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 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
##
## 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_1.8.0 crisprDesign_1.8.0 crisprScore_1.10.0
## [4] crisprScoreData_1.9.0 ExperimentHub_2.14.0 AnnotationHub_3.14.0
## [7] BiocFileCache_2.14.0 dbplyr_2.5.0 BiocGenerics_0.52.0
## [10] crisprBowtie_1.10.0 crisprBase_1.10.0 crisprVerse_1.8.0
## [13] BiocStyle_2.34.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] jsonlite_1.8.9 magrittr_2.0.3
## [5] GenomicFeatures_1.58.0 rmarkdown_2.28
## [7] BiocIO_1.16.0 zlibbioc_1.52.0
## [9] vctrs_0.6.5 memoise_2.0.1
## [11] Rsamtools_2.22.0 RCurl_1.98-1.16
## [13] base64enc_0.1-3 htmltools_0.5.8.1
## [15] S4Arrays_1.6.0 progress_1.2.3
## [17] curl_5.2.3 SparseArray_1.6.0
## [19] Formula_1.2-5 sass_0.4.9
## [21] bslib_0.8.0 htmlwidgets_1.6.4
## [23] basilisk_1.18.0 Gviz_1.50.0
## [25] httr2_1.0.5 cachem_1.1.0
## [27] GenomicAlignments_1.42.0 lifecycle_1.0.4
## [29] pkgconfig_2.0.3 Matrix_1.7-1
## [31] R6_2.5.1 fastmap_1.2.0
## [33] GenomeInfoDbData_1.2.13 MatrixGenerics_1.18.0
## [35] digest_0.6.37 colorspace_2.1-1
## [37] AnnotationDbi_1.68.0 S4Vectors_0.44.0
## [39] Hmisc_5.2-0 GenomicRanges_1.58.0
## [41] RSQLite_2.3.7 filelock_1.0.3
## [43] randomForest_4.7-1.2 fansi_1.0.6
## [45] httr_1.4.7 abind_1.4-8
## [47] compiler_4.4.1 Rbowtie_1.46.0
## [49] bit64_4.5.2 backports_1.5.0
## [51] htmlTable_2.4.3 BiocParallel_1.40.0
## [53] DBI_1.2.3 biomaRt_2.62.0
## [55] rappdirs_0.3.3 DelayedArray_0.32.0
## [57] rjson_0.2.23 tools_4.4.1
## [59] foreign_0.8-87 nnet_7.3-19
## [61] glue_1.8.0 restfulr_0.0.15
## [63] grid_4.4.1 checkmate_2.3.2
## [65] cluster_2.1.6 generics_0.1.3
## [67] gtable_0.3.6 BSgenome_1.74.0
## [69] tzdb_0.4.0 ensembldb_2.30.0
## [71] data.table_1.16.2 hms_1.1.3
## [73] xml2_1.3.6 utf8_1.2.4
## [75] XVector_0.46.0 BiocVersion_3.20.0
## [77] pillar_1.9.0 stringr_1.5.1
## [79] dplyr_1.1.4 lattice_0.22-6
## [81] deldir_2.0-4 rtracklayer_1.66.0
## [83] bit_4.5.0 biovizBase_1.54.0
## [85] tidyselect_1.2.1 Biostrings_2.74.0
## [87] knitr_1.48 gridExtra_2.3
## [89] bookdown_0.41 ProtGenerics_1.38.0
## [91] IRanges_2.40.0 SummarizedExperiment_1.36.0
## [93] stats4_4.4.1 xfun_0.48
## [95] Biobase_2.66.0 matrixStats_1.4.1
## [97] stringi_1.8.4 UCSC.utils_1.2.0
## [99] lazyeval_0.2.2 yaml_2.3.10
## [101] evaluate_1.0.1 codetools_0.2-20
## [103] interp_1.1-6 tibble_3.2.1
## [105] BiocManager_1.30.25 cli_3.6.3
## [107] rpart_4.1.23 reticulate_1.39.0
## [109] munsell_0.5.1 jquerylib_0.1.4
## [111] dichromat_2.0-0.1 Rcpp_1.0.13
## [113] GenomeInfoDb_1.42.0 dir.expiry_1.14.0
## [115] png_0.1-8 XML_3.99-0.17
## [117] parallel_4.4.1 ggplot2_3.5.1
## [119] readr_2.1.5 blob_1.2.4
## [121] basilisk.utils_1.18.0 prettyunits_1.2.0
## [123] jpeg_0.1-10 latticeExtra_0.6-30
## [125] AnnotationFilter_1.30.0 bitops_1.0-9
## [127] txdbmaker_1.2.0 VariantAnnotation_1.52.0
## [129] scales_1.3.0 crayon_1.5.3
## [131] rlang_1.1.4 KEGGREST_1.46.0