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: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
##
## 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
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_0.99.23 crisprDesign_0.99.178 crisprScore_1.1.17
## [4] crisprScoreData_1.1.4 ExperimentHub_2.5.0 AnnotationHub_3.5.2
## [7] BiocFileCache_2.5.2 dbplyr_2.2.1 BiocGenerics_0.43.4
## [10] crisprBowtie_1.1.2 crisprBase_1.1.8 crisprVerse_0.99.11
## [13] BiocStyle_2.25.0
##
## loaded via a namespace (and not attached):
## [1] backports_1.4.1 Hmisc_4.7-1
## [3] lazyeval_0.2.2 splines_4.2.1
## [5] BiocParallel_1.31.13 GenomeInfoDb_1.33.12
## [7] ggplot2_3.3.6 digest_0.6.30
## [9] ensembldb_2.21.5 htmltools_0.5.3
## [11] fansi_1.0.3 checkmate_2.1.0
## [13] magrittr_2.0.3 memoise_2.0.1
## [15] BSgenome_1.65.2 cluster_2.1.4
## [17] tzdb_0.3.0 Biostrings_2.65.6
## [19] readr_2.1.3 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_0.33
## [27] dplyr_1.0.10 crayon_1.5.2
## [29] RCurl_1.98-1.9 jsonlite_1.8.2
## [31] survival_3.4-0 VariantAnnotation_1.43.3
## [33] glue_1.6.2 gtable_0.3.1
## [35] zlibbioc_1.43.0 XVector_0.37.1
## [37] DelayedArray_0.23.2 scales_1.2.1
## [39] DBI_1.1.3 Rcpp_1.0.9
## [41] htmlTable_2.4.1 xtable_1.8-4
## [43] progress_1.2.2 reticulate_1.26
## [45] foreign_0.8-83 bit_4.0.4
## [47] Formula_1.2-4 stats4_4.2.1
## [49] htmlwidgets_1.5.4 httr_1.4.4
## [51] dir.expiry_1.5.1 RColorBrewer_1.1-3
## [53] ellipsis_0.3.2 pkgconfig_2.0.3
## [55] XML_3.99-0.11 nnet_7.3-18
## [57] Gviz_1.41.1 sass_0.4.2
## [59] deldir_1.0-6 utf8_1.2.2
## [61] tidyselect_1.2.0 rlang_1.0.6
## [63] later_1.3.0 AnnotationDbi_1.59.1
## [65] munsell_0.5.0 BiocVersion_3.16.0
## [67] tools_4.2.1 cachem_1.0.6
## [69] cli_3.4.1 generics_0.1.3
## [71] RSQLite_2.2.18 evaluate_0.17
## [73] stringr_1.4.1 fastmap_1.1.0
## [75] yaml_2.3.6 knitr_1.40
## [77] bit64_4.0.5 randomForest_4.7-1.1
## [79] AnnotationFilter_1.21.0 KEGGREST_1.37.3
## [81] Rbowtie_1.37.0 mime_0.12
## [83] xml2_1.3.3 biomaRt_2.53.4
## [85] rstudioapi_0.14 compiler_4.2.1
## [87] filelock_1.0.2 curl_4.3.3
## [89] png_0.1-7 interactiveDisplayBase_1.35.1
## [91] tibble_3.1.8 bslib_0.4.0
## [93] stringi_1.7.8 basilisk.utils_1.9.4
## [95] GenomicFeatures_1.49.7 lattice_0.20-45
## [97] ProtGenerics_1.29.1 Matrix_1.5-1
## [99] vctrs_0.4.2 pillar_1.8.1
## [101] lifecycle_1.0.3 BiocManager_1.30.18
## [103] jquerylib_0.1.4 data.table_1.14.4
## [105] bitops_1.0-7 httpuv_1.6.6
## [107] rtracklayer_1.57.0 GenomicRanges_1.49.1
## [109] R6_2.5.1 BiocIO_1.7.1
## [111] latticeExtra_0.6-30 bookdown_0.29
## [113] promises_1.2.0.1 gridExtra_2.3
## [115] IRanges_2.31.2 codetools_0.2-18
## [117] dichromat_2.0-0.1 assertthat_0.2.1
## [119] SummarizedExperiment_1.27.3 rjson_0.2.21
## [121] GenomicAlignments_1.33.1 Rsamtools_2.13.4
## [123] S4Vectors_0.35.4 GenomeInfoDbData_1.2.9
## [125] parallel_4.2.1 hms_1.1.2
## [127] rpart_4.1.16 grid_4.2.1
## [129] basilisk_1.9.11 rmarkdown_2.17
## [131] MatrixGenerics_1.9.1 biovizBase_1.45.0
## [133] Biobase_2.57.1 shiny_1.7.2
## [135] base64enc_0.1-3 interp_1.1-3
## [137] restfulr_0.0.15