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 Under development (unstable) (2023-01-10 r83596)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.17-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_1.1.3 crisprDesign_1.1.24 crisprScore_1.3.1
## [4] crisprScoreData_1.3.0 ExperimentHub_2.7.1 AnnotationHub_3.7.2
## [7] BiocFileCache_2.7.2 dbplyr_2.3.1 BiocGenerics_0.45.0
## [10] crisprBowtie_1.3.4 crisprBase_1.3.1 crisprVerse_1.1.2
## [13] BiocStyle_2.27.1
##
## 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_1.51.4 rmarkdown_2.20
## [7] BiocIO_1.9.2 zlibbioc_1.45.0
## [9] vctrs_0.5.2 memoise_2.0.1
## [11] Rsamtools_2.15.1 RCurl_1.98-1.10
## [13] base64enc_0.1-3 htmltools_0.5.4
## [15] progress_1.2.2 curl_5.0.0
## [17] Formula_1.2-5 sass_0.4.5
## [19] bslib_0.4.2 htmlwidgets_1.6.1
## [21] basilisk_1.11.2 Gviz_1.43.1
## [23] cachem_1.0.7 GenomicAlignments_1.35.0
## [25] mime_0.12 lifecycle_1.0.3
## [27] pkgconfig_2.0.3 Matrix_1.5-3
## [29] R6_2.5.1 fastmap_1.1.1
## [31] GenomeInfoDbData_1.2.9 MatrixGenerics_1.11.0
## [33] shiny_1.7.4 digest_0.6.31
## [35] colorspace_2.1-0 AnnotationDbi_1.61.0
## [37] S4Vectors_0.37.4 Hmisc_4.8-0
## [39] GenomicRanges_1.51.4 RSQLite_2.3.0
## [41] filelock_1.0.2 randomForest_4.7-1.1
## [43] fansi_1.0.4 httr_1.4.5
## [45] compiler_4.3.0 Rbowtie_1.39.1
## [47] bit64_4.0.5 backports_1.4.1
## [49] htmlTable_2.4.1 BiocParallel_1.33.9
## [51] DBI_1.1.3 biomaRt_2.55.0
## [53] rappdirs_0.3.3 DelayedArray_0.25.0
## [55] rjson_0.2.21 tools_4.3.0
## [57] foreign_0.8-84 interactiveDisplayBase_1.37.0
## [59] httpuv_1.6.9 nnet_7.3-18
## [61] glue_1.6.2 restfulr_0.0.15
## [63] promises_1.2.0.1 grid_4.3.0
## [65] checkmate_2.1.0 cluster_2.1.4
## [67] generics_0.1.3 gtable_0.3.1
## [69] BSgenome_1.67.4 tzdb_0.3.0
## [71] ensembldb_2.23.2 data.table_1.14.8
## [73] hms_1.1.2 xml2_1.3.3
## [75] utf8_1.2.3 XVector_0.39.0
## [77] BiocVersion_3.17.1 pillar_1.8.1
## [79] stringr_1.5.0 later_1.3.0
## [81] splines_4.3.0 dplyr_1.1.0
## [83] lattice_0.20-45 deldir_1.0-6
## [85] survival_3.5-3 rtracklayer_1.59.1
## [87] bit_4.0.5 biovizBase_1.47.0
## [89] tidyselect_1.2.0 Biostrings_2.67.0
## [91] knitr_1.42 gridExtra_2.3
## [93] bookdown_0.32 ProtGenerics_1.31.0
## [95] IRanges_2.33.0 SummarizedExperiment_1.29.1
## [97] stats4_4.3.0 xfun_0.37
## [99] Biobase_2.59.0 matrixStats_0.63.0
## [101] stringi_1.7.12 lazyeval_0.2.2
## [103] yaml_2.3.7 evaluate_0.20
## [105] codetools_0.2-19 interp_1.1-3
## [107] tibble_3.1.8 BiocManager_1.30.20
## [109] cli_3.6.0 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_1.35.15 dir.expiry_1.7.0
## [119] png_0.1-8 XML_3.99-0.13
## [121] parallel_4.3.0 ellipsis_0.3.2
## [123] ggplot2_3.4.1 readr_2.1.4
## [125] blob_1.2.3 basilisk.utils_1.11.2
## [127] prettyunits_1.1.1 jpeg_0.1-10
## [129] latticeExtra_0.6-30 AnnotationFilter_1.23.0
## [131] bitops_1.0-7 VariantAnnotation_1.45.1
## [133] scales_1.2.1 crayon_1.5.2
## [135] rlang_1.0.6 KEGGREST_1.39.0