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 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.11.0 crisprDesign_1.11.0 crisprScore_1.13.0
## [4] crisprScoreData_1.13.0 ExperimentHub_2.99.0 AnnotationHub_3.99.0
## [7] BiocFileCache_2.99.0 dbplyr_2.5.0 BiocGenerics_0.55.0
## [10] generics_0.1.3 crisprBowtie_1.13.0 crisprBase_1.13.0
## [13] crisprVerse_1.11.0 BiocStyle_2.37.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] jsonlite_2.0.0 magrittr_2.0.3
## [5] GenomicFeatures_1.61.0 farver_2.1.2
## [7] rmarkdown_2.29 BiocIO_1.19.0
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.25.0 RCurl_1.98-1.17
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.9.0 progress_1.2.3
## [17] curl_6.2.2 SparseArray_1.9.0
## [19] Formula_1.2-5 sass_0.4.10
## [21] bslib_0.9.0 htmlwidgets_1.6.4
## [23] basilisk_1.21.0 Gviz_1.53.0
## [25] httr2_1.1.2 cachem_1.1.0
## [27] GenomicAlignments_1.45.0 lifecycle_1.0.4
## [29] pkgconfig_2.0.3 Matrix_1.7-3
## [31] R6_2.6.1 fastmap_1.2.0
## [33] GenomeInfoDbData_1.2.14 MatrixGenerics_1.21.0
## [35] digest_0.6.37 colorspace_2.1-1
## [37] AnnotationDbi_1.71.0 S4Vectors_0.47.0
## [39] Hmisc_5.2-3 GenomicRanges_1.61.0
## [41] RSQLite_2.3.9 filelock_1.0.3
## [43] randomForest_4.7-1.2 httr_1.4.7
## [45] abind_1.4-8 compiler_4.5.0
## [47] Rbowtie_1.49.0 bit64_4.6.0-1
## [49] backports_1.5.0 htmlTable_2.4.3
## [51] BiocParallel_1.43.0 DBI_1.2.3
## [53] biomaRt_2.65.0 rappdirs_0.3.3
## [55] DelayedArray_0.35.1 rjson_0.2.23
## [57] tools_4.5.0 foreign_0.8-90
## [59] nnet_7.3-20 glue_1.8.0
## [61] restfulr_0.0.15 grid_4.5.0
## [63] checkmate_2.3.2 cluster_2.1.8.1
## [65] gtable_0.3.6 BSgenome_1.77.0
## [67] tzdb_0.5.0 ensembldb_2.33.0
## [69] data.table_1.17.0 hms_1.1.3
## [71] xml2_1.3.8 XVector_0.49.0
## [73] BiocVersion_3.22.0 pillar_1.10.2
## [75] stringr_1.5.1 dplyr_1.1.4
## [77] lattice_0.22-7 deldir_2.0-4
## [79] rtracklayer_1.69.0 bit_4.6.0
## [81] biovizBase_1.57.0 tidyselect_1.2.1
## [83] Biostrings_2.77.0 knitr_1.50
## [85] gridExtra_2.3 bookdown_0.43
## [87] ProtGenerics_1.41.0 IRanges_2.43.0
## [89] SummarizedExperiment_1.39.0 stats4_4.5.0
## [91] xfun_0.52 Biobase_2.69.0
## [93] matrixStats_1.5.0 stringi_1.8.7
## [95] UCSC.utils_1.5.0 lazyeval_0.2.2
## [97] yaml_2.3.10 evaluate_1.0.3
## [99] codetools_0.2-20 interp_1.1-6
## [101] tibble_3.2.1 BiocManager_1.30.25
## [103] cli_3.6.5 rpart_4.1.24
## [105] reticulate_1.42.0 jquerylib_0.1.4
## [107] dichromat_2.0-0.1 Rcpp_1.0.14
## [109] GenomeInfoDb_1.45.0 dir.expiry_1.17.0
## [111] png_0.1-8 XML_3.99-0.18
## [113] parallel_4.5.0 ggplot2_3.5.2
## [115] readr_2.1.5 blob_1.2.4
## [117] basilisk.utils_1.21.0 prettyunits_1.2.0
## [119] jpeg_0.1-11 latticeExtra_0.6-30
## [121] AnnotationFilter_1.33.0 bitops_1.0-9
## [123] txdbmaker_1.5.0 VariantAnnotation_1.55.0
## [125] scales_1.4.0 crayon_1.5.3
## [127] rlang_1.1.6 KEGGREST_1.49.0