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 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-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_1.10.0 crisprDesign_1.10.0 crisprScore_1.12.0
## [4] crisprScoreData_1.11.0 ExperimentHub_2.16.0 AnnotationHub_3.16.0
## [7] BiocFileCache_2.16.0 dbplyr_2.5.0 BiocGenerics_0.54.0
## [10] generics_0.1.3 crisprBowtie_1.12.0 crisprBase_1.12.0
## [13] crisprVerse_1.10.0 BiocStyle_2.36.0
##
## 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_1.60.0 rmarkdown_2.29
## [7] BiocIO_1.18.0 vctrs_0.6.5
## [9] memoise_2.0.1 Rsamtools_2.24.0
## [11] RCurl_1.98-1.17 base64enc_0.1-3
## [13] htmltools_0.5.8.1 S4Arrays_1.8.0
## [15] progress_1.2.3 curl_6.2.2
## [17] SparseArray_1.8.0 Formula_1.2-5
## [19] sass_0.4.10 bslib_0.9.0
## [21] htmlwidgets_1.6.4 basilisk_1.20.0
## [23] Gviz_1.52.0 httr2_1.1.2
## [25] cachem_1.1.0 GenomicAlignments_1.44.0
## [27] lifecycle_1.0.4 pkgconfig_2.0.3
## [29] Matrix_1.7-3 R6_2.6.1
## [31] fastmap_1.2.0 GenomeInfoDbData_1.2.14
## [33] MatrixGenerics_1.20.0 digest_0.6.37
## [35] colorspace_2.1-1 AnnotationDbi_1.70.0
## [37] S4Vectors_0.46.0 Hmisc_5.2-3
## [39] GenomicRanges_1.60.0 RSQLite_2.3.9
## [41] filelock_1.0.3 randomForest_4.7-1.2
## [43] httr_1.4.7 abind_1.4-8
## [45] compiler_4.5.0 Rbowtie_1.48.0
## [47] bit64_4.6.0-1 backports_1.5.0
## [49] htmlTable_2.4.3 BiocParallel_1.42.0
## [51] DBI_1.2.3 biomaRt_2.64.0
## [53] rappdirs_0.3.3 DelayedArray_0.34.0
## [55] rjson_0.2.23 tools_4.5.0
## [57] foreign_0.8-90 nnet_7.3-20
## [59] glue_1.8.0 restfulr_0.0.15
## [61] grid_4.5.0 checkmate_2.3.2
## [63] cluster_2.1.8.1 gtable_0.3.6
## [65] BSgenome_1.76.0 tzdb_0.5.0
## [67] ensembldb_2.32.0 data.table_1.17.0
## [69] hms_1.1.3 xml2_1.3.8
## [71] XVector_0.48.0 BiocVersion_3.21.1
## [73] pillar_1.10.2 stringr_1.5.1
## [75] dplyr_1.1.4 lattice_0.22-7
## [77] deldir_2.0-4 rtracklayer_1.68.0
## [79] bit_4.6.0 biovizBase_1.56.0
## [81] tidyselect_1.2.1 Biostrings_2.76.0
## [83] knitr_1.50 gridExtra_2.3
## [85] bookdown_0.43 ProtGenerics_1.40.0
## [87] IRanges_2.42.0 SummarizedExperiment_1.38.0
## [89] stats4_4.5.0 xfun_0.52
## [91] Biobase_2.68.0 matrixStats_1.5.0
## [93] stringi_1.8.7 UCSC.utils_1.4.0
## [95] lazyeval_0.2.2 yaml_2.3.10
## [97] evaluate_1.0.3 codetools_0.2-20
## [99] interp_1.1-6 tibble_3.2.1
## [101] BiocManager_1.30.25 cli_3.6.4
## [103] rpart_4.1.24 reticulate_1.42.0
## [105] munsell_0.5.1 jquerylib_0.1.4
## [107] dichromat_2.0-0.1 Rcpp_1.0.14
## [109] GenomeInfoDb_1.44.0 dir.expiry_1.16.0
## [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_1.20.0 prettyunits_1.2.0
## [119] jpeg_0.1-11 latticeExtra_0.6-30
## [121] AnnotationFilter_1.32.0 bitops_1.0-9
## [123] txdbmaker_1.4.0 VariantAnnotation_1.54.0
## [125] scales_1.3.0 crayon_1.5.3
## [127] rlang_1.1.6 KEGGREST_1.48.0