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 4.4.0 beta (2024-04-15 r86425)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.19-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_1.5.2 crisprDesign_1.5.4 crisprScore_1.7.3
## [4] crisprScoreData_1.7.0 ExperimentHub_2.11.3 AnnotationHub_3.11.5
## [7] BiocFileCache_2.11.2 dbplyr_2.5.0 BiocGenerics_0.49.1
## [10] crisprBowtie_1.7.0 crisprBase_1.7.1 crisprVerse_1.5.0
## [13] BiocStyle_2.31.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.16.0
## [3] jsonlite_1.8.8 magrittr_2.0.3
## [5] GenomicFeatures_1.55.4 rmarkdown_2.26
## [7] BiocIO_1.13.0 zlibbioc_1.49.3
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.19.4 RCurl_1.98-1.14
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.3.7 progress_1.2.3
## [17] curl_5.2.1 SparseArray_1.3.5
## [19] Formula_1.2-5 sass_0.4.9
## [21] bslib_0.7.0 htmlwidgets_1.6.4
## [23] basilisk_1.15.5 Gviz_1.47.1
## [25] httr2_1.0.1 cachem_1.0.8
## [27] GenomicAlignments_1.39.5 lifecycle_1.0.4
## [29] pkgconfig_2.0.3 Matrix_1.7-0
## [31] R6_2.5.1 fastmap_1.1.1
## [33] GenomeInfoDbData_1.2.12 MatrixGenerics_1.15.1
## [35] digest_0.6.35 colorspace_2.1-0
## [37] AnnotationDbi_1.65.2 S4Vectors_0.41.6
## [39] Hmisc_5.1-2 GenomicRanges_1.55.4
## [41] RSQLite_2.3.6 filelock_1.0.3
## [43] randomForest_4.7-1.1 fansi_1.0.6
## [45] httr_1.4.7 abind_1.4-5
## [47] compiler_4.4.0 Rbowtie_1.43.0
## [49] bit64_4.0.5 backports_1.4.1
## [51] htmlTable_2.4.2 BiocParallel_1.37.1
## [53] DBI_1.2.2 biomaRt_2.59.1
## [55] rappdirs_0.3.3 DelayedArray_0.29.9
## [57] rjson_0.2.21 tools_4.4.0
## [59] foreign_0.8-86 nnet_7.3-19
## [61] glue_1.7.0 restfulr_0.0.15
## [63] grid_4.4.0 checkmate_2.3.1
## [65] cluster_2.1.6 generics_0.1.3
## [67] gtable_0.3.4 BSgenome_1.71.4
## [69] tzdb_0.4.0 ensembldb_2.27.1
## [71] data.table_1.15.4 hms_1.1.3
## [73] xml2_1.3.6 utf8_1.2.4
## [75] XVector_0.43.1 BiocVersion_3.19.1
## [77] pillar_1.9.0 stringr_1.5.1
## [79] dplyr_1.1.4 lattice_0.22-6
## [81] deldir_2.0-4 rtracklayer_1.63.2
## [83] bit_4.0.5 biovizBase_1.51.0
## [85] tidyselect_1.2.1 Biostrings_2.71.5
## [87] knitr_1.46 gridExtra_2.3
## [89] bookdown_0.39 ProtGenerics_1.35.4
## [91] IRanges_2.37.1 SummarizedExperiment_1.33.3
## [93] stats4_4.4.0 xfun_0.43
## [95] Biobase_2.63.1 matrixStats_1.3.0
## [97] stringi_1.8.3 UCSC.utils_0.99.7
## [99] lazyeval_0.2.2 yaml_2.3.8
## [101] evaluate_0.23 codetools_0.2-20
## [103] interp_1.1-6 tibble_3.2.1
## [105] BiocManager_1.30.22 cli_3.6.2
## [107] rpart_4.1.23 reticulate_1.36.0
## [109] munsell_0.5.1 jquerylib_0.1.4
## [111] dichromat_2.0-0.1 Rcpp_1.0.12
## [113] GenomeInfoDb_1.39.14 dir.expiry_1.11.0
## [115] png_0.1-8 XML_3.99-0.16.1
## [117] parallel_4.4.0 ggplot2_3.5.0
## [119] readr_2.1.5 blob_1.2.4
## [121] basilisk.utils_1.15.2 prettyunits_1.2.0
## [123] jpeg_0.1-10 latticeExtra_0.6-30
## [125] AnnotationFilter_1.27.0 bitops_1.0-7
## [127] txdbmaker_0.99.9 VariantAnnotation_1.49.7
## [129] scales_1.3.0 crayon_1.5.2
## [131] rlang_1.1.3 KEGGREST_1.43.0