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)## Warning: replacing previous import 'utils::findMatches' by
## 'S4Vectors::findMatches' when loading 'AnnotationDbi'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 (2023-04-13 r84269)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.2 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_1.2.0 crisprDesign_1.2.0 crisprScore_1.4.0
## [4] crisprScoreData_1.3.0 ExperimentHub_2.8.0 AnnotationHub_3.8.0
## [7] BiocFileCache_2.8.0 dbplyr_2.3.2 BiocGenerics_0.46.0
## [10] crisprBowtie_1.4.0 crisprBase_1.4.0 crisprVerse_1.2.0
## [13] BiocStyle_2.28.0
##
## 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_1.52.0 rmarkdown_2.21
## [7] BiocIO_1.10.0 zlibbioc_1.46.0
## [9] vctrs_0.6.2 memoise_2.0.1
## [11] Rsamtools_2.16.0 RCurl_1.98-1.12
## [13] base64enc_0.1-3 htmltools_0.5.5
## [15] progress_1.2.2 curl_5.0.0
## [17] Formula_1.2-5 sass_0.4.5
## [19] bslib_0.4.2 htmlwidgets_1.6.2
## [21] basilisk_1.12.0 Gviz_1.44.0
## [23] cachem_1.0.7 GenomicAlignments_1.36.0
## [25] mime_0.12 lifecycle_1.0.3
## [27] pkgconfig_2.0.3 Matrix_1.5-4
## [29] R6_2.5.1 fastmap_1.1.1
## [31] GenomeInfoDbData_1.2.10 MatrixGenerics_1.12.0
## [33] shiny_1.7.4 digest_0.6.31
## [35] colorspace_2.1-0 AnnotationDbi_1.62.0
## [37] S4Vectors_0.38.0 Hmisc_5.0-1
## [39] GenomicRanges_1.52.0 RSQLite_2.3.1
## [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_1.40.0
## [47] bit64_4.0.5 backports_1.4.1
## [49] htmlTable_2.4.1 BiocParallel_1.34.0
## [51] DBI_1.1.3 biomaRt_2.56.0
## [53] rappdirs_0.3.3 DelayedArray_0.26.0
## [55] rjson_0.2.21 tools_4.3.0
## [57] foreign_0.8-84 interactiveDisplayBase_1.38.0
## [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_0.3.3
## [69] BSgenome_1.68.0 tzdb_0.3.0
## [71] ensembldb_2.24.0 data.table_1.14.8
## [73] hms_1.1.3 xml2_1.3.3
## [75] utf8_1.2.3 XVector_0.40.0
## [77] BiocVersion_3.17.1 pillar_1.9.0
## [79] stringr_1.5.0 later_1.3.0
## [81] dplyr_1.1.2 lattice_0.21-8
## [83] deldir_1.0-6 rtracklayer_1.60.0
## [85] bit_4.0.5 biovizBase_1.48.0
## [87] tidyselect_1.2.0 Biostrings_2.68.0
## [89] knitr_1.42 gridExtra_2.3
## [91] bookdown_0.33 ProtGenerics_1.32.0
## [93] IRanges_2.34.0 SummarizedExperiment_1.30.0
## [95] stats4_4.3.0 xfun_0.39
## [97] Biobase_2.60.0 matrixStats_0.63.0
## [99] stringi_1.7.12 lazyeval_0.2.2
## [101] yaml_2.3.7 evaluate_0.20
## [103] codetools_0.2-19 interp_1.1-4
## [105] tibble_3.2.1 BiocManager_1.30.20
## [107] cli_3.6.1 rpart_4.1.19
## [109] xtable_1.8-4 reticulate_1.28
## [111] munsell_0.5.0 jquerylib_0.1.4
## [113] dichromat_2.0-0.1 Rcpp_1.0.10
## [115] GenomeInfoDb_1.36.0 dir.expiry_1.8.0
## [117] png_0.1-8 XML_3.99-0.14
## [119] parallel_4.3.0 ellipsis_0.3.2
## [121] ggplot2_3.4.2 readr_2.1.4
## [123] blob_1.2.4 basilisk.utils_1.12.0
## [125] prettyunits_1.1.1 jpeg_0.1-10
## [127] latticeExtra_0.6-30 AnnotationFilter_1.24.0
## [129] bitops_1.0-7 VariantAnnotation_1.46.0
## [131] scales_1.2.1 crayon_1.5.2
## [133] rlang_1.1.0 KEGGREST_1.40.0