43] filelock_1.0.3 randomForest_4.7-1.2
## [45] httr_1.4.7 abind_1.4-8
## [47] compiler_4.5.2 Rbowtie_1.50.0
## [49] bit64_4.6.0-1 backports_1.5.0
## [51] htmlTable_2.4.3 S7_0.2.1
## [53] BiocParallel_1.44.0 DBI_1.2.3
## [55] biomaRt_2.66.0 rappdirs_0.3.3
## [57] DelayedArray_0.36.0 rjson_0.2.23
## [59] tools_4.5.2 foreign_0.8-90
## [61] nnet_7.3-20 glue_1.8.0
## [63] restfulr_0.0.16 grid_4.5.2
## [65] checkmate_2.3.3 cluster_2.1.8.1
## [67] gtable_0.3.6 BSgenome_1.78.0
## [69] tzdb_0.5.0 ensembldb_2.34.0
## [71] data.table_1.17.8 hms_1.1.4
## [73] XVector_0.50.0 BiocVersion_3.23.1
## [75] pillar_1.11.1 stringr_1.6.0
## [77] dplyr_1.1.4 lattice_0.22-7
## [79] deldir_2.0-4 rtracklayer_1.70.0
## [81] bit_4.6.0 biovizBase_1.58.0
## [83] tidyselect_1.2.1 maketools_1.3.2
## [85] Biostrings_2.78.0 knitr_1.50
## [87] gridExtra_2.3 ProtGenerics_1.42.0
## [89] IRanges_2.44.0 Seqinfo_1.0.0
## [91] SummarizedExperiment_1.40.0 stats4_4.5.2
## [93] xfun_0.54 Biobase_2.70.0
## [95] matrixStats_1.5.0 stringi_1.8.7
## [97] UCSC.utils_1.6.0 lazyeval_0.2.2
## [99] yaml_2.3.10 evaluate_1.0.5
## [101] codetools_0.2-20 cigarillo_1.0.0
## [103] interp_1.1-6 tibble_3.3.0
## [105] BiocManager_1.30.27 cli_3.6.5
## [107] rpart_4.1.24 reticulate_1.44.1
## [109] jquerylib_0.1.4 dichromat_2.0-0.1
## [111] Rcpp_1.1.0 GenomeInfoDb_1.46.0
## [113] dir.expiry_1.18.0 png_0.1-8
## [115] XML_3.99-0.20 parallel_4.5.2
## [117] ggplot2_4.0.1 readr_2.1.6
## [119] blob_1.2.4 prettyunits_1.2.0
## [121] jpeg_0.1-11 latticeExtra_0.6-31
## [123] AnnotationFilter_1.34.0 bitops_1.0-9
## [125] txdbmaker_1.6.0 VariantAnnotation_1.56.0
## [127] scales_1.4.0 crayon_1.5.3
## [129] rlang_1.1.6 KEGGREST_1.50.0