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 4.3.0 RC (2023-04-18 r84287)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_1.3.1 crisprDesign_1.3.1 crisprScore_1.5.0
## [4] crisprScoreData_1.5.0 ExperimentHub_2.9.0 AnnotationHub_3.9.1
## [7] BiocFileCache_2.9.0 dbplyr_2.3.2 BiocGenerics_0.47.0
## [10] crisprBowtie_1.5.0 crisprBase_1.5.0 crisprVerse_1.3.0
## [13] BiocStyle_2.29.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.14
## [3] jsonlite_1.8.4 magrittr_2.0.3
## [5] GenomicFeatures_1.53.0 rmarkdown_2.21
## [7] BiocIO_1.11.0 zlibbioc_1.47.0
## [9] vctrs_0.6.2 memoise_2.0.1
## [11] Rsamtools_2.17.0 RCurl_1.98-1.12
## [13] base64enc_0.1-3 htmltools_0.5.5
## [15] S4Arrays_1.1.4 progress_1.2.2
## [17] curl_5.0.0 SparseArray_1.1.5
## [19] Formula_1.2-5 sass_0.4.6
## [21] bslib_0.4.2 htmlwidgets_1.6.2
## [23] basilisk_1.13.0 Gviz_1.45.0
## [25] cachem_1.0.8 GenomicAlignments_1.37.0
## [27] mime_0.12 lifecycle_1.0.3
## [29] pkgconfig_2.0.3 Matrix_1.5-4.1
## [31] R6_2.5.1 fastmap_1.1.1
## [33] GenomeInfoDbData_1.2.10 MatrixGenerics_1.13.0
## [35] shiny_1.7.4 digest_0.6.31
## [37] colorspace_2.1-0 AnnotationDbi_1.63.1
## [39] S4Vectors_0.39.1 Hmisc_5.1-0
## [41] GenomicRanges_1.53.1 RSQLite_2.3.1
## [43] filelock_1.0.2 randomForest_4.7-1.1
## [45] fansi_1.0.4 httr_1.4.6
## [47] compiler_4.3.0 Rbowtie_1.41.0
## [49] bit64_4.0.5 backports_1.4.1
## [51] htmlTable_2.4.1 BiocParallel_1.35.1
## [53] DBI_1.1.3 biomaRt_2.57.0
## [55] rappdirs_0.3.3 DelayedArray_0.27.3
## [57] rjson_0.2.21 tools_4.3.0
## [59] foreign_0.8-84 interactiveDisplayBase_1.39.0
## [61] httpuv_1.6.11 nnet_7.3-19
## [63] glue_1.6.2 restfulr_0.0.15
## [65] promises_1.2.0.1 grid_4.3.0
## [67] checkmate_2.2.0 cluster_2.1.4
## [69] generics_0.1.3 gtable_0.3.3
## [71] BSgenome_1.69.0 tzdb_0.4.0
## [73] ensembldb_2.25.0 data.table_1.14.8
## [75] hms_1.1.3 xml2_1.3.4
## [77] utf8_1.2.3 XVector_0.41.1
## [79] BiocVersion_3.18.0 pillar_1.9.0
## [81] stringr_1.5.0 later_1.3.1
## [83] dplyr_1.1.2 lattice_0.21-8
## [85] deldir_1.0-9 rtracklayer_1.61.0
## [87] bit_4.0.5 biovizBase_1.49.0
## [89] tidyselect_1.2.0 Biostrings_2.69.1
## [91] knitr_1.42 gridExtra_2.3
## [93] bookdown_0.34 ProtGenerics_1.33.0
## [95] IRanges_2.35.1 SummarizedExperiment_1.31.1
## [97] stats4_4.3.0 xfun_0.39
## [99] Biobase_2.61.0 matrixStats_0.63.0
## [101] stringi_1.7.12 lazyeval_0.2.2
## [103] yaml_2.3.7 evaluate_0.21
## [105] codetools_0.2-19 interp_1.1-4
## [107] tibble_3.2.1 BiocManager_1.30.20
## [109] cli_3.6.1 rpart_4.1.19
## [111] xtable_1.8-4 reticulate_1.28
## [113] munsell_0.5.0 jquerylib_0.1.4
## [115] dichromat_2.0-0.1 Rcpp_1.0.10
## [117] GenomeInfoDb_1.37.1 dir.expiry_1.9.0
## [119] png_0.1-8 XML_3.99-0.14
## [121] parallel_4.3.0 ellipsis_0.3.2
## [123] ggplot2_3.4.2 readr_2.1.4
## [125] blob_1.2.4 basilisk.utils_1.13.1
## [127] prettyunits_1.1.1 jpeg_0.1-10
## [129] latticeExtra_0.6-30 AnnotationFilter_1.25.0
## [131] bitops_1.0-7 VariantAnnotation_1.47.0
## [133] scales_1.2.1 crayon_1.5.2
## [135] rlang_1.1.1 KEGGREST_1.41.0