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 4.3.1 (2023-06-16)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Monterey 12.6.7
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
##
## 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_1.2.0 crisprDesign_1.2.0 crisprScore_1.4.0
## [4] crisprScoreData_1.4.0 ExperimentHub_2.8.0 AnnotationHub_3.8.0
## [7] BiocFileCache_2.8.0 dbplyr_2.3.2 BiocGenerics_0.46.0
## [10] crisprBowtie_1.4.0 crisprBase_1.4.0 crisprVerse_1.2.0
## [13] BiocStyle_2.28.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.14
## [3] jsonlite_1.8.5 magrittr_2.0.3
## [5] GenomicFeatures_1.52.1 rmarkdown_2.22
## [7] BiocIO_1.10.0 zlibbioc_1.46.0
## [9] vctrs_0.6.3 memoise_2.0.1
## [11] Rsamtools_2.16.0 RCurl_1.98-1.12
## [13] base64enc_0.1-3 htmltools_0.5.5
## [15] S4Arrays_1.0.4 progress_1.2.2
## [17] curl_5.0.1 Formula_1.2-5
## [19] sass_0.4.6 bslib_0.5.0
## [21] htmlwidgets_1.6.2 basilisk_1.12.1
## [23] Gviz_1.44.0 cachem_1.0.8
## [25] GenomicAlignments_1.36.0 mime_0.12
## [27] lifecycle_1.0.3 pkgconfig_2.0.3
## [29] Matrix_1.5-4.1 R6_2.5.1
## [31] fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [33] MatrixGenerics_1.12.2 shiny_1.7.4
## [35] digest_0.6.31 colorspace_2.1-0
## [37] AnnotationDbi_1.62.2 S4Vectors_0.38.1
## [39] Hmisc_5.1-0 GenomicRanges_1.52.0
## [41] RSQLite_2.3.1 filelock_1.0.2
## [43] randomForest_4.7-1.1 fansi_1.0.4
## [45] httr_1.4.6 compiler_4.3.1
## [47] Rbowtie_1.40.0 bit64_4.0.5
## [49] backports_1.4.1 htmlTable_2.4.1
## [51] BiocParallel_1.34.2 DBI_1.1.3
## [53] biomaRt_2.56.1 rappdirs_0.3.3
## [55] DelayedArray_0.26.6 rjson_0.2.21
## [57] tools_4.3.1 foreign_0.8-84
## [59] interactiveDisplayBase_1.38.0 httpuv_1.6.11
## [61] nnet_7.3-19 glue_1.6.2
## [63] restfulr_0.0.15 promises_1.2.0.1
## [65] grid_4.3.1 checkmate_2.2.0
## [67] cluster_2.1.4 generics_0.1.3
## [69] gtable_0.3.3 BSgenome_1.68.0
## [71] tzdb_0.4.0 ensembldb_2.24.0
## [73] data.table_1.14.8 hms_1.1.3
## [75] xml2_1.3.4 utf8_1.2.3
## [77] XVector_0.40.0 BiocVersion_3.17.1
## [79] pillar_1.9.0 stringr_1.5.0
## [81] later_1.3.1 dplyr_1.1.2
## [83] lattice_0.21-8 deldir_1.0-9
## [85] rtracklayer_1.60.0 bit_4.0.5
## [87] biovizBase_1.48.0 tidyselect_1.2.0
## [89] Biostrings_2.68.1 knitr_1.43
## [91] gridExtra_2.3 bookdown_0.34
## [93] ProtGenerics_1.32.0 IRanges_2.34.1
## [95] SummarizedExperiment_1.30.2 stats4_4.3.1
## [97] xfun_0.39 Biobase_2.60.0
## [99] matrixStats_1.0.0 stringi_1.7.12
## [101] lazyeval_0.2.2 yaml_2.3.7
## [103] evaluate_0.21 codetools_0.2-19
## [105] interp_1.1-4 tibble_3.2.1
## [107] BiocManager_1.30.21 cli_3.6.1
## [109] rpart_4.1.19 xtable_1.8-4
## [111] reticulate_1.30 munsell_0.5.0
## [113] jquerylib_0.1.4 dichromat_2.0-0.1
## [115] Rcpp_1.0.10 GenomeInfoDb_1.36.1
## [117] dir.expiry_1.8.0 png_0.1-8
## [119] XML_3.99-0.14 parallel_4.3.1
## [121] ellipsis_0.3.2 ggplot2_3.4.2
## [123] readr_2.1.4 blob_1.2.4
## [125] basilisk.utils_1.12.1 prettyunits_1.1.1
## [127] jpeg_0.1-10 latticeExtra_0.6-30
## [129] AnnotationFilter_1.24.0 bitops_1.0-7
## [131] VariantAnnotation_1.46.0 scales_1.2.1
## [133] crayon_1.5.2 rlang_1.1.1
## [135] KEGGREST_1.40.0