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 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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_1.9.0 crisprDesign_1.9.0 crisprScore_1.11.0
## [4] crisprScoreData_1.10.0 ExperimentHub_2.15.0 AnnotationHub_3.15.0
## [7] BiocFileCache_2.15.0 dbplyr_2.5.0 BiocGenerics_0.53.3
## [10] generics_0.1.3 crisprBowtie_1.11.0 crisprBase_1.11.0
## [13] crisprVerse_1.9.0 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.17.1
## [3] sys_3.4.3 jsonlite_1.8.9
## [5] magrittr_2.0.3 GenomicFeatures_1.59.1
## [7] rmarkdown_2.29 BiocIO_1.17.1
## [9] zlibbioc_1.52.0 vctrs_0.6.5
## [11] memoise_2.0.1 Rsamtools_2.23.1
## [13] RCurl_1.98-1.16 base64enc_0.1-3
## [15] htmltools_0.5.8.1 S4Arrays_1.7.1
## [17] progress_1.2.3 curl_6.0.1
## [19] SparseArray_1.7.2 Formula_1.2-5
## [21] sass_0.4.9 bslib_0.8.0
## [23] htmlwidgets_1.6.4 basilisk_1.19.0
## [25] Gviz_1.51.0 httr2_1.0.7
## [27] cachem_1.1.0 buildtools_1.0.0
## [29] GenomicAlignments_1.43.0 lifecycle_1.0.4
## [31] pkgconfig_2.0.3 Matrix_1.7-1
## [33] R6_2.5.1 fastmap_1.2.0
## [35] GenomeInfoDbData_1.2.13 MatrixGenerics_1.19.0
## [37] digest_0.6.37 colorspace_2.1-1
## [39] AnnotationDbi_1.69.0 S4Vectors_0.45.2
## [41] Hmisc_5.2-1 GenomicRanges_1.59.1
## [43] RSQLite_2.3.9 filelock_1.0.3
## [45] randomForest_4.7-1.2 httr_1.4.7
## [47] abind_1.4-8 compiler_4.4.2
## [49] Rbowtie_1.47.0 bit64_4.5.2
## [51] backports_1.5.0 htmlTable_2.4.3
## [53] BiocParallel_1.41.0 DBI_1.2.3
## [55] biomaRt_2.63.0 rappdirs_0.3.3
## [57] DelayedArray_0.33.3 rjson_0.2.23
## [59] tools_4.4.2 foreign_0.8-87
## [61] nnet_7.3-19 glue_1.8.0
## [63] restfulr_0.0.15 grid_4.4.2
## [65] checkmate_2.3.2 cluster_2.1.8
## [67] gtable_0.3.6 BSgenome_1.75.0
## [69] tzdb_0.4.0 ensembldb_2.31.0
## [71] data.table_1.16.4 hms_1.1.3
## [73] xml2_1.3.6 XVector_0.47.0
## [75] BiocVersion_3.21.1 pillar_1.10.0
## [77] stringr_1.5.1 dplyr_1.1.4
## [79] lattice_0.22-6 deldir_2.0-4
## [81] rtracklayer_1.67.0 bit_4.5.0.1
## [83] biovizBase_1.55.0 tidyselect_1.2.1
## [85] maketools_1.3.1 Biostrings_2.75.3
## [87] knitr_1.49 gridExtra_2.3
## [89] ProtGenerics_1.39.1 IRanges_2.41.2
## [91] SummarizedExperiment_1.37.0 stats4_4.4.2
## [93] xfun_0.49 Biobase_2.67.0
## [95] matrixStats_1.4.1 stringi_1.8.4
## [97] UCSC.utils_1.3.0 lazyeval_0.2.2
## [99] yaml_2.3.10 evaluate_1.0.1
## [101] codetools_0.2-20 interp_1.1-6
## [103] tibble_3.2.1 BiocManager_1.30.25
## [105] cli_3.6.3 rpart_4.1.23
## [107] reticulate_1.40.0 munsell_0.5.1
## [109] jquerylib_0.1.4 dichromat_2.0-0.1
## [111] Rcpp_1.0.13-1 GenomeInfoDb_1.43.2
## [113] dir.expiry_1.15.0 png_0.1-8
## [115] XML_3.99-0.17 parallel_4.4.2
## [117] ggplot2_3.5.1 readr_2.1.5
## [119] blob_1.2.4 basilisk.utils_1.19.0
## [121] prettyunits_1.2.0 jpeg_0.1-10
## [123] latticeExtra_0.6-30 AnnotationFilter_1.31.0
## [125] bitops_1.0-9 txdbmaker_1.3.1
## [127] VariantAnnotation_1.53.0 scales_1.3.0
## [129] crayon_1.5.3 rlang_1.1.4
## [131] KEGGREST_1.47.0