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 4.2.1 (2022-06-23)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.0
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.0.0 crisprDesign_1.0.0 crisprScore_1.2.0
## [4] crisprScoreData_1.1.3 ExperimentHub_2.6.0 AnnotationHub_3.6.0
## [7] BiocFileCache_2.6.0 dbplyr_2.2.1 BiocGenerics_0.44.0
## [10] crisprBowtie_1.2.0 crisprBase_1.2.0 crisprVerse_1.0.0
## [13] BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 Hmisc_4.7-0
## [3] lazyeval_0.2.2 splines_4.2.1
## [5] BiocParallel_1.32.1 GenomeInfoDb_1.34.2
## [7] ggplot2_3.3.6 digest_0.6.29
## [9] ensembldb_2.22.0 htmltools_0.5.2
## [11] fansi_1.0.3 checkmate_2.1.0
## [13] magrittr_2.0.3 memoise_2.0.1
## [15] BSgenome_1.66.1 cluster_2.1.3
## [17] tzdb_0.3.0 Biostrings_2.66.0
## [19] readr_2.1.2 matrixStats_0.62.0
## [21] prettyunits_1.1.1 jpeg_0.1-9
## [23] colorspace_2.0-3 blob_1.2.3
## [25] rappdirs_0.3.3 xfun_0.31
## [27] dplyr_1.0.9 crayon_1.5.1
## [29] RCurl_1.98-1.7 jsonlite_1.8.0
## [31] survival_3.3-1 VariantAnnotation_1.44.0
## [33] glue_1.6.2 gtable_0.3.0
## [35] zlibbioc_1.44.0 XVector_0.38.0
## [37] DelayedArray_0.24.0 scales_1.2.0
## [39] DBI_1.1.3 Rcpp_1.0.9
## [41] htmlTable_2.4.1 xtable_1.8-4
## [43] progress_1.2.2 reticulate_1.25
## [45] foreign_0.8-82 bit_4.0.4
## [47] Formula_1.2-4 stats4_4.2.1
## [49] htmlwidgets_1.5.4 httr_1.4.3
## [51] dir.expiry_1.6.0 RColorBrewer_1.1-3
## [53] ellipsis_0.3.2 pkgconfig_2.0.3
## [55] XML_3.99-0.10 nnet_7.3-17
## [57] Gviz_1.42.0 sass_0.4.1
## [59] deldir_1.0-6 utf8_1.2.2
## [61] tidyselect_1.1.2 rlang_1.0.4
## [63] later_1.3.0 AnnotationDbi_1.60.0
## [65] munsell_0.5.0 BiocVersion_3.16.0
## [67] tools_4.2.1 cachem_1.0.6
## [69] cli_3.3.0 generics_0.1.3
## [71] RSQLite_2.2.14 evaluate_0.15
## [73] stringr_1.4.0 fastmap_1.1.0
## [75] yaml_2.3.5 knitr_1.39
## [77] bit64_4.0.5 purrr_0.3.4
## [79] randomForest_4.7-1.1 AnnotationFilter_1.22.0
## [81] KEGGREST_1.38.0 Rbowtie_1.38.0
## [83] mime_0.12 xml2_1.3.3
## [85] biomaRt_2.54.0 rstudioapi_0.13
## [87] compiler_4.2.1 filelock_1.0.2
## [89] curl_4.3.2 png_0.1-7
## [91] interactiveDisplayBase_1.36.0 tibble_3.1.7
## [93] bslib_0.3.1 stringi_1.7.8
## [95] basilisk.utils_1.10.0 GenomicFeatures_1.50.2
## [97] lattice_0.20-45 ProtGenerics_1.30.0
## [99] Matrix_1.4-1 vctrs_0.4.1
## [101] pillar_1.7.0 lifecycle_1.0.1
## [103] BiocManager_1.30.18 jquerylib_0.1.4
## [105] data.table_1.14.2 bitops_1.0-7
## [107] httpuv_1.6.5 rtracklayer_1.58.0
## [109] GenomicRanges_1.50.1 R6_2.5.1
## [111] BiocIO_1.8.0 latticeExtra_0.6-30
## [113] bookdown_0.27 promises_1.2.0.1
## [115] gridExtra_2.3 IRanges_2.32.0
## [117] codetools_0.2-18 dichromat_2.0-0.1
## [119] assertthat_0.2.1 SummarizedExperiment_1.28.0
## [121] rjson_0.2.21 GenomicAlignments_1.34.0
## [123] Rsamtools_2.14.0 S4Vectors_0.36.0
## [125] GenomeInfoDbData_1.2.8 parallel_4.2.1
## [127] hms_1.1.1 rpart_4.1.16
## [129] grid_4.2.1 basilisk_1.10.1
## [131] rmarkdown_2.14 MatrixGenerics_1.10.0
## [133] biovizBase_1.46.0 Biobase_2.58.0
## [135] shiny_1.7.1 base64enc_0.1-3
## [137] interp_1.1-3 restfulr_0.0.15