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:
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.## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 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: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] crisprViz_1.7.0 crisprDesign_1.7.2 crisprScore_1.9.2
## [4] crisprScoreData_1.9.0 ExperimentHub_2.13.1 AnnotationHub_3.13.1
## [7] BiocFileCache_2.13.0 dbplyr_2.5.0 BiocGenerics_0.51.0
## [10] crisprBowtie_1.9.0 crisprBase_1.9.1 crisprVerse_1.7.0
## [13] BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.16.0
## [3] sys_3.4.2 jsonlite_1.8.8
## [5] magrittr_2.0.3 GenomicFeatures_1.57.0
## [7] rmarkdown_2.28 BiocIO_1.15.1
## [9] zlibbioc_1.51.1 vctrs_0.6.5
## [11] memoise_2.0.1 Rsamtools_2.21.1
## [13] RCurl_1.98-1.16 base64enc_0.1-3
## [15] htmltools_0.5.8.1 S4Arrays_1.5.7
## [17] progress_1.2.3 curl_5.2.1
## [19] SparseArray_1.5.31 Formula_1.2-5
## [21] sass_0.4.9 bslib_0.8.0
## [23] htmlwidgets_1.6.4 basilisk_1.17.2
## [25] Gviz_1.49.0 httr2_1.0.2
## [27] cachem_1.1.0 buildtools_1.0.0
## [29] GenomicAlignments_1.41.0 lifecycle_1.0.4
## [31] pkgconfig_2.0.3 Matrix_1.7-0
## [33] R6_2.5.1 fastmap_1.2.0
## [35] GenomeInfoDbData_1.2.12 MatrixGenerics_1.17.0
## [37] digest_0.6.36 colorspace_2.1-1
## [39] AnnotationDbi_1.67.0 S4Vectors_0.43.2
## [41] Hmisc_5.1-3 GenomicRanges_1.57.1
## [43] RSQLite_2.3.7 filelock_1.0.3
## [45] randomForest_4.7-1.1 fansi_1.0.6
## [47] httr_1.4.7 abind_1.4-5
## [49] compiler_4.4.1 Rbowtie_1.45.0
## [51] bit64_4.0.5 backports_1.5.0
## [53] htmlTable_2.4.3 BiocParallel_1.39.0
## [55] DBI_1.2.3 biomaRt_2.61.3
## [57] rappdirs_0.3.3 DelayedArray_0.31.11
## [59] rjson_0.2.21 tools_4.4.1
## [61] foreign_0.8-87 nnet_7.3-19
## [63] glue_1.7.0 restfulr_0.0.15
## [65] grid_4.4.1 checkmate_2.3.2
## [67] cluster_2.1.6 generics_0.1.3
## [69] gtable_0.3.5 BSgenome_1.73.0
## [71] tzdb_0.4.0 ensembldb_2.29.0
## [73] data.table_1.15.4 hms_1.1.3
## [75] xml2_1.3.6 utf8_1.2.4
## [77] XVector_0.45.0 BiocVersion_3.20.0
## [79] pillar_1.9.0 stringr_1.5.1
## [81] dplyr_1.1.4 lattice_0.22-6
## [83] deldir_2.0-4 rtracklayer_1.65.0
## [85] bit_4.0.5 biovizBase_1.53.0
## [87] tidyselect_1.2.1 maketools_1.3.0
## [89] Biostrings_2.73.1 knitr_1.48
## [91] gridExtra_2.3 ProtGenerics_1.37.1
## [93] IRanges_2.39.2 SummarizedExperiment_1.35.1
## [95] stats4_4.4.1 xfun_0.47
## [97] Biobase_2.65.0 matrixStats_1.3.0
## [99] stringi_1.8.4 UCSC.utils_1.1.0
## [101] lazyeval_0.2.2 yaml_2.3.10
## [103] evaluate_0.24.0 codetools_0.2-20
## [105] interp_1.1-6 tibble_3.2.1
## [107] BiocManager_1.30.23 cli_3.6.3
## [109] rpart_4.1.23 reticulate_1.38.0
## [111] munsell_0.5.1 jquerylib_0.1.4
## [113] dichromat_2.0-0.1 Rcpp_1.0.13
## [115] GenomeInfoDb_1.41.1 dir.expiry_1.13.0
## [117] png_0.1-8 XML_3.99-0.17
## [119] parallel_4.4.1 ggplot2_3.5.1
## [121] readr_2.1.5 blob_1.2.4
## [123] basilisk.utils_1.17.2 prettyunits_1.2.0
## [125] jpeg_0.1-10 latticeExtra_0.6-30
## [127] AnnotationFilter_1.29.0 bitops_1.0-8
## [129] txdbmaker_1.1.1 VariantAnnotation_1.51.0
## [131] scales_1.3.0 crayon_1.5.3
## [133] rlang_1.1.4 KEGGREST_1.45.1