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 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-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_1.4.0 crisprDesign_1.4.0 crisprScore_1.6.0
## [4] crisprScoreData_1.5.0 ExperimentHub_2.10.0 AnnotationHub_3.10.0
## [7] BiocFileCache_2.10.0 dbplyr_2.3.4 BiocGenerics_0.48.0
## [10] crisprBowtie_1.6.0 crisprBase_1.6.0 crisprVerse_1.4.0
## [13] BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] later_1.3.1 BiocIO_1.12.0
## [3] bitops_1.0-7 filelock_1.0.2
## [5] tibble_3.2.1 basilisk.utils_1.14.0
## [7] XML_3.99-0.14 rpart_4.1.21
## [9] lifecycle_1.0.3 lattice_0.22-5
## [11] ensembldb_2.26.0 backports_1.4.1
## [13] magrittr_2.0.3 Hmisc_5.1-1
## [15] sass_0.4.7 rmarkdown_2.25
## [17] jquerylib_0.1.4 yaml_2.3.7
## [19] httpuv_1.6.12 reticulate_1.34.0
## [21] Gviz_1.46.0 DBI_1.1.3
## [23] RColorBrewer_1.1-3 abind_1.4-5
## [25] zlibbioc_1.48.0 GenomicRanges_1.54.0
## [27] AnnotationFilter_1.26.0 biovizBase_1.50.0
## [29] RCurl_1.98-1.12 nnet_7.3-19
## [31] VariantAnnotation_1.48.0 rappdirs_0.3.3
## [33] GenomeInfoDbData_1.2.11 IRanges_2.36.0
## [35] S4Vectors_0.40.0 codetools_0.2-19
## [37] DelayedArray_0.28.0 xml2_1.3.5
## [39] tidyselect_1.2.0 matrixStats_1.0.0
## [41] stats4_4.3.1 base64enc_0.1-3
## [43] GenomicAlignments_1.38.0 jsonlite_1.8.7
## [45] ellipsis_0.3.2 Formula_1.2-5
## [47] tools_4.3.1 progress_1.2.2
## [49] Rcpp_1.0.11 glue_1.6.2
## [51] gridExtra_2.3 SparseArray_1.2.0
## [53] xfun_0.40 MatrixGenerics_1.14.0
## [55] GenomeInfoDb_1.38.0 dplyr_1.1.3
## [57] BiocManager_1.30.22 fastmap_1.1.1
## [59] basilisk_1.14.0 latticeExtra_0.6-30
## [61] fansi_1.0.5 digest_0.6.33
## [63] R6_2.5.1 mime_0.12
## [65] colorspace_2.1-0 jpeg_0.1-10
## [67] dichromat_2.0-0.1 biomaRt_2.58.0
## [69] RSQLite_2.3.1 utf8_1.2.4
## [71] generics_0.1.3 data.table_1.14.8
## [73] rtracklayer_1.62.0 prettyunits_1.2.0
## [75] httr_1.4.7 htmlwidgets_1.6.2
## [77] S4Arrays_1.2.0 pkgconfig_2.0.3
## [79] gtable_0.3.4 blob_1.2.4
## [81] XVector_0.42.0 htmltools_0.5.6.1
## [83] bookdown_0.36 ProtGenerics_1.34.0
## [85] scales_1.2.1 Biobase_2.62.0
## [87] png_0.1-8 knitr_1.44
## [89] rstudioapi_0.15.0 tzdb_0.4.0
## [91] rjson_0.2.21 checkmate_2.2.0
## [93] curl_5.1.0 cachem_1.0.8
## [95] stringr_1.5.0 BiocVersion_3.18.0
## [97] parallel_4.3.1 foreign_0.8-85
## [99] AnnotationDbi_1.64.0 restfulr_0.0.15
## [101] pillar_1.9.0 grid_4.3.1
## [103] vctrs_0.6.4 promises_1.2.1
## [105] randomForest_4.7-1.1 xtable_1.8-4
## [107] cluster_2.1.4 htmlTable_2.4.1
## [109] evaluate_0.22 readr_2.1.4
## [111] GenomicFeatures_1.54.0 cli_3.6.1
## [113] compiler_4.3.1 Rsamtools_2.18.0
## [115] rlang_1.1.1 crayon_1.5.2
## [117] interp_1.1-4 stringi_1.7.12
## [119] deldir_1.0-9 BiocParallel_1.36.0
## [121] munsell_0.5.0 Biostrings_2.70.0
## [123] lazyeval_0.2.2 Matrix_1.6-1.1
## [125] dir.expiry_1.10.0 BSgenome_1.70.0
## [127] hms_1.1.3 bit64_4.0.5
## [129] ggplot2_3.4.4 KEGGREST_1.42.0
## [131] shiny_1.7.5.1 SummarizedExperiment_1.32.0
## [133] interactiveDisplayBase_1.40.0 memoise_2.0.1
## [135] bslib_0.5.1 Rbowtie_1.42.0
## [137] bit_4.0.5